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AGRI 2008, 42: 29-47

SummaryInventory of species and breeds, their populationsizes, geographic distribution and possibly theirgenetic diversity is generally undertaken as a firststep in any national programme for themanagement of animal genetic resources for foodand agriculture. The primary purpose of such anassessment is to document the current state ofknowledge in terms of a population’s ability tosurvive, reproduce, produce and provide services tofarmers. Starting an inventory requires someknowledge of the inventory items and theircharacteristic attributes. Inventory andcharacterization are, therefore, complementaryprocesses, in which the characterization stepprovides the baseline information as well as thecriteria that will be used to establish and update theinventory. Characterization provides data onpresent and potential future uses of the animalgenetic resources under consideration, andestablishes their current state as distinct breedpopulations and their risk status. As use andmanagement of animal genetic resources aredynamic processes, monitoring the status of apopulation has to be done on a regular basis. Thus,risk status indicators for use during the monitoringprocess need to be defined following the inventoryand characterization steps.

This paper discusses methods and criteriacurrently available, from research and pastexperience, for inventory, characterization andmonitoring of animal genetic resources, with theview to assist in the development of a morecomprehensive framework. Particular considerationis given to emerging tools and technologies. Thescope of the review includes all livestock speciesand their wild ancestors and wild related species.Examples focus on cattle, sheep, goats, pigs andchickens.

Inventory, characterization and monitoring

M. Tixier-Boichard1,2, W. Ayalew3 & H. Jianlin4

1Institut National de la Recherche Agronomique (INRA), AgroParisTech,UMR1236 Génétique et Diversité Animales, F-78350 Jouy-en-Josas, France

2Département sectoriel A4, “Biotechnologies - Ressources - Agronomie”, Direction Générale de la Recherche et del’Innovation, Ministère de l’Enseignement Supérieur et de la Recherche, 1 rue Descartes, F-75231 Paris, France

3National Agricultural Research Institute (NARI), P.O. Box 1639, Lae 411, Morobe Province, Papua New Guinea4CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese

Academy of Agricultural Sciences (CAAS), No. 2, Yuan Min Yuan Xi Lu, Haidian District,Beijing 100094, P.R. China

RésuméL’inventaire des espèces et des races, la taille despopulations, la distribution géographique et sipossible leur diversité génétique, est en général lepremier pas à accomplir dans un programmenational pour la gestion des ressources génétiquesanimales pour l’alimentation et l’agriculture. Leprincipal objectif de ce genre d’évaluation est dedocumenter la situation actuelle en termes deconnaissances sur la capacité de survivre et de sereproduire d’une population, ainsi que d'offrir desservices aux éleveurs. Pour initier un inventaire ilest nécessaire de disposer de certainesconnaissances sur les points principaux et sur lesattributions des caractéristiques. En outre,inventaire et caractérisation sont des procédurescomplémentaires étant donné que la caractérisationfourni l’information de base et les critères quis’utiliseront pour établir et mettre à jour l’inventaire.Tenant compte que l’utilisation et la gestion desressources génétiques animales sont des procéduresdynamiques, le suivi d’une population doit êtreréalisé sur des bases concrètes. Pour cette raison, ilest nécessaire de définir les indicateurs pour lessituations de risque qui seront utilisés pendant lesuivi tenant compte des différents points del’inventaire et de la caractérisation.

L’article présente les méthodes et critèresdisponibles actuellement à partir de la recherche etdes expériences passées pour classer, caractériser etsuivre les ressources génétiques animales dans lebut d’aider au développement d’un réseau plusefficace. Ont souligne en particulier les nouveauxoutils et technologies. L’objectif de cette révisioncomprend toutes les espèces d’élevage ainsi queleurs ancêtres sauvages et les espèces sauvagesvoisines. Certains exemples se sont centré sur lesbovins, ovins, caprins, porcins et volailles.

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30Inventory, characterization and monitoring

ResumenEl inventario de las especies y razas, el tamaño desus poblaciones, su distribución geográfica yposiblemente su diversidad genética es en generallo que se hace como primer paso en un programanacional para la gestión de los recursoszoogenéticos para la alimentación y la agricultura.El principal propósito de este tipo de evaluación esdocumentar la situación actual en términos deconocimientos sobre la capacidad de sobrevivir y dereproducirse de una población, y de proveer yproducir servicios para los ganaderos. Iniciar uninventario requiere algunos conocimientos sobre lospuntos de un inventario y la atribución de suscaracterísticas. Por lo tanto, inventario ycaracterización son procesos complementarios enlos que el paso de la caracterización proporciona lainformación de base así como los criterios que seutilizaran para establecer y poner al día elinventario. La caracterización proporciona datossobre el uso actual y potencial futuro de los recursoszoogenéticos en estudio, y establece cual es elestado actual de cada población de razas ysituación de riesgo. Teniendo en cuenta que lautilización y gestión de los recursos zoogenéticosson procesos dinámicos, el seguimiento de lasituación de una población debe llevarse a cabosobre bases regulares. Por lo tanto, se necesitandefinir indicadores sobre situaciones de riesgo parasu utilización durante el seguimiento en base a lospuntos del inventario y de la caracterización.

El articulo discute métodos y criteriosdisponibles actualmente provenientes de lainvestigación y de experiencias pasadas parainventariar, caracterizar y monitorear los recursoszoogenéticos, con vistas a asistir al desarrollo deuna red mas efectiva. Se da particular consideracióna las nuevas herramientas y tecnologías. El objetivode esta revisión incluye todas las especiesganaderas y sus antepasados salvajes así comoespecies salvajes relacionadas. Algunos ejemplos sehan centrado en bovinos, ovinos, caprinos, porcinosy especies avícolas.

Keywords: Descriptors, Relevant scales, Inventory,Characterization, Production systems, Phenotypiccharacterization, Molecular characterization, Geneticdiversity.

Conceptual frameworkGenetic diversity within a livestock species isreflected in the range of breeds and populations andin the variation present within each.

The concept of the breed

The commonly used unit of reference of animalgenetic diversity is the breed. Although the term“breed” is generally defined in terms ofmorphological, geographic, utility and geneticcriteria, it is difficult to establish a definition thatcan be universally applied in both developed anddeveloping countries. Definition of breed identitiesand characteristics requires at least a preliminarycharacterization of the breeds that are known toexist within a country. However, using the breedconcept may lead to the exclusion of localpopulations that are not well described or notidentified as breeds by the national authorities. Inorder to avoid missing data relevant to the efficientdesign of strategies for the management of animalgenetic resources, it is useful to recall the differenttypes of populations that are covered by the broadconcept of the breed and that should be included inthe inventory.

Traditional populations are mainly local and areconsidered to be adapted to their environment. Theyoften exhibit a large phenotypic diversity(particularly for coat or plumage colour). They aremanaged by the farmers with low selectionintensity, and are also affected by natural selection.Their genetic structure is mainly influenced bymigration events and mutations, which wouldgenerally be counter selected in the wild.Population size is generally large.

Standardized breeds are selected on the basis ofmorphological traits, with a recognized “standard”breed descriptor, generally established by acommunity of breeders. They derive from traditionalpopulations, but exhibit less phenotypic diversityas they are selected to meet minimum standards ofphenotype. Their genetic structure may beinfluenced by important founder effects. Totalpopulation size may be very variable, depending onhistory and breeders’ organization.

Selected breeds or commercial lines arecharacterized by an economic selection objectiveand the use of quantitative genetics methods.Molecular markers are often used, for instance forparentage testing. These populations derive fromstandardized breed or from traditional populations.Breeders are organized for pedigree and

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Tixier-Boichard et al.

performance recording. Total population size isgenerally large.

Derived lines arise from the use of specificbreeding methods. Close inbreeding leads to highlyspecialized lines which exhibit low geneticvariability. Conversely, composite breeds arederived from crosses between standardized breedsor selected lines, and exhibit a high level of geneticvariability. Experimental selected lines used forresearch are part of this group, as they are generallyderived from known breeds and selected for veryspecific traits. Transgenic lines would also belongto this group. Total population size is generallylimited, except for composite breeds, which canform the basis of a new selection programme.

These different types of population may be easilyidentifiable in highly commercialized species suchas cattle, pigs or chickens in Europe or Asia, forinstance. The classification may not apply directlyto other species such as camelids or geese, but canbe considered a general framework for all types ofdomesticated populations.

In addition to these categories, wild ancestorsand wild related species are also relevant forinventories. Indeed, spontaneous cross-breedingmay still take place between wild relatives andlivestock in interface areas. For example, themountainous regions of north Viet Nam providepermanent contact between wild species anddomesticated chicken populations. This “freebreeding” increases introgression from wildgenomes and plays an important role inmaintaining a high genetic diversity andadaptation to particular conditions. Thus, theselocal populations should undoubtedly beconsidered in any inventory.

Descriptors (items) for inventory,characterization and monitoring

Primary indicators of animal genetic diversityshould address both between-breed andwithin-breed components. Using breeds as the mainindicator of total animal genetic diversity wouldmiss out the important contribution of within-breeddiversity. National authorities need to recognize thelimitations of the breed concept and ensure that asmuch intraspecific genetic diversity as possible isaccounted for in strategies for inventory,characterization and monitoring.

Typically, inventory, characterization andmonitoring efforts will start by itemizing geneticallydistinct populations or “breeds”, the number ofanimals per population, and the number of farms

that keep these resources. As stated in The State ofthe World’s Animal Genetic Resources for Food andAgriculture (SoW-AnGR), inventory,characterization and monitoring should include theidentification, quantitative and qualitativedescription, and documentation of breedpopulations and the natural habitats andproduction systems in which they are embedded.Traits such as adaptation to a harsh environment,disease resistance, provision of environmentalservices, and product quality may receive specificattention depending on the context. Thus, it isnecessary to describe the economic, social andenvironmental context in which the breeds are used,including cultural aspects of peoples’ livelihoods.Furthermore, as socio-economic and environmentalcontexts evolve, criteria for evaluating breeds andtheir traits will also have to evolve.

Relevant scales

In principle, the strategy for inventory,characterization and monitoring should canvass allbreeding populations across relevant productionsystems within a country, and include the samplingof representative animals to generate populationdescriptor data.

However, depending on the geographicaldistribution of the breeding population, thepopulation size, breed risk status and economicsignificance, actions may be undertaken at differentscales. For endangered and at-risk populations,they may be carried out at the level of individualanimals, or populations of breeding animals infarms or stations. In the case of transboundarybreeds, the exercise may involve intercountrycollaboration, as in the case of commercial dairyand beef breeds included in multicountry breedevaluation programmes.

InventoryA nationally mandated institution for inventoryand monitoring is needed. At least in developingcountries, this institution should set up a nationalmechanism to verify whether a particular breed orpopulation represents a distinct unit of animalgenetic diversity in the country, and as such needsto be included in the primary inventory.

In any country, it will be necessary to identifythe number of farmers or communities that keep aparticular population that is registered in the

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national primary inventory. The national institutionin charge of the inventory will collect data fromgovernment extension services, as well as fromfarmers’ organizations – at any level from localcommunities to commercial companies. Involvinglivestock keepers and breeding organizations in theprocess has the added value of raising awarenessabout the value of the breeds in question. Bottom-upapproaches also exist, in which a communitydescribes a breed and brings it to the attention of theauthorities. Confidentiality issues may affectinventories of commercial lines; breedingcompanies do not always agree to divulge numbersfor the nucleus lines under selection.

In countries or areas where neither extensionservices nor breeding organizations can beidentified to provide census data, on-field countingand systematic georeferencing may be set up as aspecial effort to improve inventory. Georeferencingwill provide very useful information, as it allowsgeographical and climatic data to be linked to thedistribution of breeds within a country.

CharacterizationThe first step of characterization is the primaryassessment or baseline survey, which shouldinclude collection of data on population size andstructure, geographical distribution, productionsystems in which the breed is found, phenotypicattributes (physical features, performance levels andany unique features), historical development of thebreed through exchange, upgrading and selection,and the genetic connectedness of populations whenthese are found in more than one country (e.g. theN’Dama cattle breed of West Africa). Thewithin-population genetic diversity is measuredboth at the phenotypic level (phenotypic breeddiversity) and at molecular level; the two arecomplementary. All these data are needed to informdecisions on the utilization, improvement andconservation of the population.

Production systems and socialorganizations

As noted in the SoW-AnGR, the term “breed” is oftenaccepted as a cultural rather than a biological ortechnical term. Hence, in order to depict direct andindirect use values of breeds, they need to becharacterized in the context of the productionsystems and social structures in which they are

used. The objective is to allow comprehensiveinput/output analysis of the genetic resources inthe context of the agro-ecosystems of which theyform a part. The environmental impact of a breedingpopulation should also be considered as part of thecharacterization of the production system. Suchdata can be collected by survey. FAO has alreadydeveloped simplified formats for data collection formammals and poultry. The cost and time needed forsuch surveys should not be underestimated, butthey could benefit from being linked to trainingprogrammes, e.g. for MSc and PhD students.

Surveys will be organized differently dependingon the institutional background. In developedcountries, where commercial and conservationfarms keep registers of individual animals and theirpedigrees, structured surveys can be used to collectinformation on production systems and theenvironment. The procedure should take advantageof current data collection systems and additionalcosts should be quite limited. Yet, measurementsrelated to environmental impact of breeds and theirproduction systems are generally not included inroutine procedures and specific actions are neededto collect such information.

In countries where such data are not regularlyrecorded, specific surveys need to be set up. Fortraditional communities in pastoral and farmingproduction systems, participatory surveys andstructured interviews can be used to generate dataon breeding objectives, breed and trait preferencesand production system constraints. In the context oftraditional breeds, these descriptions give insightsinto the multitude of functions and services thatbreeds provide for their keepers. Statisticalsampling procedures can be applied to studylocalities, farms and individual animals once thesampling framework is defined.

In situations where limited documentedinformation on breed identification andcharacteristics is available, extensive exploratorysurveys may be necessary. However, exploratorysurveys have limitations; the facts generated arehighly subject to the biases of questionnairerespondents. Thus, steps need to be taken toground-truth and cross-check findings usingcomplementary procedures such as key-informantinterviews, focus-group discussions andreporting-back sessions with respondentcommunities. Consequently, these surveys becomedemanding in terms of time, skilled personnel andfinancial resources. This has been observed, forexample, in livestock breed surveys in Zimbabweand Ethiopia.

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Phenotypic characterization

The different phases of characterization involvemorphological attributes, biometrical indices,production levels (growth, reproduction, milk, egg,fibre, traction) and specific adaptations, includingsurvival. Morphological variants may be associatedwith known genes (coat colour, morphologicalmutations) and will benefit from their molecularcharacterization.

It is important that phenotypic measurements(biometrics and performance) should not focus onmeans or averages alone, but also account forvariations. It is the variation that provides the basisfor conservation and for present as well as futureutilization. For this reason, a large proportion of thepopulation should be included in the assessment ofperformance.Performance may be assessed either by directrecording of the animals or by exploitinginformation that is available in published literature,extension service field reports and reports ofbreeding units and organizations. Performancetesting may be done either on-farm or in testingstations.

On-farm testing

When genetic evaluation is performed utilizingnational records from on-farm testing, theassociated data can be made available forcharacterization, and breeding values should beincorporated. However, this is not feasible for pig orchickens breeding schemes run by companieswhich will not share their data.

For species or countries where there is nonational on-farm testing, specific action to collect

on-farm data is required. Technicians should betrained to collect morphological data. Picturesshould be taken utilizing a tape measure todocument phenotypic variability as thoroughly aspossible. In traditional communities, indigenousknowledge and practices associated with breedidentity and unique utility should also be compiledalong with population performance descriptors. Avariety of relevant participatory methods exist,including methods that allow livestock keepers torank breed and trait preferences, including traitswith non-market values. Simple criteria such assales and survival rates provide valuableinformation.

When georeferencing of phenotypic data isavailable, further biophysical data from theenvironment (climate, soil, vegetation cover, wateravailability, type and level of disease challenges)can be overlaid, and joint analysis in GIS(geographical information system) will help toassess adaptability traits.

On-station testing

On-station characterization makes it possible toevaluate breed performance and potential in arelatively defined and controlled productionenvironment. The limitations are that animals maynot necessarily be adapted to the controlledenvironment and that some traits such as grazingbehaviour and response to environmental stressorscannot be measured. Thus, the specific advantagesof a local population may not be recognized. Indeed,it is currently difficult to find objective criteria todescribe the adaptation of local populations tospecific climatic or feed conditions. Research isneeded in this field – identifying morphological and

Box 1. The Management of Farm Animal Genetic Resources in theSADC Sub-Region project

The implementation of the animal genetic resources characterization project for theSouthern African Development Community between 2000 and 2004 demonstrated thatthe human, financial and networking resources of public institutions and internationalresearch and development organizations can be harnessed to run large-scale exploratorysurveys. In this particular case, the United Nations Development Programme providedfunding; FAO and the International Livestock Research Institute provided expert adviceand guidance in the design, execution and evaluation of breed characterization surveys.

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physiological predictors for heat tolerance orwalking ability, for instance. Moreover, suchunknown adaptive traits are usually not capturedin a standardized research protocol; new protocolsneed to be developed. Conversely, a controlledenvironment allows more precise measurement ofindividual performance, pedigree recording andestimation of genetic parameters, and providesopportunities to undertake multiple comparisons(breeds and production environments) acrossstations, so as to assess genotype by environmentinteractions. A positive aspect of on-stationcharacterization is that it may contribute to theestablishment of a nucleus population andcontribute to the conservation of the resource beingcharacterized.

Advanced phenotyping

Product quality is generally considered by breedingorganizations using precise descriptors, which aredefined according to the destination of the product,taking into account indications from nutritionistsand food processors. For instance, fat percentage inmilk is analysed in terms of fatty-acid composition,and protein percentage can be detailed according tothe different types of caseins. Furthermore, systemshave been set up in Europe to associate a productwith a certificate of origin, such as ProtectedGeographic Indication1 and Protected Designationof Origin2, which generally include the breed oforigin of the product (Box 2). The same concept isapplied for goat meet in Argentina (Box 3). In manyAfrican and Asian countries, specific products arealso associated with local breeds, and accuratedescription of the product should be undertaken inorder to better define it and, consequently,characterize the breed. This requirescapacity-building for the definition of productquality requirements, and the establishment of anofficial system for certifying that the product andproduction methods meet these requirements.

Disease resistance is a high priority for severalreasons: local breeds survive in harsh environmentsand this needs to be better understood; epidemicsare major threats for all animal genetic resourcesacross the world; climatic change is likely toincrease the spread of tropical diseases to temperateareas. In addition to claims that local breeds areadapted and resistant, scientific evidence has beenobtained in several instances (examples arereported in the SoW-AnGR). The effect isparticularly well documented for parasitic diseases,

which are very prevalent in tropical areas, withlocal breeds maintaining a better performance in thepresence of parasites and/or exhibiting lower levelsof parasite infestation. Generally, this condition isbetter described as tolerance, a typical examplebeing trypanotolerance in cattle. Generally, moredata are needed on exposure and response ofanimal populations to parasites, viruses andbacteria. One delicate question involves possibleconfusion between resistance and a healthy-carrierstate for a given pathogen. True resistance, in whichthe host does not allow the pathogen todisseminate, is the objective of most research studiesin developed countries. This is consistent with theassumption that it will be possible to eradicate thepathogen. However, this seems unrealistic fortropical parasites. Thus, research is focusing ondefence mechanisms, in order to better understandthe permanent race between hosts and pathogens.Furthermore, epidemiological studies suggest thatpathogens may adapt more easily to uniformgenotypes, and that genetic variation of the host isone key to limiting pathogen expansion. Thus,cooperation between Northern and Southerncountries is needed to better characterize thepotential usefulness of animal genetic resources fordisease control. This may benefit from progress ingenomics and the identification of genes forresistance to major diseases, as well as in theunderstanding of general immune response.

Molecular characterization

The impressive development of molecular tools inthe past 20 years benefits the characterization ofanimal genetic resources in many ways – which arealready well documented in the SoW-AnGR. It isimportant that countries are aware of whatquestions molecular tools can or cannot answer at

1Protected geographical indication: the name of a region,specific place or country describing a product originating inthat region, specific place or country and possessing aquality or reputation which may be attributed to thegeographical environment with its inherent natural and/orhuman components.2Protected designation of origin: the name of a region,specific place or country referring to a product originating inthat region, specific place or country and whose quality orother characteristics are essentially or exclusively due to aparticular geographical environment.

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Box 2. Differentiation in chicken meat production in France

The French production of chicken meat is differentiated into several categories: standardbroiler (SB), label chicken (LB), certified chicken (CF), organic chicken, and Appellationd’Origine Contrôlée (AOC = Protected Designation of Origin) for the Bresse breed only. WhereasLB production represented nearly 100 million chickens in 2002 (www.synalaf.fr), the BresseAOC represented 1.4 million chickens raised only in the Bresse geographical area as definedby law. The LB category was created in 1965, to promote product quality throughout theproduction process. The LB and CF legal definitions do not require reference to a particularbreed, but only slow-growing lines are eligible. These slow-growing lines are generallycharacterized by a coloured phenotype, easy to distinguish from the white plumage of SB.The philosophy of AOC is quite different since it defines a geographical district which ischaracterized by specific features of the natural conditions and production system. For theBresse, the district was defined as early as 1936 and the protection of the name “Volaille deBresse” was enshrined in law number 57-866 on August 1, 1957. The Bresse breed standardincludes white plumage and blue shanks, which is a rare association among French poultrybreeds. A fixed set of growing conditions (density, open-air access, type of feed) must beapplied for at least 9 weeks, starting from 5 weeks of age. Then, the finishing period,slaughtering conditions and carcass processing are strictly regulated. The minimal age atslaughter for the Bresse is 112 days, whereas it is 84 days for LB and 39 days for SB. Tastingpanels are regularly organized to check the meat quality. The selection procedure for theBresse breed has also been strictly regulated and is managed by a selection centre (CSB)which is working in close collaboration with farmers. The Bresse breed is the only localFrench chicken breed the population size of which has not decreased since 50 years, andcredit must be given to the AOC for this success (Verrier et al., 2005).

Box 3. Differentiation of goat meat in Argentina

The traditional goat production system from North Neuquén (Patagonia, Argentina), developed bytranshumant goat keepers is a marginal system with low economic input and fragile environmentbut with a high cultural capital, an adapted genetic resource and a product with high reputation butnot differentiated. To overcome this situation the application of a Geographical Indication wasdeveloped. This process was based on the organization of the local goat meat marketing chain andthe description of technological properties of the product of the Neuquén Criollo breed. The chainactors developed a common vision about the system and its identity, which is reflected in the Protocolof the Designation of Origin of the “Criollo Kid of North Neuquén”. A study on the product’s typicalcharacteristics and quality has contributed to define quality indicators and traceability of the product.As a result, the goat keepers’ organizations have been empowered, a common ground ofcommunication has been established enhancing the understanding level among local actors, whichwas previously not existent. This has reinforced regional development and given projection tosustainability of the system and genetic resource (Pérez Centeno et al., 2007)

present, and how this may change in the future. It isalso important to consider that the broad array oftools that is available in the case of the “big five”species is not available for species with a morelimited geographic distribution, but which shouldnot be neglected.

Some practical considerations

The first step is to collect samples of sufficientquality from representative animals of thepopulation to be described – either a well-knownbreed or a non-described population (FAO, 1993).

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The general recommendation is to sample 30 to50 unrelated individuals, in flocks or herdscovering a wide geographical area, taking intoconsideration historical exchange of breedingstocks, and agro-ecological zones as possiblebarriers to gene flow between populations. Theseare minimum numbers. Ideally, half the sampleshould be females and half males. A cleardescription of the sampling procedure is needed,both for immediate use of the samples and to allowthe samples to be used for future studies. Ideally, theanimals sampled should also have been subject tophenotypic characterization.

The required DNA quality depends on theintended future use. Several protocols are available,and good quality should be the aim. Blood orear-tissue samples are ideal for typing nuclear andmitochondrial DNA (mtDNA) markers, but suchsampling is not always accepted by the farmer. It ispossible to extract sufficient DNA from hair bulbs toallow the typing of microsatellite DNA markers, butsuch samples are not easy to work with in the caseof mtDNA and other markers. Extraction kits areexpensive, but should provide repeatable quality.Manual extraction needs trained personnel.Whatever the protocol, DNA quality should bechecked before samples are used or sent forgenotyping.

Molecular markers involve genomic and mtDNAloci. Microsatellite markers are most commonlyused because they are multi-allelic and numerous,and can be genotyped on automatic machines. Newmicrosatellite marker sets of 20 to 30 loci per speciesrecommended by the International Society ofAnimal Genetics (ISAG)/FAO Standing Committeeare available for most species (FAO/ISAG, 2004). Itis highly recommended that a core set of a minimumof 15 markers be included so as to allowcomparative studies across countries. Merginggenotype data sets produced in differentlaboratories has proven to be possible though quitechallenging. Exchange of reference samplesbetween laboratories is mandatory, and training oftechnicians to score the genotypes following thesame procedure is necessary. Statistical methods formeta-analysis are also under development to makethe best possible use of available data in order tomerge all information and facilitate internationalcomparisons. The problem of standardizingmicrosatellite typing is not encountered in the caseof typing single nucleotide polymorphisms (SNPs)because technologies are available to providestandardized reading of SNPs and to produce datathat can be merged between laboratories. SNPs arediscussed in more details in Box 7.

Assessment of genetic diversity with anonymousDNA markers

The first question that anonymous DNA markerscan answer relates to the diversity level within apopulation, which can be described by number ofalleles, number of private alleles, or observed andexpected heterozygosity. Generally, the diversitylevel of domestic breeds/populations has beenfound to be lower than that of wild relatives andancestors. Diversity can be expected to havegradually declined during the dispersal of livestockpopulations from their centres for domestication ororigin to their current locations, mainly as a resultof random genetic drift. However, this pattern maybe distorted by the introduction of exotic breeds,cross-breeding between populations, admixture ofpopulations from different centres of domesticationand human selection. Thus a careful examination ofthe population’s history is warranted. It is also wellknown that heterozygosity estimates are not sosensitive to the change of number of alleles,particularly in the case of multi-allelic microsatellitemarkers. Therefore, the adjusted mean number ofalleles according to sample sizes could be a betterparameter to measure genetic diversity withinbreeds or populations.

Methods have been proposed, and are still underdevelopment, to estimate the effective populationsize of a breed or population from molecular data,particularly from linked markers. It is also possibleto detect departure from the equilibrium state eitherdue to excessive inbreeding or to populationfragmentation in subgroups that have few or noexchanges between them. Thus, DNA markers canbe used for monitoring conservation programmesaimed at avoiding inbreeding, genetic bottlenecksand fragmentation. Furthermore, they can be used toidentify “livestock biodiversity hotspots” as priorityareas for conservation of indigenous livestockpopulations. Typically, populations containinglarge variation at anonymous loci are expected alsoto exhibit large variation for functional traits. Thus,DNA markers could be most useful in cases wherelittle information on population history is available.However, anonymous markers do not at presentprovide a reliable prediction of phenotype; they donot replace performance measurements and shouldnot be used alone to make conservation decisions.

The second area in which DNA markers provideuseful answers includes questions of relatednessbetween populations, detection of admixture,introgressions and breed identity. Between-breedvariation may be described by geneticdifferentiation indices, such as FST for which

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statistical significance can be calculated in order toconclude whether or not genetic differentiationtakes place between pairs of populations. Allelicfrequencies for molecular loci also provide the basison which to calculate genetic distances. Asmentioned in the SoW-AnGR, phylogeneticreconstruction of the evolution of breeds orpopulations is not well adapted to the dynamics ofdomesticated populations, which do not divergestrictly from a common ancestor and may includecross-breeding, admixture and introgression eventsin their histories (Box 4). In the case of selected linesderived from the same breed, phylogeneticreconstruction with neighbour-joining tree canreveal clustering (Box 5).

Multivariate methods offer a different approach,which unlike phylogenetic trees, does not rely onany evaluative assumption. Bayesian clustering hasbeen shown to be very efficient for the assignment ofindividuals to breeds or populations and as ameans to detect population structure and admixturewithout any prior information on populationancestry. Recent results obtained in chickenpopulations, both traditional and commercial lines,showed that more than 90 percent of individualscould be assigned to their true breed of originaccording to their genotypes for microsatellitemarkers (Box 6).

Thus, DNA markers allow the definition of thegenetic entity behind the breed. This can clarify theprocedure of inventories and identify the basepopulation for conservation programmes.Knowledge of the molecular identity of certainbreeds or populations may also be used to establishbiological identification systems for certificationand traceability of living animals and derivedproducts.

In addition to nuclear markers, both mtDNA andmarkers from the Y chromosome of mammalsprovide additional information on the history ofdomestication and introgression events. Veryinteresting results have been obtained for ruminantsin this respect. These data may also be usefulbecause they shed light on peculiar adaptive traitsthat these populations may have accumulated overtime.

Known genes and functional diversity

Progress in genome annotation and quantitativetrait loci (QTL) programmes has led to theidentification of many candidate genes that arelikely to influence traits of interest. QTLprogrammes and genome databases are availablefor the “big five” species. Comparative genomicsmay also facilitate the assessment of functionaldiversity by transferring knowledge betweenspecies. Significant progress has been made in themolecular identification of genetic abnormalities aswell as major genes affecting meat quality ormuscular growth. Some causal mutations, as wellas diagnostic methods for these mutations, havebeen patented, and new alleles may be present insome indigenous populations. Therefore, the issueof intellectual property (IP) arising from thediscovery of functional diversity and exclusive ornon-exclusive use of this IP has to be addressed. Asfar as QTL are concerned, finding genes responsiblefor the quantitative effect on the performance is stillrare. Furthermore, the effect of a QTL region maydepend on the genomic background: epistaticinteractions are known to take place, so that a givenQTL region identified in one population may not be

Box 4. Sheep biodiversity

The ECONOGENE project combined a molecular analysis of biodiversity, socio-economicsand geostatistics to address the diversity and conservation of small ruminants in marginalagro-ecosystems. The population structure and genetic diversity of 57 European and MiddleEastern sheep breeds from 15 countries were analysed by typing 31 microsatellite markers,thereby extending the available knowledge of sheep diversity at the molecular level. Thedomestication centre for sheep lies in the Near and Middle East, and the results showedhigh levels of genetic variation among Middle-Eastern and South-eastern European breeds.The analysis of markers and of the spatial distribution revealed the occurrence of twoclusters, one with north-western European breeds and the other withMiddle-Eastern/southeastern European breeds.Source: Peter et al. (2007)

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Box 5. Pig biodiversity

The European PigBiodiv project used 50 microsatellite markers to assess the between- and thewithin-breed genetic diversity for a set of 59 pig breeds. The resulting structure of eight groups(bootstrap) showed within-breed clustering of pig lines. The national populations of majorbreeds and the commercial lines were clustered around their breeds of reference (Duroc,Hampshire, Landrace, Large White and Pietrain) in most cases. The Meishan breed representeda specific outgroup. Local breeds did not group into one cluster and appeared to be scatteredwithin the global frame. Using only 18 markers decreased the reliability of the clustering,particularly for the Landrace breed.Source: San Cristobal et al., (2006).

Box 6. Breed assignment with anonymous markers

The AvianDiv project used 27 microsatellite markers to genotype 30 animalsfrom 20 chicken populations, ranging from the wild ancestor to highlyselected commercial lines. After an analysis with the “Structure” software,it was possible to assign birds to their correct breeds with 90% efficiencyusing 12 markers. After 24 markers, efficiency remained close to 97%. Correctassignment of commercial birds to their true line of origin was the mostdifficult and required all markers.

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Figure adapted from Rosenberg et al. (2001).

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relevant for another population. An integratedstrategy using molecular markers would be to mapthe genetic diversity among indigenous livestockbreeds/populations to test hypotheses about whichof them may carry unique QTL for diseaseresistance.

The transcriptomics approach has enabled theexploration of gene expression patterns forthousands of genes simultaneously. But thisapproach has not been used to a large extent fordiversity studies. It raises a number of questions,regarding the tissue to be sampled, the stage ofsampling, and very often requires animals to beslaughtered. The best examples deal with the studyof disease resistance, where multigenic expressionpatterns can efficiently describe the mechanismsinvolved in defence responses, and can identifyrelevant differences between breeds. Thus, moreexperimental data are needed before geneexpression patterns are incorporated intocharacterization.

The final effector molecules are proteins.Proteomics has also made significant progress,although it raises delicate methodological issuesand has not yet been applied to the characterizationof genetic diversity. Research is needed to improvethis approach which may open the way to intensivephenotyping.

Prospects with high-density single nucleotidepolymorphisms

The full genome sequence is or will soon beavailable for chickens, cattle, pigs and sheep (andgoats) and large numbers of single nucleotidepolymorphisms (SNPs) are becoming available(Box 7). As compared to microsatellites, mtDNA andpolymorphisms of known genes, the use ofhigh-density SNP markers offers quite newperspectives: these markers are so numerous thatthey may unravel the fine structure of the genomeand identify chromosomal segments showingselection signatures. This will greatly improve ourknowledge of population genetic make-up.Large-scale SNP typing has already started inselection programmes for cattle (dairy and beef) andchickens. Performance recording is still necessary atcrucial steps of characterization programmes, todefine the association between genotypes anddesired phenotypes. Alleles, haplotypes orquantitative trait nucleotides (QTN) could then beused to estimate a breeding value genome-wide.This represents one step forward from the currentmarker-assisted selection programmes, which track

a limited number of QTL regions to whole genomeselection. Thus, the whole organization of datacollection may change in the coming years. FAO’sinformation system will have to be updated to takeinto account these trends.

Advanced inventory andmonitoringAll countries need an active inventory andmonitoring strategy for their animal geneticresources – to better understand, use, develop,maintain, conserve and access these resources. TheGlobal Plan of Action for Animal Genetic Resourcesrecognizes the need to have a country-basedstrategy so that activities for inventory andmonitoring can be linked and coordinated withrelevant country-level action plans such asagricultural censuses or livestock populationsurveys. Indicators are needed for populationtrends, breed risk status and changes in theproduction environment. Apart from theopportunity of carrying out meta-analysis ofnationwide data to establish trends andinformation gaps, country-based strategies alsoencourage the establishment of informationdatabases of animal genetic resource inventorywhich can provide a comprehensive source ofinformation for research, development of breedingstrategies, conservation programmes, policyframeworks and even training.

Monitoring driving forces and describingproduction environments

Production environments are dynamic, albeit atdifferent scales and rates. As discussed in theintroductory paper to this series, the major driversof change that are of relevance to the management ofanimal genetic resource diversity are populationgrowth, urbanization, and the associated changesin the structure and volume of demand for livestockproducts, globalization, climate change and globalhealth hazards such as avian influenza. All of thesedrivers should be monitored to predict futurescenarios and allow improved preparedness to meetfuture challenges.

Indicators related to production environmentwere elaborated at an FAO expert consultationwhich met in Armidale, Australia in 1998. Fivemain criteria (climate; terrain; disease, disease

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complexes and parasites; resource availability; andmanagement) were identified as the basis for thecharacterization of production environments for alllivestock species, with three to seven indicators foreach criterion (FAO, 1998). The framework isdemanding in terms of resource requirements andneeds to be operationalized, but can be used toselect priority criteria and indicators that better meetspecific needs.

The application of georeferencing tools can makea major contribution to improving the scope andscale of advanced inventory and monitoring both atcountry and global levels.

Monitoring animal populations

Through their ratification of the Convention onBiological Diversity, countries are committed toinventory and monitoring of the status of theiranimal genetic resources. However, country reportsprepared during the SoW-AnGR reporting processshow that national inventories have either not beencarried out or are still incomplete.

Monitoring requires regular checking ofpopulation status, and the evaluation of trends inthe size and structure of breed/populations, theirgeographical distribution, risk status and geneticdiversity. If breeders’ associations or other groupsinterested in breed maintenance and promotionexist, it may be possible to update the inventoryannually. In the absence of such groups, themandated national institutions must ensure that

periodic assessment of breed status are carried outideally on annual or biennial basis, or at least atintervals of one generation for the species inquestion. This would require comprehensiveupdating at intervals of about eight years for horsesand donkeys, five years for cattle, buffaloes, sheepand goats, three years for pigs and two years forchickens. Once a breed has been identified as atrisk, a more intensive monitoring programme isneeded on an ongoing basis.

As noted in the SoW-AnGR, monitoring can bean extremely expensive aspect of the managementand should take as much advantage as possible ofexisting resources and activities.

Defining indicators for animal geneticdiversity

A compromise has to be found between the ideal listof indicators needed to provide accurateinformation, and the cost of collection and ease ofinterpretation. As stated by OECD (2001), four maincriteria may be used to assess the value ofindicators: policy relevance, analytical soundness,measurability and interpretation. In general, a smallnumber of indicators is preferable in terms ofmeasurability and communication, but relevantinformation needs to be captured in order tosupport sound decisions.

The existing FAO definitions of breed risk status(extinct, critical, endangered and not at risk) are

Box 7. A new approach of genome diversity with SNPs

Large numbers of SNPs have been or will be generated as companion programmes ofthe genome sequencing efforts undertaken for the “big five” species. SNPs are mainlybi-allelic due to the low frequency of mutations. Therefore, only a higher number ofSNPs can achieve information content comparable to that obtained using a givennumber of microsatellite markers. Characterization of the same set of ten chickenbreeds using 29 microsatellite markers and 145 SNPs confirmed that increasing thenumber of SNPs had a higher impact on the reliability of the results than increasingthe sample size (Hillel et al., 2007). Heterozygosity and allelic-richness estimatesobtained for SNP markers exhibit a lower order of magnitude as compared tomicrosatellite markers, with values in the range of 0.34 and 1.94, respectively, acrossa set of Holstein-Friesian bulls (Zenger et al., 2007). It is likely that systematic molecularstudies of animal genomes will use SNPs and handle questions of selection andmanagement of genetic diversity at the same time. Cost of typing SNPs is steadilydecreasing, but SNPs are valuable only when they are very numerous (e.g. more than3 000). Therefore, the absolute cost of typing is still a matter to be considered.

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based on numbers of breeding females and males,but do not relate to how matings are handled(e.g. random or high selection intensity withinbreeds, use of crossbreeding). Major drivers ofchange can lead to rapid changes in the populationsize and structures of locally adapted breeds.Regular monitoring is therefore required, at least forthose breeds classified as critical or endangered. Atpresent, most national livestock censuses do notcontain breed-level data; therefore, regular reportingof breed population numbers does not usually takeplace. In addition to population size, the number offarms and number of breeding organizations couldbe considered. The number of breeding malesshould be made available. Such a monitoringscheme can serve as the basis for national earlywarning, so that timely management interventionscan be planned. Monitoring programmes need toensure that feedback is provided to farmers,researchers and other stakeholders.

Recent research suggests that several issuesneed to be taken into account for the development ofindicators for animal genetic diversity:• the concept of the breed as a genetic entity for

measuring diversity would benefit from the useof molecular markers for the assignment ofindividuals to breeds .

• the assessment of breed risk status should notrely on population size alone, but would benefitfrom more accurate parameters calculated on thebasis of extensive pedigree analysis, such asinbreeding coefficients of current breedinganimals, or the number of ancestors with acumulated contribution of 50 percent of the totalgene pool.

• in the absence of pedigree recording, loss indiversity may be monitored using molecularmarkers, particularly on the basis of the adjustedmean number of alleles calculated for referencesets of microsatellite markers.

• occurrence of introgressions or fragmentationsmay be monitored with molecular markers,combining nuclear markers and mtDNA,provided that reference data sets for a range ofpopulations are available for comparativeanalysis within a country or region.Target values for country-based early warning

tools are yet to be developed. It is essential toestablish both baseline (inventory) and follow-up(monitoring) assessments to effectively informdecision-making in the management and utilizationof animal genetic diversity. Monitoring of diversityshould address both the level of between-breeds

diversity, with setting up conservation programmesfor endangered populations, and the level ofwithin-breed diversity with updating rules for thegenetic management of the population (Fikse &Philippson, 2007).

Conclusions andrecommendationsInventory and characterization of animal geneticresources should be an iterative process. Regularupdates are necessary, because animal geneticresources are exposed to strong driving forces, bothfrom the viewpoint of production systems andemerging technologies.

Data from all types of populations are relevantfor the Domestic Animal Diversity InformationSystem (DAD-IS) managed by FAO. In order tominimize information gaps, the concept of the breedshould be understood in a broad sense. Inventoryshould include criteria to assess within-breeddiversity. National databases have to be set up andshould be coordinated at a regional level and withFAO, in order to facilitate the comparisons and theupdating of information.

A comprehensive description of productionenvironments is needed in order to betterunderstand the comparative adaptive fitness ofspecific animal genetic resources. It will also help toidentify threats and options for the management ofthese resources.

On-field and on-station phenotypiccharacterization are complementary. Performancedata should focus on variability as much aspossible and not only include means. Defencemechanisms against pathogens should be apriority, given the significance of the threats posedby epidemics and climate change.

It is likely that microsatellite markers will remainthe first choice for the analysis of genetic diversityin many domestic species in the near future. Stepsshould be taken to support comprehensivemulticountry studies, and to facilitatemeta-analysis. On the technical side, this requiresimproved exchange of reference samples andstandardization of genotyping procedures. From themethodological perspective, appropriate modelsneed to be developed and tested.

Anonymous markers provide a range ofinformation, from population history to breedidentity. However, the number of markers which issufficient for population genetics studies does notallow any prediction of performance. Thus,

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available molecular genetic markers should be usedtogether with phenotypic data.

Recent technologies for large-scale geneexpression studies and high-throughputSNP genotyping are likely to greatly modifycharacterization tools, with the prospect of betterconnecting phenotypes to genotypes. Costs are stilltoo high for these procedures to be used insystematic surveys of genetic diversity, but inspecies such as cattle and chickens in which thegenome has been sequenced, these technologies arelikely to rapidly prove their usefulness in achievinga comprehensive approach to the assessment ofgenetic diversity.

Data on production systems, phenotypes andmolecular markers should be used altogether in anintegrated approach to characterization. Decisionsregarding conservation should incorporate alldescriptors. Conserving without documentingwould be useless. National authorities should beaware that sharing information and data isessential to support cost-effective decisions in themanagement of animal genetic resources.

List of referencesFAO. 1993. Secondary Guidelines for

Development of National Farm Animal GeneticResources Management Plans. Measurement ofDomestic Animal Diversity (MoDAD): OriginalWorking Group Report. Rome.

FAO. 1998. Report: Working group onproduction environment descriptors for farmanimal genetic resources. Report of a WorkingGroup, held in Armidale, Australia, 19–21 January1998. Rome.

FAO. 2007. The State of the World’s AnimalGenetic Resources for Food and Agriculture, editedby B. Rischkowsky & D. Pilling. Rome, (alsoavailable at ftp://ftp.fao.org/docrep/fao/010/a1250e/a1250e.pdf), pp. 511.

FAO/ISAG. 2004. Secondary Guidelines.Measurement of Domestic Animal Diversity(MoDAD): New recommended microsatellitemarkers. (also available at. http://dad.fao.org/cgi-bin/getblob.cgi?sid=-1,50005882).

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Pérez Centeno, M., Lanari, M.R., Romero, P.,Monacci, L., Zimerman, M., Barrionuevo, M.,Vázquez, A., Champredonde, M., Rocca, J.,López Raggi F. & Domingo, E. 2007. Puesta envalor de un sistema tradicional y de sus recursosgenéticos mediante una Indicación Geográfica: Elproceso de la Carne Caprina del Norte Neuquino enla Patagonia Argentina. Animal Genetic ResourcesInformation Bulletin, 41, 17-24

Peter, C, Bruford, M., Perez, T.,Dalamitra, S., Hewitt, G., Erhardt, G. & TheEconogene Consortium, 2007. Genetic diversity andsubdivision of 57 European and Middle-Easternsheep breeds Animal Genetics, 38: 37–44

Rosenberg, N.A., Burke, T., Elo, K.,Feldman, M.W., Freidlin, P.J., Groenen, M.A.M.,Hillel, J., Maki-Tanila, A., Tixier-Boichard, M.,Vignal, A., Wimmers, K., Weigend, S. 2001.Empirical evaluation of genetic clustering methodsusing multilocus genotypes from 20 chicken breeds.Genetics, 159, 699–713.

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& Cardellino, R. 2006. Genetic diversity within andbetween European pig breeds using microsatellitemarkers. Animal Genetics, 37: 189–198.

Verrier, E., Tixier-Boichard, M.,Bernigaud, R. & Naves, M. 2005. Conservation andvalue of local livestock breeds: usefulness of nicheproducts and/or adaptation to specificenvironments. Animal Genetic ResourcesInformation Bulletin, 36, 21–32

Zenger, K.R., Khatkar, M.S.,Cavanagh, J.A.L., Hawken, R.J. & Raadsma, H.W.2007. Genome-wide genetic diversity of HolsteinFriesian cattle reveals new insights into Australianand global population variability, including impactof selection. Animal Genetics, 38: 7–14.

Bibliography for further readingAyalew, W., van Dorland, A. & Rowlands, J.

(Eds). 2004. Design, execution and analysis of thelivestock breed survey in Oromia Regional State,Ethiopia. Nairobi, OADB (Oromia AgriculturalDevelopment Bureau), Addis Ababa, and ILRI(International Livestock Research Institute), pp. 260.

Berthier, D., Chantal, I., Thévenon, S.,Marti, J., Piouemal, D. & Maillard, J.C. 2006. Bovinetranscriptome analysis by SAGE technology duringan experimental Trypanosoma congolenseinfection. The Annals of the New York Academy ofSciences, 1081: 286–299.

Cunningham, E.P. & Meghen, C.M. 2001.Biological identification systems: genetic markers.Revue scientifique et technique de l’Officeinternationale des epizooties, 20: 491–499.

Doherty, M.K., McLean, L. & Beynon, R.J.2007. Avian proteomics: advances, challenges andnew technologies. Cytogenetics and GenomeResearch, 117: 358–369.

Drucker, A., Gomez, V. & Anderson, S.2001. Economic valuation of farm animal geneticresources: a survey of available methods. EcologicalEconomics, 36 (1): 1–18.

Eaton, D., Windid J., Hiemstra, S.J.,van Heller, M., Trach, N.X., Hao P.X., Doan, B.H. &Hu, R., 2006. Indicators for livestock and cropbiodiversity. Centre for Genetic Resources,CGN/DLO foundation, report 2006/05,Wageningen, the Netherlands.

FAO. 2006. A System of IntegratedAgricultural Censuses and Surveys, Volume 1,World Programme for the Census of Agriculture2010, (SDS No. 11). (also available at www.fao.org/es/ess/census/default.asp).

FAO. 2006. The role of biotechnology inexploring and protecting agricultural geneticresources, edited by J. Ruane & A. Sonnino. Rome.(also available at www.fao.org/docrep/009/a0399e/a0399e00.htm).

Freeman, A.R., Bradley, D.G., Nagda, S.,Gibson, J.P. & Hanotte, O. 2006. Combination ofmultiple microsatellite datasets to investigategenetic diversity and admixture of domestic cattle.Animal Genetics, 37: 1–9.

Gandini, G.C., Ollivier, L., Danell, B.,Distl, O., Georgoudis, A., Groeneveld, E.,Martyniuk, E., van Arendonk, J.A.M., &Woolliams. J.A. 2004. Criteria to assess the degree ofendangerment of livestock breeds in Europe.Livestock Production Science, 91:173–182.

Gibson, J.P. & Bishop, S.C. 2005. Use ofmolecular markers to enhance resistance oflivestock to disease: a global approach. Revuescientifique et technique de l’Office internationaledes epizooties, 24: 343–353.

Gibson, J.P., Ayalew, W. & Hanotte, O. 2007.Measures of diversity as inputs for decisions inconservation of livestock genetic resources. In:D.I. Jarvis, C. Padoch & H. D. Cooper (Eds).Managing biodiversity in agricultural ecosystems.New York, Columbia University Press, pp. 117-140.

Hanotte, O., Bradley, D.G., Ochieng, J.,Verjee, Y., Hill, E.W. & Rege, J.E.O. 2002. Africanpastoralism: genetic imprints of origins andmigrations. Science, 296(5566): 336–339.

Kadarmideen, H.N., von Rohr, P. &Janss, L.L.G. 2006. From genetical genomics tosystems genetics: potential applications inquantitative genomics and animal breeding.Mammalian Genome, 17: 548–564.

Moazami-Goudarzi, K. & Laloe, D. 2002. Is amultivariate consensus representation of geneticrelationships among populations alwaysmeaningful? Genetics, 162: 473–484.

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Mburu, D.N., Ochieng, J.W., Kuria, S.G.,Jianlin, H., Kaufmann, B., Rege, J.E.O. &Hanotte, O. 2003. Genetic diversity andrelationships of indigenous Kenyan camel(Camelus dromedarius) populations: implicationsfor their classification. Animal Genetics, 34: 26–32.

Muchadeyi, F.C., Eding, H., Wollny, C.B.A.,Groeneveld, E., Makuza, S.M., Shamseldin, R.,Simianer, H. & Weigend, S. 2007. Absence ofpopulation substructuring in Zimbabwe chickenecotypes inferred using microsatellite analysis.Animal Genetics, 38: 332–339.

Pritchard, J.K., Stephens, M. & Donnelly, P.2000. Inference of population structure usingmultilocus genotype data. Genetics, 155: 945–959.

Tano, K., Kamuanga, M., Faminow M.D. &Swallow, B. 2003. Using conjoint analysis toestimate farmers’ preferences for cattle traits in WestAfrica. Ecological Economics, 45(3): 393–408.

Tuggle, C.K., Wang Y.F. & Couture, O. 2007.Advances in swine transcriptomics. InternationalJournal of Biological Sciences, 3: 132–152.

Vignal, A., Milan, D., SanCristobal, M. &Eggen, A. 2002. A review on SNP and other types ofmolecular markers and their use in animal genetics.Genetics Selection Evolution, 34: 275–305.

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Mr Richard Clarke, Rare Breeds Survival Trust(RBST), United Kingdom

As the first NGO interested in the conservation offarm animal genetic resources we fully support theapproach presented in this paper. Inventory,characterization, monitoring and utilization are thecore principles that have driven the work of theRBST since its creation in 1973.

Since 1973, the RBST followed these principlesfor over 70 breeds of large livestock native to theUnited Kingdom. Since 1976, RBST has sought toshare its awareness of breeds at risk through thepublication of an annual watchlist. Eligibility isbased on numerical, distribution and geneticfactors. Over the past thirty years RBST hasoverseen the movement of 11 breeds from an“at risk” classification to mainstream.

Initially the Trust was independent ofgovernmental agencies, but now is working moreclosely with them. Surveys of endangered breedshave been undertaken by RBST since 1976, but since1994 the RBST, in close association withgovernment agencies, has undertaken surveys of alllivestock breeds in the United Kingdom. Surveyshave been every 4–5 years.

In the past twelve months much of the work ofthe RBST has been encapsulated in the DEFRA(Department of Environment, Food and RuralAffairs) UK National Action Plan on Farm AnimalGenetic Resources.

Finally, I would like to make a couple ofobservations concerning issues raised in this paper.

From the RBST’s years of experience inconsidering breeds at risk of extinction, apreoccupation on numbers at the cost of anawareness of within-breed diversity, andgeographical distribution can be dangerous.

This paper clearly demonstrates how technologyis rapidly developing to allow us to better connectphenotype to genotype, but with it comes the threatthat these technologies will allow more rapidselection for a specific phenotype, thus threateninggenetic diversity.

Mr Milan Zjalic, International Committee forAnimal Recording (ICAR), ItalyAnimal identification and recording as tools incharacterization of animal genetic resources

“Characterization of AnGR encompasses all activitiesassociated with the identification, quantitative andqualitative description, and the documentation of breedpopulation…” (State of the World report, Part 4 –Section B, Methods for characterization).

Identification and registration (I&R) areimportant tools at all stages of an animal’s life, aswell as in any part of the food production processsuch as:• Farm and herd management.• Animal recording.• Animal breeding.• Animal health and disease surveillance.• Trade.

Animal marking is associated to thedomestication of different animal species byhumans. Identification techniques are classifiedaccording to characters used and to theirpermanence on the animal. Main artificialpermanent systems are branding (hot-iron andfreezing), tattooing, ear notching, ear tagging (metaland plastic) and electronic identification (injectable,ear tags and bolus), but natural systems are alsoused (mainly retinal imaging and molecularmarkers). Recent experience has shown thatelectronic identification in spite of its high-technature is the most suitable method of identification,also for developing countries. In this respect, the useof boluses for ruminants and injectables formonogastric animals are recommended. Molecularmarkers are routinely used in parentageregistration.

Description and documentation of phenotypiccharacteristics of the breed population includesrecording all traits of economic importance such asproduct yield, quality of products, longevity andreproduction traits. For decision-making onconservation strategies and on developments ofbreeds, it is necessary also to collect data on birthweight, age at sexual maturity, daily gain andothers. Data should be collected, stored andprocessed in a uniform and standardized manner,so that they can be retrieved and compared withfuture data as well with data related to other localor mainstream breeds.

Panellists’ comments and discussion

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The International Committee for AnimalRecording (ICAR) is composed of national andlocal organizations involved in animalidentification, recording and genetic evaluation.The object of ICAR is to promote the developmentand improvement of performance recording andevaluation of farm animals through establishingdefinitions and standards for measuring animalcharacteristics having economic importance.Working together, Members of ICAR establish rules,standards and guidelines for the purpose ofidentifying animals, the registration of theirparentage, recording their performance, evaluatingtheir genetics and publication of such.

The present structure of ICAR as a registerednon-profit INGO provides for full participation ofits members in developing guidelines andrecommendations on the basis of the soundscientific evidence. Guidelines represent minimumrequirements set up to ensure a satisfactory degreeof uniformity of recording among member countriesand a maximum flexibility in the choice of methods.ICAR’s logo – an antique Roman scale andinscription in Latin “Quod scriptum est manet” (whatis written remains) symbolizes the message that onecan measure animal traits using available tools andthat data should be registered for future use.However, only standardized methods ensureuniformity of data and adequate evaluation of traits.

Animal identification, performance recordingand genetic evaluation are of particular importancefor the sustainable utilization of animal geneticresources and development of animal production indeveloping countries. For this reason, ICARencourages and supports experts from countrieswith prevailingly low to medium input productionsystems in developing standards and guidelinessuitable for their specific conditions. The ICAR TaskForce Developing Countries promotes participationof experts from developing countries in ICARresearch and training activities and promotes theestablishment of country-specific identification andrecording systems. Success stories, such asguidelines for buffalo milk recording,recommendations for animal identification andbreeding programmes in low to medium inputsystems and activities of ICAR Members fromdeveloping countries in Africa, Asia and LatinAmerica, indicate that this type of internationalcooperation is necessary also in support ofconservation and sustainable utilization of localand endangered breeds.

Mr Jacob Wanyama, VETAIDMozambique/LIFE Network, Mozambique

The paper covers different levels and methods ofcharacterization, and highlights the importance ofcovering more than only production. It providesdetails on the role of emerging technologies formolecular characterization. It provides a usefulbasis for conducting the inventory and monitoringanimal genetic resources.

However, from the points of view of the livestockkeepers:• The breed definition does not give justice to the

fact that many local breeds are products ofdeliberate manipulations by their keepers. Itdoes not capture the selection criteria of breedersin the communities.

• Documentation methods should put moreemphasis on the participation of stakeholders inthe communities.

• If collecting materials for molecularcharacterization, those doing the inventoriesshould obtain the prior informed consent of theowners of the animals!The paper outlines what needs to be done. But it

lacks information on transparent procedures onhow the information is stored and used. It should beclear:• Who has access to the data.• Who can use them.• How the data will be used.

The monitoring describes an early warningsystem. But again, it does not recognize theimportant role that livestock keepers can play inthis process.

The future:• NGOs have the direct contacts to livestock

keepers in communities and therefore have theability to aid communities in the inventory,characterization and monitoring of their breeds.

• The information collected should be stored incommunity-based and driven documentationcentres. NGOs have the capacity to facilitatesuch process. They can build the capacity ofcommunities to document their own breeds.

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Summary of plenary discussionThe meeting was then opened for generaldiscussion and interventions from the floor. Issuesraised during this discussion included:• The practical steps needed to improve inventory

and monitoring.• The need to ensure that results of

characterization processes are widelydisseminated.

• The need to consider legal issues – such as thoserelated to intellectual property rights associatedwith methods for characterization and theanimal genetic resources themselves.

The authors’ responses and concludingcomments included the following points:• The need for a multi-disciplinary approach to

characterization and for the appropriateallocation of roles in the characterizationprocess.

• The importance of encouraging participation ofbreeders and livestock keepers and theirorganizations.

• The need for clear explanation of how theinformation gathered will be used, and for thosethat provide the information to be involved inthe analysis and use of this information.

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AGRI 2008, 42: 49-69

SummarySustainable use of animal genetic resources foragriculture and food production is proposed as thebest strategy for maintaining their diversity.Achievement of sustainable use would continue tosupport livelihoods and minimize the long-termrisk for survival of animal populations. The conceptof sustainable use has economic, environmentaland socio-cultural dimensions. Sustainable use ofanimal genetic resources also contributes to foodsecurity, rural development, increasing employmentopportunities and improving standards of living ofkeepers of breeds. Supporting the rearing of breedsthrough better infrastructure, services, animalhealth care, marketing opportunities and otherinterventions would make a significant contributionto the sustainable use of animal genetic resources.

Sustainable use envisages the use andimprovement of breeds that possess high levels ofadaptive fitness to the prevailing environment. Italso encompasses the deployment of sound geneticprinciples for sustainable development of the breedsand the sustainable intensification of theproduction systems themselves. Sustainable useand genetic improvement rely on access to a widepool of genetic resources.

Genetic improvement programmes need to beconsidered in terms of national agriculture andlivestock development objectives, suitability to localconditions and livelihood security as well asenvironmental sustainability. Genetic improvementcan involve choice of appropriate breeds, choice of asuitable pure breeding or crossbreeding system andapplication of within-breed genetic improvement.The choice of appropriate breeds and crossbreedingsystems in developed countries has been a majorcontributor to the large increases in productivity,

Sustainable use and genetic improvement

C. Nimbkar1, J. Gibson2, M. Okeyo3, P. Boettcher4 & J. Soelkner5

1Animal Husbandry Division, Nimbkar Agricultural Research Institute,P.O. Box 23, Phaltan 415 523, Maharashtra, India

2The Institute for Genetics and Bioinformatics, C.J. Hawkins Homestead, University of New England,Armidale, NSW 2351, Australia

3International Livestock Research Institute, P.O. Box 30709, Nairobi 00100, Kenya4Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, International Atomic Energy Agency,

P.O. Box 100, A-1400 Vienna, Austria5University of Natural Resources and Applied Life Sciences, Vienna, Austria

and has benefited greatly from the fact thatdeveloped country animal genetic resources arewell characterized and relatively freely exchanged.Where proper steps have been followed by carefulassessment of demand, execution, delivery, impactand cost–benefit analyses, successful within-breedimprovement has been realized within indigenouspopulations in developing countries. Breedingobjectives and programmes for subsistence orientedand pastoralist systems are likely to be entirelydifferent from conventional programmes.Crossbreeding has been most successful where it isfollowed by a rigorous selection programmeinvolving livestock owners’ participation andsubstantial public sector investment in the form oftechnical support. In any genetic improvementprogramme, inbreeding needs to be monitored andcontrolled.

Within-breed genetic improvement is normalpractice in the developed world, and has become ahighly technical enterprise, involving a range ofreproduction, recording, computing and genomictechnologies. Emerging genomic technologiespromise the ability to identify better, use andimprove developing world animal genetic resourcesin the foreseeable future. Useful systems can,however, be established without the need forapplication of advanced technology or processes.

RésuméOn propose une utilisation durable des ressourcesgénétiques animales pour l’agriculture etl’alimentation comme meilleure stratégie pour laconservation de la diversité. Atteindre l’utilisationdurable permettra d’améliorer la qualité de vie etdiminuera le risque à long terme de la survie despopulations animales. Le concept d’utilisation

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50Sustainable use and genetic improvement

durable entraîne des mesures économiques,environnementales et socioculturelles. L’utilisationdurable des ressources génétiques animalescontribue aussi à la sécurité alimentaire, audéveloppement rural, à l’augmentation desopportunités d’emploi et à l’amélioration desstandards de vie des éleveurs. Soutenirl’amélioration des races à travers une meilleureinfrastructure de services, de santé animale,d'opportunités de marché et d’autres interventionspourrait aider de façon significative à l’utilisationdurable des ressources génétiques animales.L’utilisation durable comporte l’utilisation etamélioration des races qui possèdent des hautsniveaux d’adaptation physique aux principauxmilieux. Cela comporte aussi l’application deprincipes génétiques adéquats au développementdurable des races et à l’intensification durable dessystèmes de production en soi. L’utilisation durableet l’amélioration génétique se basent sur l’accès àune large gamme de ressources génétiques.

Les programmes d’amélioration génétiquedoivent être considérés en termes d’agriculturenationale et développement des objectifs d’élevage,ainsi que compatible avec les conditions locales demoyens d’existence et d’environnement durable.L’amélioration génétique peut entraîner le choix deraces plus appropiées, races plus pures adaptées ouun système de croisement de races et l’applicationde l’amélioration génétique à l’intérieur de la raceelle-même. Le choix de la race et des systèmes decroisement de races dans les pays endéveloppement a été un des facteurs qui a influencéle plus l’augmentation de la productivité et abénéficier largement le fait que dans les paysdéveloppés les ressources génétiques animalessoient bien caractérisées et puissent bénéficier d’unmouvement relativement libre. Là où les démarchesappropriées ont été suivies à travers des évaluationscorrectes sur la demande, l’exécution, la remise,l’impact et l’analyse de coût-bénéfice, le succès del’amélioration à l’intérieur de la race a tout de suiteété atteint avec les population indigènes dans lespays en développement. Les objectifs d’améliorationet les programmes pour la subsistance et lessystèmes de pâturage seront différents desprogrammes conventionnels. Les croisements deraces ont eu plus de succès lorsqu’un programmede sélection rigoureux a été suivi et quand laparticipation des éleveurs et une partie du secteurpublic a été présente en forme d’investissement etappui technique. Dans tout programmed’amélioration génétique il est nécessaire decontrôler et faire un suivi de la consanguinité.

L’amélioration génétique de la race est unepratique normale dans le monde développé et estdevenue une entreprise hautement technique quimet ensemble les domaines de la reproduction, lecontrôle, l’identification et technologies du génome.Les nouvelles technologies du génome promettentdans un futur proche une meilleure capacitéd’identification et l’utilisation et amélioration desressources génétiques animales dans le monde endéveloppement. Des systèmes utiles peuventcependant être établis sans la nécessité d’appliquerdes procédures ou des technologies à l’avant-garde.

ResumenSe propone una utilización sostenible de losrecursos zoogenéticos para la agricultura y laalimentación como mejor estrategia para elmantenimiento de su diversidad. Alcanzar el usosostenible contribuirá a la mejora de la calidad devida y minimizara el riesgo a largo plazo de lasupervivencia de las poblaciones animales. Elconcepto de utilización sostenible conllevadimensiones económicas, ambientales ysocioculturales. La utilización sostenible de losrecursos zoogenéticos también contribuye a laseguridad alimentaria, el desarrollo rural, elaumento de oportunidades de empleo y la mejora delos estándares de vida de los ganaderos. Apoyar lacría de razas a través de una mejor infraestructura,servicios, cuidados sanitarios de los animales,oportunidades de mercado y otras intervencionescontribuiría de forma significativa a la utilizaciónsostenible de los recursos zoogenéticos.

La utilización sostenible comporta el uso ymejora de las razas que poseen altos niveles deadaptación de su forma física a los principalesambientes. También conlleva el despliegue deprincipios genéticos adecuados para el desarrollosostenible de las razas y la intensificaciónsostenible de los sistemas de producción en símismos. La utilización sostenible y la mejoragenética se basan en el acceso a un amplia gama derecursos genéticos.

Los programas de mejora genética necesitan serconsiderados en términos de agricultura nacional ydesarrollo de objetivos ganaderos, así comocompatibilidad con las condiciones locales yseguridad de sustento y sostenibilidad ambientales.La mejora genética puede implicar la elección de lasrazas más apropiadas, la raza más pura adecuadao un sistema de cruce de razas y la aplicación demejora genética dentro de la raza. La elección de laraza adecuada y de los sistemas de cruces de razas

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en los países en vía de desarrollo ha sido uno de losfactores que más ha influido en el incremento de laproductividad, y se ha beneficiado ampliamente delhecho que en los países desarrollados los recursoszoogenéticos están bien caracterizados y gozan deun intercambio relativamente libre. Donde se hanseguido los pasos adecuados con evaluacionescorrectas sobre la demanda, ejecución, consigna,impacto y análisis de costo-beneficio, el éxito de lamejora dentro de la raza ha sido alcanzado conpoblaciones indígenas en países en vía dedesarrollo. Los objetivos de mejora y los programaspara la subsistencia y sistemas pastorales seránmayormente distintos de los programasconvencionales. Los cruces de razas han tenidomayor éxito donde se ha seguido un programa deselección riguroso que implique la participación deganaderos y parte substancial del sector publico enforma de inversión y soporte técnico. En todoprograma de mejora genética es necesario controlary monitorear la consanguinidad.

La mejora genética dentro de la raza es unapráctica normal en el mundo desarrollado y se haconvertido una empresa altamente técnica quecubre los campos de reproducción, control, computoy tecnologías de genoma. Las nuevas tecnologías degenoma prometen la capacidad para identificarmejor y la utilización y mejora de los recursoszoogenéticos del mundo en vía de desarrollo en unfuturo próximo. Los sistemas útiles pueden sinembargo ser establecidos sin la necesidad de aplicarprocedimientos o tecnologías de vanguardia.

Keywords: Targeting breeds, Production systems,Market access, Adding value, Dissemination, Sustainablebreeding programmes, Technology, Intellectualproperty.

IntroductionSustainable use “is the use of components of biologicaldiversity in a way and at a rate that does not lead to thelong-term decline of biological diversity, therebymaintaining its potential to meet the needs andaspirations of present and future generations”. This isthe definition of “sustainable use” proposed inArticle 2 of the Convention on Biodiversity (CBD).The State of the World’s Animal Genetic Resources forFood and Agriculture (SoW-AnGR) (FAO, 2007)identified key elements of this concept as it appliesto animal genetic resources. It reviewed existingconcepts but did not attempt a comprehensivedescription of the state of the art. The generalconclusions of the SOW-AnGR were that there is a

need for the concept of “sustainable use” to be“interpreted in the context of agricultural biodiversity,and for concrete management strategies to be developedfor AnGR”. After the drafting of SOW-AnGR, FAOheld an expert meeting that identified the guidingprinciples of sustainable use, made specificrecommendations addressing relevant aspects ofthe concept and focused on work required to clarifyand develop the concept further (FAO, 2006a; FAO,2008). This paper describes the state of the art ofscientific thinking on the key technical issues,options and opportunities in relation to sustainableuse of AnGR.

Animals are reared in production systems, eachwith its unique geographical, environmental,cultural and socio-economic context. Sustainableuse of animals for agriculture and food productionin robust, ecologically compatible productionsystems is widely accepted to be the best strategy tomaintain their diversity. Continued use of animalgenetic resources within the environment in whichthey were developed provides a number ofadvantages, including maintenance of localknowledge about how best to manage the animal,maintenance of the production environment, andcontinued opportunities for the livestock to adapt tolocal production conditions and the needs of thesociety (FAO, 2006a). However, allowing movementof animal genetic resources to new locations andproduction and market systems is also a way ofpromoting their sustainability. Use of animalgenetic resources inevitably includes development.Animal genetic resources are dynamic resources,changing with each generation in interaction withthe physical environment and according to theselection criteria of their keepers (Wurzinger et al.,2006). The concept of sustainable use thereforeencompasses genetic improvement.

Even in the most rapidly developing countries,there are striking inequities in access to the benefitsof economic development. Many families continueto keep a few animals of traditional breeds, oftenwith very low use of external inputs, to provide awide variety of products and services for householdconsumption and for sale in local markets. Thedevelopment of opportunities for most of thesefamilies to intensify production and participate innational or niche markets or to find more lucrativenon-agricultural employment is not likely to occurin the near future. In the meantime, continuedaccess to well-adapted, local animal geneticresources will remain important for them (FAO,2006b). Support for sustainable use of animals indeveloping countries will thus contribute to thebroader socio-economic goals of livelihood security

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and rural development, increasing employmentopportunities and standards of living in rural areasand reducing migration to cities. Animal geneticresources play an important role in maintainingvital rural areas in developed countries also. Inaddition, in both developing and developedcountries, animal genetic resources supplynutritious, protein-rich foods to people.

This paper discusses opportunities to enhancesustainable use of animal genetic resources, giventhe identified drivers of change articulated in thefirst paper in this series, mainly in agropastoralsystems in marginal areas and crop–livestocksystems in high potential areas. This focus isjustified because industrial production systemsusing commercial breeds are already welldeveloped, supported by heavy investment ofcapital, other resources and knowledge, and haveefficient monitoring and corrective mechanisms inplace if needed. The paper also presents the currentscientific understanding in the area of geneticimprovement and sustainable breedingprogrammes for development of animal geneticresources. The impact of revolutionary technologiesin the field of genetic improvement and issuesrelated to intellectual property rights are alsodiscussed.

Facilitating sustainable usewithin production systemsAnimal genetic resources form the basis of thelivelihood and the cultural identity of a largenumber of farming and pastoral groups. Livestockhave a critical role in maintaining sustainableagricultural systems, assuring food security andalleviating poverty. This role is especially importantgiven the prospect of climate change or emergingdiseases and the unpredicted rate andconsequences of such change. It is expected thatsustainable use would lead to the maintenance ofvibrant and vigorous populations of breeds in theirappropriate production systems. Increasing theprofitability of rearing animals, particularly byincreasing their market value, as well as enhancingtheir non-market values can maximize theprobability of their continued use in the long term.Adaptive fitness and increased productivity can beachieved and maintained more effectively byimproving inputs, environmental conditions andgenetic resources concurrently. There is a range ofalternatives and opportunities available for suchfacilitation including institutional strengthening.

There are, however, also many examples whereopportunities have been wasted or inadequatelyexploited due to inappropriate policies and lack ofsupport in critical areas (Philipsson, Rege andOkeyo, 2006).

Targeting breeds that requireinterventions

In general, more effort to promote sustainable useneeds to be directed to those breeds that are likely tobecome threatened without support. Another factorto be considered in the targeting of interventions isthe specific characteristics of breeds that make themunique – for example, adaptive traits such asdisease and heat-resistance or specific feedingbehaviour. Other criteria might include a focus onbreeds that are specific to restricted regions or areunique in terms of their genetic, morphological,functional or cultural characteristics or the productsthat they produce. Development of a breed is likelyto be more successful where there is a localcommunity that highly values the breed in questionand has a long history of local knowledge andexperience of working with the animals.Continuous monitoring of the status of breeds byperiodic breed surveys and censuses would help toprovide information on population trends andimpending threats. Such data can informdecision-making and help in formulating sounddevelopment schemes. This aspect is dealt withmore comprehensively in the companion paper oncharacterization.

Strengthening production systems

Breeds fit into specific production systems andagricultural landscapes. If particular productionsystems disappear, the associated animalpopulations may no longer continue to be usedsustainably. Strengthening these productionsystems so that they are robust in the face ofchanging circumstances would support thesustainable use of animal genetic resources. Variousways of strengthening these systems are elaboratedbelow.• Opportunities for small changes in farming

systems. Small changes in farming systems,designed according to the prevailing climate,resource profile and agricultural practices, canmake livestock rearing more profitable andbeneficial to the farming system and thus more

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sustainable. One example is to use novel ways ofintegrating crop farming and livestock rearingsuch as ley farming. Another example of analternative model of farming using livestock isgrowing grass/leguminous forage on marginal,rainfed lands and rearing livestock instead ofsowing grain crops that usually do not yield anygrain because of inadequate rainfall.

• Provision of technical services. In some cases,technical improvements to animal nutrition,management and health may improve theeconomic viability of animal populations. Thesustainability of animal genetic resources inexisting production systems could be improvedsubstantially by provision of basic veterinaryservices, including disease prevention measuressuch as vaccination. Improvements inmanagement and genetics go together in realityas changes in one create new opportunities forthe other. Provision of credit to purchaseanimals and for capital expenditure and areliable supply of feed resources can providesignificant impetus to the rearing of endangeredbreeds. These services may have to be tailored tospecific needs – for example, they need to bemobile for nomadic herding. Otherimprovements to rural and agriculturalinfrastructure would also encourage livestockrearing in addition to other general benefits, forexample by improving market access throughprovision of market information and objectivepricing structures.

• Ensuring continued resource availability tolivestock keepers. Sustainable use of animalgenetic resources is closely linked to thecontinued availability of adequate grazing andwater. Pastoralist production systems areincreasingly under threat worldwide. Thereasons for this are numerous:- deterioration of natural pastures as a result of

droughts, inappropriate management ofgrazing and soil erosion;

- curtailed access of livestock to commonproperty resources;

- diversion of grazing lands to other uses suchas irrigated crop-farming, establishment ofindustries, urbanization or creation ofnational parks;

- increasing difficulties in migration owing toincreased cross-border disease-relatedcontrols, and traffic and highway codes thatrestrict livestock movement along and acrossmajor highways.

There are also other increasing demands, suchas for biofuel production, on common property

resources and government lands in almost allcountries. A pragmatic approach would be to takeinto account the vital role of animal geneticresources in diverse spheres, from production ofmuch-demanded animal protein to maintenance offertility of farmlands and creation of space foranimal genetic resources in land-use plans(Köhler-Rollefson and LIFE Network, 2007).• Capacity building. Training will help to inform

livestock keepers of the latest scientificdevelopments applicable to their livestock, suchas availability of new vaccines, and will help toprotect them from inappropriate advice(Malmfors et al., 2002). Training should buildupon existing local knowledge of the productionsystem and enable livestock keepers to makeinformed decisions.

• Improving the status of animal genetic resourcesby raising awareness among policy- anddecision-makers. Sustainable use of animalgenetic resources has not achieved a highpriority in the strategies of many governments ornational and international funding agencies. Inthe Consultative Group on InternationalAgricultural Research (CGIAR), institutionalcapacity and availability of funds are generallyskewed heavily towards the plant sector (FAO,2006b). Animal husbandry usually gets a rawdeal compared to crop farming in governmentalfinancial allocations because of inadequateawareness of policy-makers of the importance oflivestock. It is therefore necessary to raise theawareness of the contribution of livestock tonational economies and to the well-being oflarge numbers of families to give a higher profileand status to livestock rearing. Raisingawareness will help in encouragingpolicy-makers to develop sound policies that arebeneficial for sustainable use of animal geneticresources rather than policies that may have anadverse impact on livestock rearing. Forexample, supportive public policy and long-termtechnical support systems are largelyresponsible for the success of the dairy subsectorin India (Kumar, Birthal and Joshi, 2003).

• Promoting “organizations” of livestock keepers. Akey aspect to promoting sustainable use iscreating or strengthening structures to organizethe keepers of animals and help motivatecommunal efforts (Kosgey & Okeyo, 2007).Organizations are stronger than individuals andcan safeguard group interests better, byadvocacy with authorities. In the longer term,building these structures may serve acapacity-building role – allowing livestock

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keepers better access to information,strengthening their position in relation toextension services, facilitating the organizationof training and improving bargaining powerwhen marketing products. In Europe, there arestrong farmer cooperatives and breedingorganizations that go back a century and havealso received much public support over theyears.

Improving market access and promotingnovel uses of animal genetic resources

Developing markets for livestock breeds, theirproducts and services

The value of animal production can be increased bymarketing products more effectively. Ease ofmarketing and lucrative prices for animals and theirproducts can provide the biggest boost forcontinued use of animal genetic resources (Boxes 1and 2).

Development of niche markets is also importantfrom the perspective of promoting sustainableutilization. Niche markets rely on creatingperceived value regarding the conditions ofproduction, product quality or a combination ofthese. Consumers that particularly value foodquality or specific production methods are the mostlikely to purchase specialized niche products suchas Parmigiano Reggiano cheese produced fromRegianna cattle in Italy, high-value cured porkproducts from Iberian pigs reared in oak-forestproduction environments in Spain and meat fromthe black boned chicken breed in Viet Nam, knownfor its medicinal value. One of the ways to createdemand for products of breeds reared in pastoralistsystems with no chemical inputs is to market themas “range-fed” or “fed on natural vegetation”. Suchproducts could also benefit from “geographicalindication” recognition.

In almost all areas of India, a niche market forlocal breed chickens and eggs, perceived to be“high-quality” and therefore more expensive, existsside by side with broiler chicken and commerciallayer hen eggs. Similarly, in Malaysia, meat from theKampong chicken is considered to be better tastingthan the commercial breeds. In the United Kingdom,a ready market was developed for beef from Anguscattle as high-quality beef (with high marbling),which served to increase the Angus population. Themeasures adopted for this included promoting

Angus beef through a restaurant chain. The fragilityof some such niche markets is, however,demonstrated by the collapse of the restaurantchain following the outbreak of mad cow disease.

Novel uses for animals and animal products

New uses have been developed for animals andtheir products with desirable consequences forcontinued maintenance of animal genetic resources.The unique immune system enhancementproperties of Panchagavya (a mixture of milk, curd,ghee, urine and dung of indigenous cows preparedaccording to a recipe from ancient Ayurveda[Sushruta Samhita, 1985]), identified by newresearch (Chauhan et al., 2004) have led to newmarketing possibilities in India and Sri Lanka. Anon-governmental organization (NGO) inRajasthan, India, has successfully introduced camelmilk ice cream (desert dessert) as part of acomprehensive strategy to make camel rearing moreprofitable. Research in the United States of Americaon “aversive conditioning” using boluses withlithium chloride (Mueller, Poore and Skroch, 1999)shows that sheep can be trained to bypass thetender shoots of grapevines and trees for the weedssprouting underneath.

Promoting use of animals in landscapeconservation

Use of traditional grazing livestock for landscapeheritage and biodiversity maintenance and fornurturing more complete ecosystems is a growingmanagement practice in many developed countries.In the United Kingdom and Europe, and specificallythe Balkans, the role of grazing livestock has beenrecognized as critical in the maintenance of wildlifeand native plant biodiversity in many high naturevalue ecosystems. In the Mediterranean, grazing forshrub control helps to reduce forest fires. Culturaltourism associated with the unique culture ofrearing local breeds has been expanding rapidly inEurope and also in South America where camelidsare great attractions at parks and tourist sites.Similar approaches are needed in other developingcountries, since here too particular breeds haveshaped certain landscapes. Functioning pastoralistsystems also have value as tourist attractions,besides contributing to ecosystem health.

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Box 1. Adding value to Nguni cattle

The Nguni of South Africa is an African taurine breed with a slight admixture of zebu blood that reachedthe region together with southward migrating pastoralists in about 300 AD. After white settlers arrivedwith exotic cattle, the Nguni cattle were long perceived as inferior because of smaller carcass size,non-uniform colour pattern and lack of information on their production potential. Even the people whohad originally kept this breed started crossbreeding or keeping exotic cattle. Research in the 1980s thenrevealed that the Nguni breed is very tick-tolerant, can maintain its condition during seasonal foodshortages, can obtain optimal nutritional value from the available forage, is a good walker and verydocile. Its adaptation to harsh extensive production systems offers many advantages to smallholders.The Animal Improvement Institute has therefore initiated a project to supply selected Nguni bulls tosmallholders together with training and infrastructural support. Nguni cattle have a wide range ofcolours. The colour variation indicates the cultural heritage of the breed, which has been raised byAfrican stockmen for centuries. Colour variation frequently had a ceremonial and symbolic importance.The colourful Nguni hides are much in demand these days for pelts that are tanned with the hair on, foruse as rugs, clothing and home furnishings. Being able to predict and generate specific colours has takenon a new economic aspect as these uses have recently increased. In addition, certain colours orpigmentation patterns (such as pigmented skin beneath white hair) can be helpful in adaptation ofanimals to harsh conditions of high solar radiation. All three of these factors (tradition, utility, adaptation)combine to make colour important for Nguni breeders, and unravelling the details of colour genetics canbe useful for them (Köhler-Rollefson, 2004; Sponenberg, 2007).

Box 2. Value-adding to peri-urban dairy farming inLatin America

Straddling the border of Peru and Bolivia, the Altiplano – a high-altitudeplain at 4 000m above sea level – is one of the poorest regions in theworld. At such high altitudes, the environment is unforgiving: droughtand extreme cold are common. The region supports six million people,who mostly depend on agriculture. Potato is the staple but crop failureis a regular occurrence and many families live in extreme poverty.However, for some Altiplano farming families living close to urbancentres, nutritional and income stability is not completely unattainable.Milk production is growing in importance in the region and a pilotproject, under the ALTAGRO initiative of the International Potato Center(CIP) and its partners, has created a market in several large towns forcheese made from local cows’ milk. Most households in the area earnaround US$1 per day. With this initiative, dairy producers have morethan doubled their income, with some now earning up to US$850 peryear. The ALTAGRO project, financed by the Canadian Government,has supported the construction of two small dairies in Atuncolla-Illpa,a Peruvian town with a population of 10 000 people. A training plantset up at the experimental station of the Instituto Nacional deInvestigación Agraria (INIA, Peru’s National Agricultural ResearchInstitute) is providing technical assistance to farmers and processors inhow to transport the milk and process it into cheese (www.new-ag.info/07/04/focuson/focuson1.php).

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Research and dissemination of researchresults

Public-funded applied research needs to focus onimproving livestock rearing as an integral part ofproduction systems and finding innovativesolutions to real problems rather than on obscuretheoretical topics. Successes as well as failures needto be published in order to capitalize onexperiences. Research on the beneficialinterrelationships between livestock and theirenvironment and the necessity of livestock tomaintain the sustainability of the landscapes theyuse is likely to provide enlightening results (Lewis,2003). It is important to publish research results inaccessible sources to ensure wider dissemination.

Promoting sustainability as the mainobjective

The supporting interventions should be such thatthey create an enabling environment to makelivestock rearing self-sustained in the long termrather than dependent on outside support. Ifsupport is withdrawn due to a change in themacroeconomic situation or in the government, thelivestock rearing system it has strengthened shouldnot collapse. In fact, consequences of interventionscould be tested against the potentiality that thesupport may be terminated.

Appropriate strategies for sustainable use willdiffer from country to country or among groups ofcountries because of the large differences amongareas of the world, especially in terms of grossnational product and available technology(Gandini and Oldenbroek, 2007).

Genetic improvement andsustainable breedingprogrammes

Introduction

The concept of sustainable use encompasses thedevelopment of animal genetic resources, ensuringthat they remain a functional part of productionsystems, and the sustainable intensification of theseproduction systems. Genetic improvement is thesystematic exploitation of genetic variation inimportant traits among individuals within or

between breeds. Breeding programmes for animalgenetic resources are generally undertaken in orderto improve their productivity and the quality of foodand products derived from them and to ensure theavailability of such food/products at affordableprices. Genetic improvement of livestock has madeand will continue to make major contributions toagricultural development, food security,sustainability and livelihoods. In high-inputproduction systems, which are common in thedeveloped world, modern chicken and pig hybridsconsume less than half the feed per kilogram ofmeat produced than the strains of 50 years ago.Such genotypes cannot, however, stand the harshrigours (disease challenge, poor-quality feed, hightemperature) of the low-input, livelihood-focusedsystems in most of the developing countries. Thehigh feed conversion efficiency has allowed thedemand for meat of affluent societies to be met froma greatly reduced land area, thus releasing largeareas of agricultural land that would otherwisehave been required to produce poultry and pig feed.The importation of these improved genetics alongwith their associated production systems intodeveloping countries has benefited consumersthrough availability of cheap broiler meat and porkand has also brought profits to farmers, althoughsome other farmers were crowded out of marketsbecause of these developments. There are otherexamples of benefits (with some qualifications) inthe developing world. For example, the use ofimproved dairy genotypes has allowed thedevelopment of a large informal milk market thathas dramatically improved smallholder livelihoodsand human nutrition in the densely populatedhighlands of Kenya. A recent study has, however,shown that these animals are of higher milkpotential than tropical climates and feed resourcescan support. In some situations, this resulted indrastic reductions in farmers’ profits (King et al.,2006).

Genetic improvement can take many forms, butgenerally and logically follows an orderedhierarchy of events. This starts with understandingof the production and marketing systems, choice ofappropriate breeds or strains (sometimes resultingin replacement of existing breeds), establishment ofan effective pure breeding or crossbreeding system,and then further improvement through selection ofsuperior genotypes within populations that bestsuit the production and market conditions. The past50 years have seen a drastic change in breed use. Asa consequence, genetic improvement in thedeveloped world is now primarily based on a fewbreeds and within-breed improvement. Almost all

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pigs in developed country markets are, however,crossbred and some strategic crossbreeding is beingundertaken increasingly in cattle and sheep. In thedeveloping world, most genetic change is takingplace through change of breeds via crossbreedingprogrammes aimed at “grading up” of indigenousbreeds towards exotics from the developed world.Systematic within-breed improvement is much lessprevalent, although livestock keepers themselvescontinuously make decisions to keep and cullanimals according to criteria they considerimportant. However, apart from a few cases, most ofthe structured breeding programmes have seenlimited success, mainly because of inadequateunderstanding of the prevailing agro-ecological andmarketing conditions.

Within-breed improvement

Within-breed genetic improvement programmes areroutine for all the breeds and strains of livestockused in the dominant livestock production systemsof the developed world. The genetic improvementtypically accounts for 40 to 60 percent of the annualproductivity gains in these systems. In thedeveloping world, however, within-breedimprovement to improve productivity is notcommon and has not often been sustainable. Therelative lack of effort is partly due to the perceptionthat greater genetic change is possible through thechoice of specialized and improved exotic breedsand strains and crossbreeding systems. However,inadequately planned crossbreeding programmeshave seen as much failure, if not more, aswithin-breed improvement programmes. Lack ofsuitable infrastructure, expertise and sustainedgovernment support has also hampered theestablishment of within-breed improvementprogrammes in developing countries. Many factorshave contributed to the lack of success in existingprogrammes – inadequate initial characterization oflocal populations, lack of participation ofsmallholder beneficiaries, inadequatedissemination mechanisms, inadequate orunsustainable infrastructure and expertise and/orrapid evolution of production systems (such asbreed replacement), apparently eliminating the needor demand for the improved stock. Successfulapplication of within-breed improvement isundoubtedly attainable in the developing world,but requires more careful assessment of demand,execution, delivery, impact and cost–benefitanalyses.

Within-breed improvement presents a particularchallenge in subsistence-oriented systems. It has tobe based on adequate knowledge of the breeds inquestion and of the production system. Seriousconsideration has to be given to social, economicand environmental sustainability in this situation.Potential strategies for breed developmentappropriate to the local conditions and in keepingwith the country’s overall livestock developmentobjectives should then be identified, assessed andprioritized (Box 3).

Generally, breeding objectives have focused onincreasing productivity, often measured at theindividual animal level. However, breedimprovement should take into account the fullrange of attributes that make production systemssustainable. Selective breeding efforts can vary inscope from highly organized breeding programmesthrough to simple culling decisions based onindividual phenotypic information under lesscontrolled environments. The choice of methodswill depend on the objectives of the breedingprogramme, their acceptability to the wholespectrum of stakeholders, access to improvedgenetic resources and the technology andinfrastructure available.

In harsh mountainous or arid rangelands andpastoral systems where the environment andmarkets are unlikely to change in the medium tolong term and where existing genotypes are welladapted, simple within-breed selection programmesfocusing on as few traits as possible provide thebest approach. The traits to be included need to beeasily recorded for the animals to be selected anddepend on the primary use of a breed. They will bemultiple for multipurpose breeds. While naturalselection will take care of many adaptive traits,fertility of male animals needs to be consideredbased on the results of a first mating season. Whenthe environment and market requirements arechanging, then more planning, better designs andinstitutional integration/coordination are required.

Where proper steps have been followed,successful within-breed improvement has beenrealized, even within indigenous populations indeveloping countries. The improved Boran cattle inKenya, the Nguni cattle in South Africa, the Tulicattle of Zimbabwe and the Murrah buffaloprogramme of India (with some limitations) aresuccess stories in regions where many programmeshave failed. What is unique about all theseexamples is that the production, policy and marketenvironments were well understood, the locallyavailable genetic resources/breeds were well

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evaluated and simple selection criteria agreed uponand implemented.

Intensive selective breeding will inevitably resultin some reduction in genetic diversity within thebreed. Systems for allocating breeding males tofemales based on the relative genetic contributionsof parents have been developed to optimize geneticimprovement while minimizing the rate ofinbreeding (e.g. Sonesson and Meuwissen, 2000).These are used in commercial breeding and can beapplied to local breeds if animals are appropriatelyidentified and their pedigrees recorded accurately.

Choice of breeds and cross-breeding

The matching of appropriate breeds to evolvingproduction systems has been a major contributor togrowth in productivity and improvement of productquality in the developed world. This has beenpossible because developed world breeds and

strains are relatively well characterized and areeasily accessible through established processessuch as genetic evaluation rankings and semen andbreeding male distribution schemes. In thedeveloping world, most animal genetic resourcesare inadequately characterized and access toanimal genetic resources from other developingcountries is often difficult or impossible. In fact it isironic that recently developed well-intentionedinstruments such as the Convention on Biodiversitymay hamper the sharing of breeds across countrieseven if it appears to be the most technically logicaloption and would actually contribute to themaintenance of agricultural biodiversity. Unlesslivestock genetic resources of the developing worldare better characterized and made more accessible,it is inevitable that the choice of breeds and strainsfor breed replacement and crossbreeding will bedominated by those of the developed world. This isevident, given the strong marketing strategies of theimproved livestock genetics companies from the

Box 3. Community sheep breeding programme inPeru

In the highlands of the Sierra Central in Peru (an isolated highmountain range environment at an altitude of about 4 000 metres abovesea level), dual purpose Corriedale sheep and native-type sheep withdifferent levels of exotic upgrading are kept in an extensive pastoralsystem. A survey conducted in 1996 identified three types of sheepproduction systems: individual family flocks, communal flocksbelonging to villages and multicommunal flocks managed bycooperatives often involving several villages in a region. The surveyidentified two major requests of farmers related to breeding: the needfor suitable rams and the need for training in breeding techniques.After extensive discussions, an interesting breeding structure basedon the open nucleus concept was established and made functional.The land and labour necessary to run the nucleus were provided bythe communities based on a series of arrangements and technicalsupport was provided by the university. The nucleus was establishedby mating imported and locally produced top rams with 50 “best”females of each of nine communal and multicommunal flocks. Half ofthe ewes were returned pregnant to the suppliers and the other halfwere used for starting a central nucleus providing improved rams tocommunal and regional flocks, which in turn also provided rams tofamily flocks. Incidentally, the progeny of local rams proved to bebetter suited to the local market conditions than the progeny ofimported rams. Farmer organization and farmer training are thebackbone of this successful community-based sheep breedingprogramme, which is still in operation (Mueller, Flores and Gutierrez,2002).

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high-input systems of some developed countries.This may severely restrict the options of developingcountries to develop their local breeds to meet goalsfor agricultural and economic development,sustainability and improvement of livelihoods.

With now widely predicted climate changesthrough direct and indirect effects (i.e. reducednumber of growing days, hence herbage yields,increased disease outbreaks and challenges), thedeveloping regions of the world’s productionsystems are likely to be severely affected. Therefore,the need to source appropriate (those that bestmatch the predicted future scenarios) breeds andgenes from one developing country to anotherwould be the most logical option. For example, if, asa result of global climate change, most of thesub-Saharan regions receive less rainfall and havehotter climates than currently is the case, theninstead of embarking on long-term within-breedimprovement of local breeds to match the predictedfuture environments in the affected areas, it wouldbe better to access and move breeds. For example,Kenana and Butana cattle breeds of the Sudan thatare already naturally adapted and reasonablyproductive under a harsh environment could bemoved to those areas where harsher conditions areexpected in future. Such realities add a newdimension to the potential utility of indigenousbreeds.

In pastoral systems, and when marketopportunities for improved milk and meatproduction exist but where large erraticenvironmental changes such as droughts arecommon, livestock keepers may maintain a range ofdiverse genotypes, some of which can survivedrought conditions. Traditionally, pastoralists maykeep a mix of species and breeds in their herds tomaximize the advantages of good seasons and toreduce risk during bad seasons. For example,crossbred animals generated by crossing locallyadapted females to an improved “exotic” breed malemay be more profitable than their local purebredmothers when conditions are good, but may be thefirst to die when there is a bad drought. Farmersmay use some indigenous breed sires and someexotic sires on parts of their herds/flocks whilepractising within-breed selection in part of theherd/flock. A good example is the Ankole cattlebreed in the African Great Lakes region, wheremany keepers of large herds adopt a strategy ofsplitting their herds in this manner (Wurzinger etal., 2006). Better planning is then necessary to find abalance between high-profit/high-risk andlow-profit/low-risk and to ensure a goodbio-economic balance.

The use of crossbreeding has also made majorcontributions to productivity and product quality inthe developed world. Structured cross-breedingsystems, such as “terminal crossing” where firstgeneration cross-bred (F1) animals are slaughteredor where specialized crossbred dam lines are used,are common. Cross-breeding may also be used forgradual breed replacement with upgrading or thecontrolled maintenance of various proportions ofexotics leading to formation of composites. The needto maintain pure breeds for the production ofcrossbred animals or commercial production iseither managed by farmers or by commercialcompanies. Farmers have had extensive supportand training and now understand the need tomaintain a balance of breeds to make the systemsustainable in the long term.

There are also examples of successfulcrossbreeding programmes in developing countries.In some situations, carefully conceived andexecuted crossbreeding programmes have merit as arapid method of introducing desirable traits intolocal well-adapted breeds. The development of theDorper sheep is one of the most successfulprogrammes of composite breed development for alow-input production environment (de Waal andCombrinck, 2000). The breed was developed inSouth Africa by crossing Dorset Horn sheep withthe fat-rumped, black-headed Persian sheep, a localSomali breed. Other successful crossbreedingprogrammes include the formation of the Sunandinisynthetic dairy cattle in Kerala State, India (Box 4),the Boer goat of South Africa (Malan, 2000) and theBrazilian Milking Hybrid (MLB) cattle (Madalena,2005). Crossbreeding has been most successfulwhere it was followed by a rigorous selectionprogramme involving livestockowners’ participation and substantial public sectorinvestment in the form of technical support.

However, very often, crossbreeding has beenindiscriminate and the local breeds that underpinthe crossbreeding programme have been lostbecause of a lack of understanding by theauthorities, companies and/or farmers involvedthat these pure breeds must be maintained tosupport the system. The strategic use ofcrossbreeding as a way out of a narrowed geneticbase in commercial breeds is also consideredimportant. It is gaining acceptance, for example, forfixing the increasing adverse trends in reproductivetraits in commercial dairy cattle in North America.Such strategic crossbreeding is desirable to preventlong-term reduction of genetic diversity.

Finally, it should be recognized that large,highly variable and rich genetic pools of crosses

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between exotic and indigenous breeds exist indeveloping countries today. Such populationswould serve as a quick foundation for syntheticbreed formation; especially given the survivingindividuals have the combination of genes that bestfit the prevailing environments. Strategic use ofsuch crosses to develop breeds for specificproduction systems is prudent and timely. Forexample, in trypanosomiasis endemic areas, itwould make good sense to combine N’dama crossesthat have survived and are productive withpurebreds or crosses of equally tolerant cattle breedssuch as the Orma Boran of Kenya and Sheko ofEthiopia (which is at risk). This underlines theimportance of sorting out the problem ofcross-country access to such genetics.

Applications of technology ingenetic improvement

Current use of technology

Breeding programmes in the industrial productionsystems are complex and have evolved over manyyears of technical inputs in terms of design,determination of breeding objectives, calculation of

economic weights, genetic evaluation methods,breeding strategies and delivery of services, as wellas structures and techniques for dissemination ofimproved genetics. They involve the extensive use oftechnologies for data recording and storage,advanced computing and statistical analysis,reproduction, genetics and genomics. For example,dairy cattle improvement generally involvesautomatic milk recording of several hundredthousand cows each year, compositional qualityassessment, data download to a central database,large computers and advanced computeralgorithms that estimate the genetic merit ofmillions of animals simultaneously, artificialinsemination of millions of cows and embryotransfer of several thousand cows, laboratoryassays to determine parentage and, increasingly,molecular genetic testing to determine whichanimals carry particularly desirable sets of genes.

In the developing world, advanced technologiesare more difficult to implement because of high cost,lack of expertise and infrastructure and areconsequently not widely used. A contrastingsituation, however, exists in some developingcountries (such as India) where several top researchinstitutes pursue the use of mainly moleculartechnologies for their glamour rather than forsupporting a practical breeding programme.

Box 4. The Sunandini cow in Kerala, India

Conditions in the State of Kerala in southern India are generally not conducive to classicaldairy farming. These conditions are: the year round hot and humid climate, relentlesspressure on land for human needs, acute scarcity of fodder, high rainfall and consequentmineral depletion of the soil. However, the Kerala dairy development programme,implemented over four decades (1964–65 to 2000–01), increased the State’s average yieldper cow per day from less than a litre to nearly 7 litres and milk production from 200 000 to2.6 million tonnes per year. It has provided livelihood support to over one millionsmallholder households. The phenomenal growth in milk production can be attributed toa planned effort to develop the cattle genetically for milk production, supported by anextension programme for fodder development and a well-organized milk collection,processing and marketing system. A new composite breed, called “Sunandini” has beenestablished by crossbreeding local cattle and further selection among the crosses. Duringthe process, however, almost 80 percent of the local cattle have been converted to Sunandiniand the local Vechur breed of cattle has almost been lost. The composite has a wide geneticbase of exotic donor breeds – Brown Swiss, Jersey and Holstein Friesian and, to a lesserextent, the Indian donor breeds Sahiwal, Gir, Rathi and Kankrej. The Sunandini breedcombines the positive qualities of local cattle such as adaptability, resistance to disease andstrong hooves with the high production potential of the exotics. The level of exotic inheritanceis limited to 50 percent. Its overall average lactation milk yield is 3 400 kg with a milk fatpercentage of 4.0 (KLDB, 2004).

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Research involving use of technologies is preferredover more tedious field research, which is perceivedto be less rewarding. It is therefore necessary toensure that simple breeding programmes based onproven genetic principles are not abandoned infavour of molecular genetic technologies that, inturn, need the existence of sound breedingprogrammes to be used effectively (see Box 5 for anexample of effective use of advanced technology in abreeding programme in a developing country.) Anexample of effective use is that reproductivetechnologies, such as frozen semen or embryos, areused in several species to transfer germplasmbetween countries and sometimes to expand and/ordisseminate rapidly an imported population. Inaddition to greater efficiency and reduced costachieved, the use of such technologies greatlyreduces the risk of disease transmission comparedwith importation of live animals.

Progress with simple technology

The low level of use of advanced technologies inmost aspects of genetic improvement in thedeveloping world need not prevent effectiveimprovement being achieved (Box 6). For example, awell designed improvement programme, based onselection of the best animals assessed on their ownperformance, with no other information or analysis,can achieve from 40 to 70 percent of the maximum

possible rate of genetic improvement whencompared with the use of all advancedtechnologies. The use of advanced technologies inthe developed world is driven by the intensecompetition among breeding groups or companiesand the desire to improve characteristics that arenot easily or accurately recorded for every animal.In the absence of such intense competition indeveloping countries, there is no immediate need tointroduce expensive, advanced technologies. Alower rate of genetic progress using simplecost-effective techniques is preferable and certainlybetter than no selection.

The level of sophistication in terms of breedingstrategies to be adopted in order to ensuresustainability and effectiveness needs to becarefully considered. It will depend on the state ofthe local infrastructure, the product market andavailable supportive technical expertise andinstitutional arrangements. An example ofunsustainable levels of sophistication is the KenyanNational Dairy Cattle Breeding Programme, withsophisticated progeny testing comprisingmultibreed centralized milk and butter fat recordingand data processing systems involving severalinstitutions. The programme was modelled along aEuropean type of system without considering thelocal infrastructure and institutional limitations.The result is an ineffective system in which anunacceptably low (five or less) number of bulls perbreed are recruited each year, with up to 11 yearsbefore the test results are completed, leading to a

Box 5. Marker-assisted introgression/gene introduction in India

A good example of a clear gene effect successfully implemented in a marker-assisted introgression (MAI)programme is found in India. The Booroola gene is being introgressed from the small Garole breed intothe local Deccani breed that is suitable for meat production but has a limited reproductive performance.The Booroola gene has tremendous economic effects in this production system, increasing the weaningrate by nearly 50 percent. The breeding programme is undertaken by a research institute, but there areclear strategies and activities to ensure that the improved stock finds its way to shepherd flocks. Evaluationof the results in these shepherd flocks is an explicit part of the project, and initial results look verypromising. Long-term impact, however, needs to be assessed. Early results also indicate that the littersize of Booroola carriers has a direct correlation with feed availability during mating/pregnancy. Thismeans shepherds would be able to reap the benefits of the higher litter size during “good” years while theflock’s average litter size would not be unsustainably high during “bad” years. Shepherds may also liketo keep a mixed flock of Booroola carrier and non-carrier animals as a risk insurance. MAI should not beruled out for breeding programmes in developing countries, but should be assessed based on the meritof each case (van der Werf, 2007).

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near-zero genetic gain. In this situation, a simplernucleus-herd-based young bull scheme would havebeen more effective and sustainable, given the verylimited number of herds actually contributing togenetic improvement. Location and management ofthe nucleus and recorded herds should ensure thatproduction conditions in such herds match ormimic those of the smallholder and/or commercialfarms under which most of the progenies of thebulls are raised.

Emerging technology applications

Reproduction, data and statistical analysistechnologies continue to show regular incrementalimprovements and are expected to benefit but notfundamentally change the current design andoperation of genetic improvement programmes.After decades of research and development, sexedsemen has recently become available on acommercial basis (Johnson et al., 1987, Weigel,2004). The use of sexed semen could be especiallybeneficial in countries such as India where religiousbeliefs preclude the consumption of beef. In suchcountries, the male animals are neglected and are awasted resource. Technologies for management offemale reproduction, such as synchronization ofoestrus and (non) pregnancy diagnosis, cancontribute to faster genetic improvement bydecreasing the intervals between successive

parturitions and increasing the number ofcandidates for selection.Some technologies, such as the LivestockIdentification and Trace-Back System (LITS)implemented in Botswana as a deterrent to cattlethefts (http://practicalaction.org/?id=peace5_cattle_tracking_botswana), could have hugepotential for a genetic improvement programmewhere lack of individual identification is one of themain hurdles. The digital identification system usesradio frequency identification technology, is safe,environmentally friendly and tamperproof, and isused to identify individual livestock throughout thecountry. Other than managing cattle records anddeterring cattle thefts, the system would alsopotentially open up access to important livestockmarkets such as the European Union (EU). The EUbeef market regulation requires that imported beefbe traceable from the export slaughter facilities tothe individual animal that the meat came from.

Genomic technologies that have emerged fromthe human genome project are rapidly beingdeveloped for livestock. For example, in the past twoyears the ability to detect variations in the geneticcode of individual cattle has risen from testing twoor three variations in a single test to50 000 variations in a single test, and the cost oftesting has dropped more than a hundredfold (seecompanion paper on characterization). Suchtechnology developments are truly revolutionaryand provide prospects for radical changes in

Box 6. Simplifying phenotypic measurement of performance

The marginal gain obtained by increasing the precision of information onphenotypic traits is subject to the law of diminishing returns. For this reason,developing countries that are attempting to implement an open nucleus breedingscheme may be advised to begin by collecting “low tech”, simple measurementsof phenotypes from more animals and farms, rather than asking a few farmersto record complicated measures. For example, recording of milk yield could bebi-monthly or quarterly, rather than monthly. Lactation milk yield estimatesbased on only two test-days have been shown in some studies to have acorrelation of greater than 0.85 with estimates based on ten test-days(Vasconcelos et al., 2004). Measurements of heart girth can serve as a proxy forbody weight when scales are not available, as the traits are both highly heritableand highly correlated genetically (Janssens and Vandepitte, 2004). For traitssuch as overall likeability, temperament and general disease resistance thatwould be difficult or expensive to measure objectively, farmers can be asked toassign simple, ordered categorical scores for phenotypes.

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genetic characterization and improvement. Severalgroups have already demonstrated that using suchtests it is possible to determine the genetic merit ofindividual animals for most commerciallyimportant characteristics, without the need for anyprior phenotypic information on the animal(Meuwissen, Hayes and Goddard, 2001). Hugequantities of molecular level data are, however,needed. The ramifications of this are still beingexplored, but it is clear that radical changes indesign and operation of genetic improvement in thedeveloped world could emerge. The ability to applysuch technologies for routine genetic improvementin the developing world will require substantialreductions in cost, which seem likely to be achievedbut cannot be guaranteed. However, it is alreadyclear that these new technologies can be applied toachieve a much greater understanding of thefunctional genetic variation of developing anddeveloped world animal genetic resources, whichcan then be used indirectly to better target geneticimprovement globally.

Intellectual property issues

Virtually all the processes of relevant reproduction,data capture, statistical analysis and computingtechnology are in the public domain. Proprietarysoftware is either readily available at reasonablecost or can easily be duplicated withoutinfringement of proprietary rights. A small numberof commercially valuable molecular genetic testshave been patented. In most cases these patentshave not been registered in developing countriesand therefore provide little or no restriction on usein developing countries. Coupled with the fact thatsuch existing patents are for inventions with littlepractical value in the developing world, thewillingness of patent owners to provide free orlow-cost access to the developing world does notappear to have been tested. The recent developmentof high-throughput tests for genetic variants has ledto several applications for patents for simultaneoususe of large numbers of genetic polymorphisms. It isunderstood that in recent months the United StatesPatent Office has ruled that such patents are notvalid and that the test for each polymorphism mustbe patented separately. The most likely consequenceof this is that inventors will seek to protect suchintellectual property (IP) by maintainingcommercial secrecy rather than applying forthousands of separate patents. This will mean thatthe technology will be available to competingcompanies or countries, but the exchange of

information will be hindered. It may also meanmore difficulties for inventors to share IP withothers, even where no commercial competitionexists. This is because of the risk that keyinformation might be leaked, thereby devaluing theIP. This situation is likely to be more damaging totechnology use in the developing world whereresources are less likely to be available to duplicatediscoveries that have been protected by commercialsecrecy.

ConclusionsEnhanced use and development of animal geneticresources in all relevant production systems playkey roles in achieving food security and alleviatingpoverty. Ongoing utilization is also regarded as aneffective means of maintaining diversity andensuring the availability of resources for the future.Utilization is likely to continue if the breeds areperceived to provide genuine benefits – whetherthese are private benefits for the livestock keeper orpublic benefits for which society is willing to pay.

Continued increases in animal production andproductivity will be necessary to enhance foodsecurity and provide critical income, products andservices to hundreds of millions of poor families.Strategies involving incremental improvements inthe production potential and productivity oftraditional breeds, and corresponding gradualimprovements in management and access toveterinary services, supplemental feeds andmarkets, appear most promising. The continued useof traditional breeds is likely to remain the mosteffective strategy for resource-poor farmers in manyof the least-developed countries. However,opportunities may exist both to improve localbreeds and for carefully managed and limitedintroductions of exotic breeds in areas of greatestproduction potential. These opportunities must beseized when genuinely available.

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Mr Jan Philipsson, Interbull Centre, Sweden

This paper essentially concludes that the beststrategy to maintain animal genetic diversity isbased on the sustainable use of the AnGR. This is apro-active way of considering the conservationissue and it includes economic as well as naturalresource aspects, and has environmental andsociocultural dimensions. Interesting exampleswith diverse use of the AnGR are given asillustrations, primarily from developing countries.

In reviewing the options for the sustainable useof AnGR these may indeed vary considerablybetween developed and developing countries, dueto differences in climatic challenges, resources andinfrastructure. It is underlined that geneticimprovement of livestock productivity in most casesis a prerequisite for sustainability and thatproduction systems also will be intensified. It is animportant task to investigate how this can best beachieved in different regions and productionsystems considering possible environmentalimpacts. However, intensification by suchinterventions leading to increased fertility, survivalrate and health of animal populations would undermany circumstances mean considerably higherproductivity and less environmental stress.

The authors emphasize the need to make use ofboth traditional as well as new, molecular genetictools to catch the opportunities for geneticimprovement of livestock populations. However,they also point out that considerable improvementscan be achieved already with traditional knowledgeand rather simple techniques. They point forexample to both the use of nucleus herd selectionschemes and cross-breeding for the formation ofcomposite breeds to improve productivity whilemaintaining adaptation to the environment.Effective use is thereby made of genes from differentpopulations, a method that historically always hasbeen practised in the dynamic forming of breeds.The proposed wider use geographically oftropically adapted breeds is important and shouldbe further explored.

Obstacles for sustainable use of AnGR which Ithink need to be further addressed are:1. Improper definitions of breeding objectives to be

sustainable in relation to both market conditionsand a broad range of traits in animals. This isstill lacking in many populations of the

developed world, and may lead to seriousbiological problems with the animals(e.g. declining fertility and disease resistance). Indeveloping countries the choice of exotic breedsfor use in pure-breeding and cross-breeding hastoo often not been properly assessed beforeembarking on breeding systems, that laterproved to be non-sustainable, partly because of alack of long-term breeding strategies.

2. The role of farmer involvement needs to beemphasized even more. There are neithershort- nor long-term benefits of knowledge ingenetics or animal breeding if this knowledgecannot be transferred to the farming communityfor their action. More research on this technologytransfer issue and its proper consideration indevelopment projects are needed.

3. There are generally too few trained animalbreeding scientists and extension staff in mostdeveloping countries to effectively supportimplementation and running of sustainablebreeding programmes. Also in the developedcountries there is a shortage of quantitativegeneticists needed for development of AnGR.Increased research supporting the sustainableuse of AnGR and intensified capacity-buildingis therefore necessary.In conclusion, this paper emphasizes the

sustainable use of AnGR as the best method tomaintain necessary genetic diversity. For that tohappen, I would like to emphasize that geneticimprovement programmes are greatly dependentnot only on genetics, but also on policy,organizational and infrastructural issues to besustainable.

The issue of short-term vs. long-term benefits ofgenetic improvement programmes was raised. Itwas stated that it simply takes too long for thebenefits to be visible.

My answer to this is that the time it takes to seethe results of genetic improvement programmesdepends very much on the species, breedingstrategies chosen and the production system. Forspecies with short generation intervals, such aspoultry and pigs, results of both pure-breeding andcross-breeding are realized within one to two years,whereas effects of within-breed selection of dairycattle takes five to ten years if germplasm from othermore productive strains of the same breed cannot beused. On the other hand, all genetic effects are

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accumulated for each generation of selection. Thelater you start a selection programme with a breed,the more it will fall behind other breeds undercontinuous selection. However, geneticimprovement can be achieved much faster throughcross-breeding with a superior breed assessed to besuitable for the environment in question, andprovided that a long-term strategy has been workedout and considered feasible. In many cases such astrategy ends up with a new synthetic breed as theauthors of this paper have indicated.

The other point I would like to raise on thisissue, and which has an impact on the outcome, isthat genetic improvement programmes should notbe seen in isolation. First of all they must beapplicable to the prevailing environment andproduction systems. Secondly, improvements inmanagement and feeding must also be made, andsome of these improvements may be realized evenbefore the genetic ones. A holistic view of animprovement programme must be aimed for, wherethe genetics is just one component, but an importantone. Whatever the strategy chosen, a long-termperspective must always be taken.

Mr Raúl Perezgrovas, Instituto de EstudiosIndígenas, Chiapas, México

I would like to thank FAO for the invitation to be apanellist during the Scientific Forum, and for theopportunity to share some comments on the paperon “Sustainable use and genetic improvement of AnimalGenetic Resources”. I would like to congratulateChanda and the co-authors of the paper for thecomprehensive coverage of such a wide number oftopics regarding the sustainable use of AnGR.

I have been requested to present some reactions,and, as an animal scientist I can easily relate to allof the strategies and technical approachespresented by the different authors. It was possible toidentify the key words, as they were constantlymentioned throughout the document, and some ofthem were:• Animal genetic resources.• Farm animal breeds.• Livestock.• Breed improvement.• Genomic technologies.• Animal productivity; to mention just a few.

However, as a social scientist, I noticed the lowfrequency in the use of “other” key words, such as:• Livestock keepers.• Small-scale farmers.• Livelihoods.

• Local knowledge.And this is very important when the topic under

discussion is precisely the “sustainable use andgenetic improvement of AnGR”, because we know thatsustainability has a social, an economic and acultural component.

So, I present here a couple of suggestions to beconsidered by the agricultural technicians, theextension workers, the university professors andresearchers, and the policy-makers.

First, we all need to take a more humbleapproach and recognize that livestock keepers canteach us a few things regarding the sustainableutilization of farm animals; it is they who haveconserved and improved many indigenous or localanimal breeds, making them a vital part of theirlivelihoods.

And second, there are many participatorymethodologies that will allow the livestock keepersand the researchers, and the policy-makers toundertake a fruitful learning experience for all.

There is in the paper a very good example ofhow to integrate the local peoples’ expertise. Whentalking about “capacity-building and training”, I cameacross the following statement, and I quote:

“…training should build upon existing knowledge of theproduction system, and enable livestock keepers to make

informed decisions…”

I would suggest that the same spirit isconsidered also when we speak of geneticimprovement, promoting novel uses of animalgenetic resources, and the design of sustainablebreeding programmes.

Earlier today, the issue of Livestock Keepers’Rights was raised as necessary in a global actionplan. I suggest that the issue of “Listening toLivestock Keepers’ Voices” needs also to bediscussed.

Ms Xuan Li, South Centre, Switzerland

First of all, I would like to extend my appreciation toFAO for inviting me to be a panellist today. Irepresent the South Centre, an intergovernmentalorganization and think tank of the developingcountries, with its headquarter in Geneva,Switzerland. The member states of the South Centrecomprise G-77 and China. Our mandate is toprovide strategic vision and technical support forthe developing countries, particularly in the field ofintellectual property, trade and global governance.

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Coming to the paper, sustainable use andgenetic improvement is considered one of fourstrategic components of the Global Plan of Action forAnimal Genetic Resources. The paper properlydemonstrates that there is no inherentincompatibility between conservation andutilization if animal genetic resources are properlymanaged. The immediate questions arising are,what are the challenges and what managementstrategy will work?

Before addressing the challenges, I would like togive a brief picture on what is happening in majorinternational fora in the field of animal geneticresources in Geneva. In WIPO-IGC (WorldIntellectual Property OrganizationIntergovernmental Committee on IntellectualProperty and Genetic Resources, TraditionalKnowledge and Folklore), the issue is rather limitedto the discussion of plant genetic resources, and nobinding international agreement has been achieved.In WTO (World Trade Organization), the matter isovershadowed by the debate on “disclosure of source”and “prior informed consent”. In WHO (World HealthOrganization), emphasis has been made to urgemember states to establish mechanisms that ensurethe routine and timely sharing of biologicalmaterials and isolates from both humans andanimals, and no proper benefit-sharing scheme isavailable. In short, neither effective incentive topromote sustainable use of animal genetic resourcesnor proper international regulation on geneticresource protection has been provided.

Reading from the paper, in my view, there are atleast four challenges that we are facing to ensure asustainable use of animal genetic resources. Thefirst challenge is to re-think livestock sector policiesthat “distort the playing field” on which indigenousbreeds compete. As we have seen, farmers are oftendisadvantaged by subsidies on feed, artificialinsemination and other inputs that tend to favourexotic breeds. From a policy perspective, there is aneed to conduct some systematic policy analysis toassess the implications of the existing livestockpolicies, and respond accordingly.

The second challenge is, from an economicperspective, that appropriate incentive and fundingmechanisms to foster innovation is crucial. Choiceneeds to be made between patent and alternativemechanisms, whichever is more cost-effective tofoster sustainable use and innovation.

The third challenge is that the interface betweenanimal genetic resources and intellectual property(IP) seems to be underestimated. The statement “allthe processes of relevant reproduction, data capture,statistics analysis, etc are in the public domain” is

inaccurate. In addition, a range of rapidlydeveloping molecular and reproductivebiotechnologies also has important implications foranimal genetic resources management. In order toensure a sustainable use of animal geneticresources, efforts must be made to carefully examinethe interface between animal genetic resourcesand IP.

The fourth challenge is that a proper scheme toensure access to animal genetic resources andtechnology transfer as well as benefit-sharing isnecessary. Specifically, there is a strong need toestablish an international binding treaty tostimulate the sustainable conservation and use ofanimal genetic resources. Such a treaty should cover“any genetic material of animal origin of actual orpotential value for food and agriculture”. The objectiveshould target the conservation and sustainable useof animal genetic resources for food and agricultureand the fair and equitable sharing of benefitsderived from their use, in harmony with theConvention on Biological Diversity, for sustainableagriculture and food security. The InternationalTreaty on Plant Genetic Resources for Food andAgriculture serves as an excellent analogy.Considering the slow movement in WIPO, WTOand WHO on genetic resource discussion, Memberstates are encouraged to work towards theestablishment of an efficient, effective andtransparent multilateral system at FAO, to facilitateaccess to animal genetic resources for food andagriculture, and to share the benefits in a fair andequitable way.

To conclude, if properly managed, a globalaction plan for animal genetic resources will be amajor contribution to the implementation of theConvention on Biological Diversity in the field offood and agriculture. Efforts should be made toestablish a series of coherent policy and legalregimes to achieve the purpose above.

Summary of plenary discussionThe meeting was then opened for generaldiscussion and interventions from the floor. Keyissues raised during this discussion included:• The need to reinforce research, human resources

and institutions, particularly in the developingworld.

• The significance of buffaloes in the context ofSouth Asia and the limited attention that thisspecies attracts from international donors andresearchers.

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• The need to better utilize existing technologiesand not always rush to adopt new technologies.

• The importance of characterization as anelement in the process of promoting sustainableuse – for example in the identification of breedswith specific attributes such as diseaseresistance.

• The need for information on breedcharacteristics to be effectively disseminated.

• The problem of reconciling the short-term needsof farmers with the longer-term objectivesassociated with sustainable utilization.Responses and final comments of the authors

included the following points:• Better understanding of animal genetic resources

is vital to achieving sustainable utilization.

• Existing knowledge, including local knowledge,needs to built upon and better integrated intomanagement strategies.

• Community-based structures are the buildingblocks of sustainability.

• In addition to North–South collaboration,South–South cooperation in the utilization ofanimal genetic resources is needed.

• Ensuring sufficient resources for themanagement of animal genetic resourcesrequires better awareness of the importance oflivestock production.

• There are links between the utilization of cropand animal genetic resources, and researchefforts in the two fields can be complementary.

adfbgdd

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AGRI 2008, 42: 71-89

SummaryLivestock production faces major challengesthrough the coincidence of major drivers of change,some with conflicting directions. These are:1. An unprecedented global change in demands for

traditional livestock products such as meat, milkand eggs.

2. Large changes in the demographic and regionaldistribution of these demands.

3. The need to reduce poverty in rural communitiesby providing sustainable livelihoods.

4. The possible emergence of new agriculturaloutputs such as bio-fuels making a significantimpact upon traditional production systems.

5. A growing awareness of the need to reduce theenvironmental impact of livestock production.

6. The uncertainty in the scale and impact ofclimate change. This paper explores thesechallenges from a scientific perspective in theface of the large-scale and selective erosion ofour animal genetic resources, and concludes thatthere is a stronger and more urgent need thanever before to secure the livestock geneticresources available to humankind through acomprehensive global conservation programme.

RésuméLa production animale se trouve face à des défisimportants dus à la coïncidence de différentsfacteurs de changements, certains en évident conflitpar rapport à leur orientation. C’est-à-dire:1. Changement sans précédent de la demande au

niveau mondial de produits traditionnels telsque la viande, le lait et les œufs.

2. Changements importants dans la distributiondémographique et géographique de la demande.

3. Le besoin de réduire la pauvreté dans lescommunautés rurales en offrant un moyend'existence durable.

4. L’émergence due à la possibilité de nouveauxproduits de l’agriculture tels que le combustiblebiologique qui a un impact significatif sur lessystèmes traditionnels de production.

5. Une majeure considération de la nécessité deréduire l’impact environnemental dû à laproduction animale.

6. L’incertitude sur le niveau et l’impact duchangement climatique. Cet article étudie lesdéfis du point de vue scientifique dans le casd’une érosion sélective des ressourcesgénétiques animales à large échelle. Enconclusion, il existe plus que par le passél’urgence d’assurer la disponibilité desressources génétiques animales pourl’utilisation humaine à travers un programmemondial de conservation.

ResumenLa producción ganadera se enfrenta conimportantes desafíos debido a la coincidencia devarios factores de cambio, algunos de los cuales enclaro conflicto con respecto a su orientación. Estosson:1. Un cambio sin precedentes en la demanda a

nivel mundial de productos tradicionales talescome la carne, la leche y los huevos.

2. Importantes cambios en la distribucióndemográfica y geográfica de la demanda.

3. La necesidad de reducir la pobreza en lascomunidades rurales ofreciendo una rentasostenible.

4. La emergencia debido a la posibilidad de nuevosproductos de la agricultura tales como elcombustible biológico que tienen un impactosignificativo sobre los sistemas tradicionales deproducción.

5. Una mayor conciencia de la necesidad dereducir el impacto ambiental debido a laproducción ganadera.

Conservation of animal genetic resources: approaches andtechnologies for in situ and ex situ conservation

J.A. Woolliams1, O. Matika1 & J. Pattison2

1Roslin Institute (Edinburgh), Roslin, Midlothian, EH25 9PS, United Kingdom2Centre for African Studies, University of Edinburgh, School of Social and Political Studies,

University of Edinburgh, 21 George Street, Edinburgh EH8 9LL, United Kingdom

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72Conservation of AnGR: approaches and technologies

6. La incertidumbre sobre el nivel y el impacto delcambio climático. Este artículo estudia estosdesafíos desde un punto de vista científico en elcaso de una amplia escala y erosión selectiva delos recursos zoogenéticos. En conclusión, existemás que nunca una fuerte y mayor urgencia deasegurar la disponibilidad de recursoszoogenéticos para uso humano a través unprograma mundial de conservación.

Keywords: Cryoconservation, Breed erosion, Climatechange, Genomic revolution, Managing uncertainty,Inbreeding, Somatic cell nuclear transfer (SCNT).

Darwin, Dylan and egg baskets:the scientific case forconservationThe first of this series of papers has described thetrends that are operating on animal geneticresources for food and agriculture throughout theproduction systems of the world. A much simplifiedsummary is that livestock are a focal point for manydrivers of change related to their ability to lift peopleout of poverty and into sustainable livelihoods, tosatisfy global demand for livestock products andpromote international trade, and the need forlivestock production to reduce its impact on theenvironment and its contribution to globalwarming. A broad conclusion is that there will be aneed for sustainable intensification of livestockproduction. The other papers in this series haveindicated the scientific background of how thismight be better achieved both now and in the future,and the needs for scientific information to supportdecisions on animal genetic resources.

The current drivers of change have led to a largenumber of breeds slipping between the cracks asproduction environments change, and changerapidly. Production environments are now shapedin part, to a greater or lesser extent, by theeconomics of the current global market, both forinputs such as feed and water for animals, andoutputs such as meat, milk and eggs. Broadly,breeds survive if they are fit for the marketconditions that prevail, and decline towardsextinction if they are not, a parallel of Darwin andnatural selection. The decline in numbers furtherincreases vulnerabilities to other catastrophicevents, such as conflict, disease, flood or drought.box 1 examines the scale of erosion of the world’sanimal genetic resources using data from The State

of the World’s Animal Genetic Resource for Food andAgriculture (FAO, 2007a) and concludes that asmany as one in three breeds may be at risk ofextinction, with a further one in ten already extinct.

Is this breed erosion a problem? Maybe not, ifthere is certainty and stability, but otherwisedefinitely yes. Unfortunately science tells us that, toquote Bob Dylan1, “the times they are a-changin’” andthat some of our past certainties may disappear.There is now an established scientific consensusthat there will be a period of relatively rapidclimatic warming over this century, and that humanactivity has contributed, and continues to contributeto this trend (IPPC, 2007).

As an example, box 2 shows the projectedchange in just one key agricultural parameter forone continent, the length of the growing season inAfrica; other parameters such as the projectedchanges in the frequency and severity of droughtsand floods are equally relevant. Box 2 illustrates animportant additional point in that the degree ofchange and its agricultural and socio-economicconsequences (see section 2.A.3 of The State of theWorld report for a brief overview of some of these)will depend on our future actions and theircoordination on a global scale. These actionsremain uncertain, but if they are limited orineffective, more far-reaching consequences areexpected. Further, as in all models, there areuncertainties resulting from limitations in ourscientific knowledge and understanding: somescientists think the consensus positionunderestimates the extent of change, while othersthink the change is overestimated. Therefore,beyond the familiar uncertainties of market trendsand the economic values of products, there is nowan additional uncertainty of a magnitude anddimension that is beyond the experience of themodern world. In short, there is change rather thanstability, with uncertainty writ large.

As a consequence of these developments, thechances are higher than ever before that what mayfit the needs of today may not fit the needs of ourchildren’s children. Science shows how the geneticdiversity that we have within any of our livestockspecies today can be regarded as being partitionedbetween breeds and within breeds. Estimates of themagnitude of the diversity between breeds are well

1Bob Dylan, 1963. The Times They Are A-Changin’. PopularSong.

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Box 1. A brief review of for mammalian and avian species based upon TheState of the World’s Animal Genetic Resources for Food and Agriculture

The table below summarizes the risk status of breeds in 2006, taking the data presented in tables 12and 13 of Part 1 – Section B.5 of The State of the World report. At first sight it might be concluded that“only” one in five of all mammalian and avian breeds are “at risk” of extinction, although closerexamination shows that only one in three can be viewed as “not at risk”. The discrepancy arises fromthe “unknown” category.

Mammalian Avian Total Risk Status Number % Number % Number % Critical 255 4.6 245 12.2 500 6.6 Critical-maintained 59 1.1 20 1.0 79 1.0 Endangered 406 7.3 287 14.3 693 9.2 Endangered-maintained 160 2.9 55 2.7 215 2.8 At risk 880 15.8 607 30.2 1 487 19.7 Not at risk 2 129 38.3 521 26.1 2 650 35.1 Unknown 1 907 34.3 825 41.3 2 732 36.1 Extinct 643 11.6 47 2.3 690 9.1 Total 5 559 100.0 2 000 100.0 7 559 100.0

It is possible to throw some light on the true state of the “unknown” breeds by analysis of the informationon breeds that were “unknown” in 1999 but for which more precise information is now available.Examination of Tables 19, 21 and 22 of The State of the World report shows that a total of 238 breeds wereclassified as “unknown” in 1999 and classified as either “at risk”, “not at risk” or “extinct” in 2006. Ofthese 40 percent were “at risk”, 57 percent were “not at risk” and 3 percent were “extinct”. Using thesefigures as predictors of the true status of “unknown” breeds in 2006, the best estimates for all breeds in2006 becomes 56 percent “not at risk”, 34 percent at risk” and 10 percent “extinct”, i.e. over one in three“at risk”, a further one in ten “extinct”, and just over one in two breeds “not at risk”. A further point tonote is that among the breeds known to be at “at risk”, only one in five have some form of in vivoconservation measure in place. In conclusion, the position of global animal genetic resources is farfrom secure.

in excess of 50 percent of the total diversity for traitsthat are related to fitness for an environment(Cundiff et al., 1986). This leads to the inescapableconclusion that the between-breed component ofdiversity is very important for addressing a broadrange of environmental conditions. The concern isthat the breeds thriving today are primarily thosefitted to high inputs and high outputs. Givenuncertainty over the production systems thatlivestock will face in the future, for example thepossible diversion of crops to biofuels, the breedsthriving today may not meet all our needs fortomorrow. Experience shows that we cannot change

the genetic constitution of existing breeds rapidlyenough to manage this uncertainty. Paradoxically,the ease of breed substitution which has placed somany breeds at risk is the primary reason why thefull range of breeds we have today is so valuable forthe future. There is a saying, “don’t put all your eggsin one basket” and currently the world is movingtowards a single basket of livestock.

The current state of insecurity of global animalgenetic resources was discussed above. Globalclimate change might be anticipated to increase theinsecurity of animal genetic resources, both directlythrough more extreme climatic events, even if the

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Box 2. Scenarios illustrating the potential impact of global climate change onthe length of the growing season in Africa, and the degree of uncertainty

arising from differing assumptions

Brief descriptions of the scenarios are given in the notes below, but the two maps represent theextremes for this attribute taken from a range of scenarios considered by the authors. The colours,from deep red, light red, white, light green to green represent loss in excess of 20 percent, loss of5-20 percent, change less than 5 percent, gain of 5–20 percent and gain in excess of 20 percentrespectively.

Notes:1. Regions gaining 5 percent or more in the growing season occupy considerably less than 1 percent

of the coloured regions for either map; examples of such regions in both maps are a minority ofthe coloured region on the North African coast, and to the south of the Great Rift Valley inEthiopia.

2. The maps are derived using the Hadley Centre Coupled Model version 3. The 2 scenariosshown are: on the left, A1F1, assuming very rapid global economic growth, global populationpeaking mid-century, rapid introduction of new and efficient technologies, with an emphasison fossil fuel energy; on the right, B1, assuming rapid change globally to service and informationeconomies, global population peaking mid-century, introduction of clean and efficient resourcetechnologies, with global planning but no new climate initiatives.

The maps are reproduced from Mapping climate vulnerability and poverty in Africa by kind permissionof P.K. Thornton.

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animal genetic resources appear well-adaptedtoday, and indirectly through competition foressential resources such as food and water leadingto an increased risk of conflict.

There is a stronger case than ever before foraction to secure animal genetic resources throughconservation measures. This case is based onmanaging the uncertainties in future food security,and extends beyond our raised awareness of theneed for managing genetic resources andecosystems that flowed from the Convention onBiological Diversity. The scientific logic is todevelop and implement a global conservationstrategy to create a secure backup, a “secondegg-basket”. This is a conclusion reached by at ameeting of experts in Montpellier (Gibson et al.,2006), and is one of the key action points identifiedby FAO in its Global Plan of Action for Animal GeneticResources (FAO, 2007b). The underlying operationalscience will be returned to later in the paper.

Opening the conservationtoolboxConservation can take different forms, dependingon needs and resources. The major classification iswhether or not the conservation is in situ or ex situ:the former describes a situation where conservationtakes place in the environment in which the breedhas been developed, and of necessity involvesconserving live animals over generations. Incontrast, ex situ conservation takes place outside thenative environment. It may or may not involve liveanimals, as there is the possibility of storinggametes, sperm or oocytes, or cells with thepotential to develop new animals, e.g. embryos,using the scientific advances of cryopreservation.There is a preference for in situ conservation,recognized by the Commission on GeneticResources for Food and Agriculture (FAO, 1998a).

Why this preference for in situ conservation? Thejustification lies in the opportunity for the breed tocontinue to develop in its native environment, andin doing so the qualities that adapt it to theenvironment continue to be maintained throughcontinued selection pressure. When theenvironment changes in one or more aspects,further selection builds upon an adaptedfoundation. Some adaptations, such as an ability towithstand drought or a resistance to a disease maybe easily observed; others may be identified as partof the characterization process; others may berecognized unexpectedly and in crises. An

illustration of the potential importance of in situconservation is the North Ronaldsay sheep, nativeto the United Kingdom, which was habitually keptin an environment where seaweed was importantcomponent of its diet. Upon removal from thisenvironment a large proportion of sheep died fromcopper toxicity. Further investigation showed thatthe ability to extract copper from the seaweed, withhigh efficiency, was an important adaptation of thebreed to their native diet. If there had been norecourse to an in situ population, the surviving exsitu population would have been strongly selectedagainst the very adaptation which had made thebreed potentially unique!

Given the potential benefits of in situconservation, why there is a need to consider ex situmeasures? The immediate answer is that resourcesand commitment of farmers may not be forthcomingin the face of the pressures that have led to the needfor the breed to be conserved, as it is seen as failingto meet the current needs. Alternative ex situ optionsare therefore necessary. These may include theestablishment of live populations of the breed ininstitutional or NGO environments that may differfrom the native environment, or by adoptingcryoconservation. The choice of conservationoptions is not a strict dichotomy, as combinations ofin situ and ex situ may be used. In particular, theidea of in situ populations supported bycryoconservation has become the method of choicein many developed countries.

Cryoconservation has a significant profile inlivestock conservation. The development,refinement and practice of the associatedcryopreservation techniques has been driven by theinterest of breeding organizations in many livestockspecies, because of the improved genetic progressthat can be achieved by using these techniqueswithin breeding programmes. Nevertheless, whilecryoconservation is a powerful option forconserving animal genetic resources, there aresignificant limitations: first, there are majordifferences among the livestock species in terms ofthe ease and effectiveness of applying thetechniques (discussed further in following sectionsof this paper); second, even in cattle wheretechniques are well developed success may beachieved only after a lot of time and resources,e.g. see Box 102, section 4.F.7 of The State of the Worldreport and third, the cryopreservation of semen,oocytes and embryos requires the use of liquidnitrogen. Use of liquid nitrogen is not a universaloption, as a significant number of countries haveno, or only limited, experience of such procedures.Box 3 summarizes the information o this topic

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presented in The State of the World report on thistopic. It is clear that global conservation capabilitieswould be advanced if the capacity to use liquidnitrogen were to be made universal.

Conservation can be viewed as the creation of agene bank containing live animals, or cryopreservedgametes and cells, or both. The gene banks securethe animal genetic resources, and in doing soprovide new opportunities. One such opportunity isto enhance the exchange of animal geneticresources, and allow the benefits from animalgenetic resources developed in one country to beshared elsewhere. Examples show that theimportance of a breed can sometimes be moresustained in a country other than the one in whichit is developed: for example the utilization ofSahiwal cattle (from South Asia) in Kenya.

Sharpening the tools: thecontribution of scienceThis section will describe how science can help tomake conservations more tractable and moreeffective, and how science currently under

development can improve matters further. The basicintegration of scientific approaches to conservationis described in the “Guidelines for management ofsmall populations at risk” developed by FAO (1998a),which cover all activities relating to conductingcensuses and compiling inventories, throughconsidering what conservation options may beappropriate for a single breed, how actions may beprioritized, through to the technical guidelines onsetting up and managing gene banks of live animalsand cryopreserved gametes. The techniques forcryopreserved gametes were reviewed and updatedmore recently by the European Regional Focal Pointfor animal genetic resources (ERFP, 2004). Thispaper will only introduce and discuss areas wherethe underlying science has developed or where newconservation needs have been identified.

How many minutes to midnight?

To be effective, conservation needs to be timely.Preserving the gametes of the last dodo would havehad little impact in terms of preventing the loss ofthe species. The proactive identification of breeds at

Box 3. A brief review of worldwide practice of techniquesrelevant for cryoconservation

The following is based upon data contained in section 3.D.2 of The State ofthe World report1 on use of artificial insemination (AI), which is a morewidespread technology and is and more widely applicable across the rangeof livestock species than embryo transfer. Only 84 percent of the 148 countriesproviding data report the use of AI in routine practice, and those not usingAI were primarily situated in SW Pacific, Africa and Asia regions. However,this fraction is an upper bound on the routine use of liquid nitrogen, sinceAI may be carried out with fresh semen, rather than frozen, without requiringcryopreservation. Furthermore, whilst the use of AI may indicate capacityfor storage and use of cryopreserved semen, it need not imply the routineuse of procedures for collection and cryopreservation of semen, bothessential for cryoconservation, as in many cases it was reported that exoticsemen was being used.

Section 3.D.2 also demonstrates that the practice of AI is primarilydirected towards cattle: whilst only one of the 84 percent of countriesreporting use of AI fails to mention cattle, only 34 percent and 21 percent ofcountries report the use of AI for pigs and sheep respectively, the two nextmost common species for AI use. As with cattle, these figures are upperbounds on the fraction of countries that routinely collect, store and usecryopreservation for these species.

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risk for conservation actions is an important tool formonitoring animal genetic resources, yet it is a toolthat remains blunt. One example is theidentification of breeds that are at risk as a result ofbeing confined to a small geographical area (acondition referred to as endemism), although theymay be locally numerous. Such breeds may be atrisk from catastrophic events. This was illustratedclearly in the United Kingdom during the foot andmouth disease epidemic of 2001. The regulations forcontrolling this disease within the European Union(EU) led the United Kingdom to cull livestock on alarge scale, with the result that few individualswithin the focus of the epidemic were left alive.Unfortunately, this focus closely coincided with thecentre of population of the Herdwick sheep breed,which is numerous locally but restricted in itsgeographical spread. Recognition of the plight ofthis breed led to a number of emergencyconservation actions during the epidemic.

Quantitative measures of the risk associatedwith endemism have not been formalized. Risk mayvary across regions; for example the area affected bya catastrophic drought may be wider than the areaaffected by a catastrophic fire. Thus, an assessmentof the risk associated with endemism requirescareful analysis of the potential impact ofcatastrophic events in the region in question.Attempts have been made (Gandini et al., 2004) todevelop approaches to the calculation of risk statusthat are not merely functions of populationnumbers. Several such methods, of varyingcomplexity, are in use, but these require furthersocio-economic and genetic inputs before they canbe considered reliable. Limitations will remain,while it may be possible to obtain better data forquantifying some risk factors, such as the degree ofcross-bred matings, other risks such as conflict maybe harder to quantify objectively.

Turning safety nets into springboards

Conservation, particularly in situ conservation, hasa dual purpose. It was introduced above as a“second egg-basket”, a form of safety net. However,considerable socio-economic research has beencarried out in an attempt to understand how thisnet can become a springboard for the return of abreed to the mainstream, in which no specialmeasures beyond the market are required tomaintain the population. In the FAO guidelines(1998a), the core approach to this transformationwas establishing the true market value of a breed,emphasizing the need to consider lifetime

performance and lifetime contributions rather thansimple measures of product yields under a regimeconducive only to high outputs. This considerationand the options that exist for improving therecognition of full market value remain important.However, it is now widely accepted that a breed’svalue exceeds the expected market value of itsproducts. Two further concepts can now be addedto the valuation process to demonstrate this: first thecontribution of a breed to managing climaticuncertainties and to recovery from environmentalcrises faced by farmers, and second the valuation ofa wide range of potential non-market services. Box 4illustrates why these concepts are important tomaintaining breed populations and securing thelivelihoods of farmers.

A more controversial area of economic scienceassociated with conservation of live animals is theuse of subsidy for maintaining breeds. An exampleof the complexity of this area is the mixed success ofmeasures implemented by the EU, which has in thepast supported such actions. While the subsidyhalted the decline in census numbers of breedscovered by the scheme, there was a barrier topopulation growth caused by existence of athreshold population size (headage) below which abreed was considered eligible for subsidy: a trendexisted for breeds to sit just below this thresholdsize for fear of losing subsidy. Therefore, subsidy isan effective safety net but an ineffectivespringboard! Consequently, subsequent EU supportis more concerned with characterization andhelping breeds to develop added values. Thisproblem with headage barriers can also be faced byNGOs. One such example is the Rare BreedsSurvival Trust in the United Kingdom, which hasre-vamped its qualifying conditions to allow it to actmore effectively as a springboard for moving breedsbeyond “at risk” status.

The genomic revolution

The genomic revolution with its tools of completegenome sequence, dense high-throughputgenotyping at increasingly affordable prices, andrapid detection of genetic polymorphism areprimarily new tools of characterization – to go fromsequence to consequence. These developments willlead to an advance of an order of magnitude beyondour current understanding, are addressed in thecompanion paper. However, in the context of thispaper, DNA has “traditionally” been used as thesource of DNA markers with which to measure agenetic distance between breeds, or to measure

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Box 4. Beyond the expected product value

Managing uncertainty. This can be illustrated by the considerable variation that exists betweenbreeds in terms of their ability to withstand drought, which is empirically seen to be muchgreater than variation within breeds. Farmers in many regions rely on their livestock as ameans of maintaining livelihoods through droughts. A breed providing this service mayperform a more vital role than a breed that provides better returns in the good times but failsin the bad times leaving the farmer without support. Therefore, the valuation of a breed’sperformance needs to take account of the foreseeable crises that affect the productionenvironment in which it is kept, rather than the average conditions. This process of valuationdoes not need to involve a straight choice between one breed and another: farmers in manyregions recognize the benefits of maintaining a mixed economy of breeds, maintaining highlyproductive breeds to capitalize on the good times, while maintaining the robust breeds asinsurance for the bad times. This latter role maintains populations, while securing livelihoodsin the fullest sense of the word “secure”.

Non-market values. Many products and services generated by livestock breeds are not marketed;these often include: transportation and traction; manure as fertilizer or fuel; fibre and skin forclothing; household meat, milk and eggs. Breeds may differ in their ability to provide theseservices. In addition livestock provide financial and socio-cultural services.

Financial services (Dorward et al., 2005) can depend on the animal having longevity in theenvironment in which it is maintained and retaining productivity in the harsher times of theproduction cycle. The ability to provide such services will clearly depend on the breed.Examples of financial services include:• buffering (or consumption smoothing) whereby investments are made in livestock during

periods when production or income exceeds consumption needs and then theseinvestments are drawn upon later in the season when lower production and income arenot sufficient to support consumption needs.

• Saving, whereby animals are kept explicitly to provide for some major expenditure (suchas a major purchase or investment, or expenditure on school fees or an important socialactivity).

• Insurance, where animals are kept solely for the provision of insurance against unexpectedevents that either reduce income or require additional expenditure, such as accidents orillness.

• Collateral for borrowing.Sociocultural services include important social integration functions in livestock

keepers’ society and culture. Traditional breeds may confer status on the individual owners,and may contribute to the sense of identity of whole communities through associations withtraditional agricultural systems or landscapes, folklore, cuisine, ceremonies, and crafts. Itshould also be kept in mind that commercial breeders gain status when their animals arepriced or exhibited.

genetic variation between and within breeds. Thesemeasures are then used to prioritize actions with aview to maximizing the diversity conserved (Eding& Bennewitz, 2007). There is an unresolved debateover the use of such methods, as there are soundarguments for basing actions on established andvalued phenotypes rather than the measures based

on anonymous marker DNA. One reason for basingactions on phenotypes is that empirically thereappears to be a poor correlation betweenquantitative measures of diversity based uponphenotypes and molecular measures of diversity(Reed & Frankham 2001). A future outcome of thegenomic revolution may be to improve this

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correlation through the richness of the informationobtained with the new genomic tools. However if, asargued previously above, there is a need to set inplace a comprehensive global conservation strategy,rather than one led by a process of choosing amongbreeds, then the issues surrounding prioritizationamong breeds may become more academic.

Dealing in diversity

One of the perennial concerns of managingpopulations in vivo in conservation schemes hasbeen the fear of inbreeding and the loss of diversity.Inbreeding is an unavoidable and natural processpresent in all populations, and as Bryson (2005)points out, to avoid all inbreeding in humans backto the time of Julius Caesar would require morehumans than have ever lived! There areconsiderable scientific arguments to show thatproblems associated with inbreeding are related tothe rate at which it occurs, not the observed degree,with faster rates associated with higher risks ofgenetic problems. This was addressed in the FAOguidelines (1998a), but science has continued toadvance in this area. New techniques have shownhow this rate of inbreeding can be managedsimultaneously with maximizing selectionopportunities under a range of circumstances.Combining these twin objectives is important for themanagement of breeding within conservationschemes, as populations may need to havedeleterious genes removed, which is a form ofselection, or may be part of a selection programme toimprove their economic viability. The same coretechnique can be modified to minimize the rate of

inbreeding given the resources available. Suchtechniques benefit from establishing the sires anddams of offspring each generation to build thepedigree. See box 5 for more details. In summary,these techniques move breeders from contemplatinga win–lose “trade-off” between selection gain andinbreeding, to taking advantage of a win–win byobtaining the maximum gain whilst managing ratesof inbreeding.

Not all the issues of inbreeding are concernedwith live animals: in cryopreserved gene banks thediversity “put in” limits the diversity “taken out”.The diversity put in depends on how donor animalsare sampled– both how many and which ones. Inthe event of a crisis, expending time consideringthis may be a luxury. However, there are establishedtechniques for identifying which individuals from abreed should contribute, and the size of theircontribution, in order to maximize the geneticvariation that can be mobilized from thecryopreserved bank, even where there areconstraints on the numbers sampled. These aremost easily applied if pedigrees are available, usingthe same core technology as for conservationschemes using live animals.

Managing expectations fromcryoconservation

In a cryopreserved gene bank there is no interest ondeposits - you only get out what you put in, at best!This observation is central to the design ofcryopreserved gene banks. Such banks requirefunds, effort and commitment to collect samples andto maintain them ready for a time of need, and it is

Box 5. Managing rates of inbreeding in live animals

Breeding schemes may have conservation or selection objectives, but all schemes can bebroadly classified into two groups: more sophisticated schemes with extensive pedigreerecording and where genetic evaluations for selection are computed by combining informationon a candidate and its relatives; and other schemes that are limited in their scope to accumulatefull pedigrees on offspring, and/or rely on mass selection procedures. For the first group ofschemes the sophistication of the scheme is sufficient to incorporate optimal contributionmethods (Meuwissen, 2007) into selection procedures to manage rates of inbreeding. For thesecond group the rate of inbreeding can be managed with the use of a simple table, based onthe ratio of number of breeding females to breeding males and the lifetime family size of abreeding female (Woolliams, 2007). The latter table is a more developed version of the T4.1 givenin the FAO Guidelines for managing small populations at risk (FAO, 1998a).

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vital that in the time of need the gene bank is fit forthe purpose. The FAO guidelines (1998a)introduced clear and valuable objectives for settingup gene banks as templates for others to developand customize to specific needs. There are nowexamples (Roughsedge et al., 2006), such as thesemen archive linked to the United Kingdom’sNational Scrapie Plan in which the samplenumbers and sampling plan are linked to theobjectives to be met in the future, after the semen iswithdrawn from the bank. What was recognized bythe FAO guidelines (1998a), and is now becomingmore widely accepted, is that the amount ofgermplasm required for worthwhile objectives maybe large and/or time consuming to acquire. It isessential that the managers of a cryopreserved genebank recognize not only what the use of the storedmaterial can achieve, but also what it can’t achieve,as false expectations inevitably lead to poorstrategic decisions.

Achieving more with less

It was already remarked in box 3 that most use ofcryopreservation techniques for breeding surroundscattle, with little use in some other species. So it is tobe expected that the effectiveness ofcryoconservation of gametes and their use postthaw varies widely between livestock species. Thisis illustrated by box 6, which is extracted from theFAO guidelines (1998a), which shows largedifferences between species in the time taken tocollect sufficient semen to achieve the same packageof measures defined by quantified outcomes fromusing the semen.

Furthermore, only for a minority of livestockspecies is it possible to routinely restore an animalwith an intact genome of a breed produced entirelyfrom cryopreserved material, i.e. an embryo, or cell,or gametes of both sexes. This is not yet possible inpractice for any poultry species. The relevance ofthis is that for those species where it is not possible,re-establishment of a breed from cryopreservedmaterial must involve another breed and repeatedbackcrossing. Important incremental advancescontinue to be made in the broad range ofcryopreservation techniques, partly through thepull of mainstream animal breeding seeking newopportunities. Examples of notable improvementare the effective cryopreservation of oocytes in cattle,and the ability to collect and cryopreserveepididymal spermatozoa in several species. Thelatter adds a back-up tool of collecting male gametesfrom abattoirs, but such a course of action must not

risk breeding males or potential breeding males of abreed at risk.. However significant and importantchallenges remain and some are listed in box 7.

One important new opportunity in conservingbreed diversity is the potential use of somatic cellnuclear transfer (SCNT), leading to cloning (Wilmutet al., 1997). This is perhaps paradoxical, as cloningacts against diversity by creating individuals withidentical genotypes! The explanation of thisparadox is that the initial steps in the processinvolving the collection, preparation and storage ofcells prior to nuclear transfer is a much moreflexible technique, requiring fewer facilities, thanthe collection of gametes for cryopreservation (FAO,1998b; Woolliams & Wilmut, 1999). FAO identifiedSCNT in 1997 as a viable option for emergencyconservation actions where other more establishedtechniques may be difficult to implement. Since thenSCNT has been demonstrated in a wider range oflivestock species, and its efficiency appears to beincreasing in many parts of the world (Box 8). Giventhe developments in this field, the scope ofapplication of SCNT and the recommendedprocedures for using SCNT in conservation actionsshould be reviewed and revised.

Ensuring best practice

The previous sections have demonstrated thatscience continues to make important and valuableadvances in sharpening the tools conservation moreeffective in achieving a diverse set of objectives. Thestate of the art in this area was drawn together in1998 by FAO to ensure best practice, and someaspects of cryopreservation were reviewed by ERFP(2004). It would be timely to comprehensivelyrefresh these guidelines.

Meeting the ChallengePreviously, it was argued that there is a need toestablish a comprehensive conservation strategy foranimal genetic resources in the face of the globaltrends and growing uncertainties described in thefirst paper in this series. Experience has shown thatsecuring animal genetic resources is best carried outproactively, giving time for the development ofeffective in situ conservation schemes whereverpossible. This will not be possible in all cases, andsecuring the full range of animal genetic resources,as argued previously, will require the resources toprovide a cryoconserved backup of all breeds. As

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Box 6. The time taken to acquire sufficient cryopreserved semen for achievingthe FAO “default” package of objectives for ten livestock species (see Note 1

below). The numbers of samples required for the package are defined byrequirements after use post-thawing, i.e. what is ultimately achieved from using

the semen

208

Mam

mal

sPo

ultr

y

123

153

191

Days required to complete sample collection

60

11

3

10

10

492

Chicken

Duck

Turkey

Horse

Pig

Rabbit

Sheep

Buffalo

Cattle

Goat

Notes1. The “default” package is detailed in Section 5.2.6 of Guidelines for management of small populations at

risk (FAO, 1998a) and includes semen for quantified sub-objectives involving re-establishment,supporting in vivo conservation, new breed development, and scientific research.

2. The numbers of samples required for the package are defined by requirements after use post-thawing,i.e. what is ultimately achieved from using the semen.

3. The times indicated are taken from Guidelines for management of small populations at risk, and arebased upon leading technology current in 1998. While these times have been reduced for somespecies as a result of subsequent research, the large differences between species in required timewill remain.

identified in box 3, such a strategy would require anextension of current capacities: cryopreservationtechniques are not yet a global technology althoughroutine in many countries, and species other thancattle would need to be addressed. There would be aneed to refine the techniques for several species,with particular attention given to poultry. However,it is best to start now with current best practicerather than wait with animal genetic resourcesunsecured and at risk.

Coordination of gene banks will be needed eitherthrough multilateral or bilateral agreements. In thiscontext, there is a need to resolve howcryoconserved material can be stored in duplicate(or more) locations, to reduce the risk of catastrophic

failure of one; how access and use can be madetimely and traceable, with appropriate security tomanage disease pathogens; and how replenishmentof the gene bank can be achieved after access anduse. These aspects are discussed in the FAOguidelines (1998a) and ERFP guidelines (ERFP,2004), but the principles contained therein need tobe fleshed out. Of primary importance is theprinciple that such gene banks should encourageuse – provided such use is equitable – as it is to thebenefit of all.

Large-scale conservation cannot be achievedovernight for more than 7 000 breeds of domesticlivestock! Operationally, in the face of the manydrivers for change in what we require from animal

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Box 7. Desirable advances in cryopreservation efficiency for thepurpose of conservation

1. Reducing the scale of variation between species in the time taken to obtaining sufficientsemen (or embryos) for delivering an identical quantified outcome post-thaw.

2. Developing a practical procedure to produce an intact genome of a poultry breedentirely from cryopreserved material.

3. Establishing reliable procedures in a range of species for obtaining thawed embryosfor transfer that have little or no variation in the numbers of embryos per embryo (oroocyte) donor. Depending on the technique used for embryo or oocyte recovery thisvariation can be considerable and can create a serious lack of diversity in the resultingoffspring. This is often ignored in simple formulae for number of embryos required,but the diversity “in” determines the diversity “out”!

4. Developing measures on semen pre-freezing to predict semen quality post-thaw. Thiswould increase success rates per unit of stored semen, reduce numbers of doses storedand the reliability of outcomes post thaw. However the time taken to collect the semenmight not be reduced.

5. Refining strategies for making best use of cryopreserved semen and embryos tore-establish extinct breeds (Boettecher et al., 2005). More rapid re-establishment wouldencourage more use of gene bank material in such cases.

genetic resources a strategy is required to capturethe diversity these breeds represent, and to ensurethat few, if any, slip between the cracks. Somecomponents of this strategy can be suggested. Asbreeds are more likely to get lost in more rapidlychanging systems, an initial step would be forinstitutions funding development programmes to beproactive in requiring project proposals to identifyconservation needs, and to supply costed andtimebound plans for addressing these needs thatwould be available for review and eligible forfunding. Such plans would be easier to draw upand organize if they were to be based upon “default”packages of quantified sub-objectives for thecryopreserved material, such as that suggested byFAO (1998a), or successor guidelines, which maythen be customized to meet particular needs, ifappropriate. A further important step is to identifyan “emergency” package for geographicallyrestricted breeds in the event of catastrophic events,such as drought and disease, and a fund for puttingthis into action when required. Such a package mayrequire a range of options, including the collectionof somatic cells, depending upon capacity in theaffected area, the need and the time available. Withthese steps in operation, gaps in ex situ collectionscould be assessed to identify the need for furtheractions. None of these steps preclude the

development of regional or national initiativesbased on their own priorities.

ConclusionLivestock production faces major challengesthrough the coincidence of major drivers of change,some with conflicting directions. These are:1. An unprecedented global change in demands for

traditional livestock products such as meat, milkand eggs.

2. Large changes in the demographic and regionaldistribution of these demands.

3. The need to reduce poverty in rural communitiesby providing sustainable livelihoods.

4. The possible emergence of new agriculturaloutputs such as biofuels making a significantimpact upon traditional production systems.

5. A growing awareness of the need to reduce theenvironmental impact of livestock production.

6. The uncertainty in the scale and impact ofclimate change. These challenges, with theirinherent unpredictability, should be met by firstsecuring the livestock genetic resources that areavailable to humankind.

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Box 8. Somatic cell nuclear transfer and cloning

Somatic cell nuclear transfer (SCNT) was first demonstrated in sheep with the creationof Dolly by Wilmut and co-workers (Wilmut et al., 1997) in 1997. In principle, thistechnique allows the creation of large numbers of animals with identical genotypes, bytransferring a nucleus from a donor cell into an enucleated oocyte to create an embryo fortransfer. Since Dolly the technique has been demonstrated in several mammalian livestockspecies: cattle (1998), goats (1999), pigs (2000), rabbits (2002) and horses (2003). Thetechnique has also been demonstrated in rodents, dogs, cats and ferrets, leading to thehypothesis that SCNT may be feasible for all mammalian species. It has yet to bedemonstrated in any avian species.

Although much of the public’s attention has been drawn to its potential use forcommercial cloning on demand, SCNT has properties that make it an attractiveproposition for use in conservation schemes. An outline procedure for use in conservationwould be to collect tissue samples, e.g. skin samples from live animals, prepare the cellsfor culture and store. When required for re-establishing a live animal, the cells would bethawed and used for nuclear transfer to create an embryo that could be then culturedin vitro and finally transferred to a recipient animal. Neither the donor of the enucleatedoocyte nor the recipient need be the same breed as the nucleus donor.

The strengths of SCNT compared to gamete or embryo cryopreservation are primarilyin the collection and storage of material:• The cost of equipment and training required for collection and initial treatment of

tissue samples is comparatively low.• Samples that have been given an initial treatment can be transported back to a central

laboratory for further processing and cryopreservation over a relatively long timeperiod, unlike the near-immediate and on-site cryopreservation required for gametesand embryos.

• In may be possible to recover and re-process cell lines after accidental thawing,providing this is identified early enough, unlike thawed gametes and embryos.The weaknesses of SCNT are primarily in the use of the cells post-thawing:

• low efficiency of providing viable embryos; and• increased risks of disorders at birth, sometimes fatal, associated with sub-optimal

embryo culture procedures.As early as 1997, FAO had identified SCNTas a viable technique for emergency

conservation actions. Since then, the technique has been shown to be feasible in severallivestock species, as described above, and there is anecdotal evidence that the efficiencyof producing viable embryos free of disorders can be considerably increased withexperience. In conclusion, it would be timely to review the potential of this techniqueand to integrate it more firmly into conservation guidelines. It may be that SCNT canonly be recommended as a desired option for a few livestock species in specialcircumstances; however it may be worth considering the cryopreservation of somaticcells even for poultry on the assumption that advances in technology may eventuallymake nuclear transfer viable in avian species. Groeneveld (2005) proposed to createnational genebanks on the basis of somatic cells.

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List of referencesBoettcher, P.J., Stella, A., Pizzi, F. &

Gandini, G. 2005. The combined use of embryosand semen for cryogenic conservation ofmammalian livestock genetic resources. GeneticsSelection Evolution, 37: 657–675.

Bryson, B. 2005. A short history of nearlyeverything. New York, USA, Broadway Books.

Cundiff, L.V., Mac Neil, M.D., Gregory, K.E.& Koch, R.M. 1986. Between and within-breedgenetic analysis of calving traits, and survival toweaning in beef cattle. Journal of Animal Science,63: 27-33

Dorward, A., Kydd, J., Morrison, J. &Poulton, C. 2005. Institutions, markets andeconomic co-ordination: Linking developmentpolicy to theory and praxis. Development andChange, 36: 1-25.

Eding, H. & Bennewitz, J. 2007. Measuringgenetic diversity in farm animals. In K. Oldenbroek,(Ed.). Utilisation and conservation of farm animalgenetic resources. Wageningen, the Netherlands,Wageningen Academic Publishers, pp. 232.

ERFP. 2004. Guidelines for the constitution ofnational cryopreservation programmes for farmanimals, edited by S-J Hiemstra. Publication No. 1 ofthe European Regional Focal Point on AnimalGenetic Resources. (also available atwww.rfp-europe.org/files/file00244.pdf).

FAO. 1998a. Secondary Guidelines forDevelopment of National Farm Animal GeneticResources Management Plans. Management ofSmall Populations at Risk. Rome.

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Gandini, G.C., Ollivier, L., Danell, B.,Distl, O., Georgoudis, A., Groeneveld, E.,Martyniuk, E., van Arendonk, J.A.M. &Woolliams, J.A. 2004. Criteria to assess the degree ofendangerment of livestock breeds in Europe.Livestock Production Science, 91: 173–182.

Gibson, J., Gamage, S., Hanotte, O.,Iñiguez, L., Maillard, J.C., Rischkowsky, B.,Semambo, D. & Toll, J. 2006. Options andstrategies for the conservation of farm animalgenetic resources. Report of an InternationalWorkshop (7–10 November 2005, Montpellier,France). Rome, CGIAR System-wide GeneticResources Programme (SGRP)/BioversityInternational, pp. 53.

Groeneveld, E. 2005. A world wideemergency programme for the creation of nationalgenebanks of endangered breeds in animalagriculture. Animal Genetic Resources InformationBulletin 36: 1–6.

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Meuwissen, T.H.E. 2007. Operation ofconservation schemes. In K. Oldenbroek, ed.Utilisation and conservation of farm animal geneticresources, pp. 167–193. Wageningen, theNetherlands, Wageningen Academic Publishers,pp. 232.

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Thornton, P.K., Jones, P.G., Owiyo, T.,Kruska, R.L., Herrero, M., Kristjanson, P.,Notenbaert, A., Bekele, N. & Omolo, A., withcontributions from Orindi, V., Ochieng, A.,Otiende, B., Bhadwal, S., Anantram, K., Nair, S.,Kumar, V. & Kelkar, U. 2006. Mapping climatevulnerability and poverty in Africa. Report to theDepartment for International Development. Nairobi,International Livestock Research Institute (ILRI).200 pp. (also available at www.dfid.gov.uk/research/mapping-climate.pdf).

Wilmut, I., Schnieke, A.E., McWhir, J.,Kind, A.J. & Campbell, K.H.S. 1997. Viableoffspring derived from fetal and adult mammaliancells. Nature, 385: 810–813.

Woolliams, J.A. & Wilmut, I. 1999. Newadvances in cloning and their potential impact ongenetic variation in livestock. Animal Science, 68:245–256.

Woolliams, J.A. 2007. Genetic contributionsand inbreeding. In K. Oldenbroek, ed. Utilisationand conservation of farm animal genetic resources,pp. 147–165. Wageningen, the Netherlands,Wageningen Academic Publishers, pp. 232.

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Mr Arthur Mariante, EMBRAPA GeneticResources and Biotechnology, Brazil

A very interesting paper, which brings back the oldquestion: in situ or ex situ, with a different approach!John and his co-authors brought some newingredients to this subject. Some of their coremessages are:• Diversity “put in” limits diversity “taken out”!• How many and which ones to include?• Gene Banks pay no interest! You get out only

what you put in!• What the use of the stored material can or cannot

achieve?• Use of SCNT for emergency conservation

actions.I would like to demonstrate some aspects of

animal genetic resources in Brazil.Most livestock are not indigenous to Brazil;

animals were brought in by the settlers, have been

submitted to natural selection, and supportedanimal production in the country for centuries. Atthe beginning of the twentieth century, exotic breedswere imported and gradually replaced theseadapted breeds.

To avoid the loss of this genetic material, in 1983Embrapa decided to include conservation of animalgenetic resources among its priorities. At that time,we decided to conserve those old breeds both ways,as suggested by John: in situ and ex situ. We agreewith the authors that there is no dichotomy, andthese two methods complement each other.

In situ conservation is carried out in nucleusherds (conservation nuclei), maintained in thehabitats where the breeds have been naturallyselected.

When there are human and physical resourcesin the nucleus, the collection and freezing of geneticmaterial are carried out on farm. When it is not

Brazilian Animal Genetic Resources NetworkBrazilian Animal Genetic Resources Network

GeneBank

NorthNortheastCentral-WestSoutheastSouth

Figure 1. Ex situ conservation - Semen and embryos are stored at the Animal Germplasm Banklocated at our Experimental Farm located in Brasilia. 65 000 semen samples and 250 embryos arebeing stored at the Animal Gene Bank (AGB), located at the Experimental Farm. More than8 000 DNA samples are being stored at the DNA Bank.

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possible, some animals are temporarily transferredto the Experimental Farm for this collection.

We agree with the conclusions by the authors,when they list six major challenges that livestockproduction is facing nowadays. The mentionedunpredictability of these challenges should really bemet by securing the animal genetic resources thatare available to mankind.This task should be shared by countries that havethe facilities and human resources to do so,building capacities in regions where this is not yetbeing done.

The time may have arrived to establish regionalgene banks, a huge project postponed by FAO in theearly 1990s, due to different animal healthlegislation of countries within the same regions. Theestablishment of subregional gene banks could bethe way to proceed in order to save endangeredbreeds of countries that are not yet prepared to doso. We are all responsible!

Ms Nitya S. Ghotge, ANTHRA, India

While on one hand the paper states that theposition of global animal genetic resources is farfrom secure, it does not adequately address therelative merits and demerits of different approachesand technologies with reference to different nationstates, which then brings one to the very crucialquestion of who will conserve the genetic material,where and how. The paper also does not touch onthe very important aspect of the ownership of genesand genetic material.

Currently, the genetic diversity of domesticatedlivestock lies in the Southern, lesser-developedcountries, often with farmers living in fragile andmarginal livelihoods. Efforts to preserve thisdiversity must go in tandem with efforts to improvethe livelihoods of these farmers, and this is wherefunds need to be channelled. The ownership of thegenetic material must remain with the communitiesand not in the private hands of industries orinstitutes.

Our organization ANTHRA which is based inIndia works with small and marginal farmers –dalits, adivasis (indigenous communities),pastoralists and landless groups – especially withwomen from these marginalized communities. Ourwork focuses on production and farming systems,and within them the crops and fodder varieties,livestock and plant genetic resources, medicinalplants and health care traditions, land and wateruse, and the indigenous knowledge connected withthese systems.

We support viable community-based livelihood-enriching interventions which use and strengthenpeoples’ knowledge systems in productive waysand make them less dependent on external forces.Towards this end we have been active insupporting local livestock production systems suchas women and backyard poultry with a specialfocus on the Aseel, Nicobari and Kadaknath breeds;local goats –the Kanchu Meka breed; local cattle –the Dangi; and local pigs – the Nicobari for differentadivasi (indigenous) communities, and the Deccanisheep for pastoral communities.

Mr Shakeel Bhatti, FAO International Treaty onPlant Genetic Resources for Food andAgriculture, Italy

Thank you, Mr Chairman.As I am on this Panel, the only commentator

from the plant genetic resource side and the onlyrepresentative of an intergovernmental body, Iwould like to add some comments on theinter-relation between the important work that liesahead for your Conference and the already existingwork and intergovernmental processes in the fieldof plant genetic resources (PGR) – in particular, ofcourse, the International Treaty on Plant GeneticResources for Food and Agriculture (ITPGRFA).

Having heard the presentations by the authors,my basic observation is that plant and animalgenetic resources are very distinct and cannot beforced into the same mould in legal and policyterms. And my basic argument would be that, intheir distinctiveness, PGR and animal geneticresources (AnGR) policy can and should becomplementary, mutually supportive and conceivedand developed in a coordinated manner.

Conservation, which is addressed underArticle 5 of the Treaty, is one of the basic objectivesof the ITPGRFA. However, the ITPGRFA comes fromthe plant side and so what I am about to say hasmostly elliptical value as a contribution to thisdebate.

Introduction to ITPGRFA

As the two areas are so different, let me, for those ofyou who are not familiar with the Treaty, recallsome of the main features of the ITPGRFA.Historically, the work of the Global Plan of Actionfor Plant Genetic Resources was purely foodcrop-based. It was during the negotiations for theITPGRFA that forages were brought in. The Treaty

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establishes a multilateral system (MLS) for a fixedlist of 64 crops and forages, established on the basisof the criteria of food security and interdependence.For these crops and forages the Treaty facilitatesaccess and regulates benefit-sharing.

Farmers’ Rights

As the paper mentions, there is a preference forin situ conservation recognized by the Commissionon Genetic Resources for Food and Agriculture(CGRFA), the prime body for policy in agriculturalgenetic resources. As we heard this morning, that iswhere the rights of pastoralists and traditionallivestock breeders, who are conserving AnGRdiversity in situ, come in. You might be interested toknow that in the context of the negotiations for theITPGRFA, we had the same discussion onrecognizing and incentivizing the enormouscontribution of farmers to the in situ conservation ofPGR. This discussion led to the adoption of Article9 of the International Treaty, entitled “Farmers’Rights”. So there has been a similar debate on therecognition of traditional communities in theconservation of PGR and the work onimplementation of Farmers’ Rights is still going on.There may be lessons to be learned there.

Linkages between PGR and AnGR

There may be a case to be made for working withecosystemic approaches that integrate perspectiveson PGR and AnGR to make overall productionsystems more effective. The linkages are, indeed,there in the production systems – AnGR productionsystems use crops and forages to produce. Thecoordination between PGR and AnGR policy mayplay a particularly important role in facilitatingsustainable intensification in crop-based livestockproduction systems and for conservation inpastoralist production systems.

AnGR and PGR are very different: differentbiology, different production systems, different useand innovation patterns, etc. Thus, whilerecognizing that they are inter-related, thedifferences must be recognized. This is wellreflected in the current policy and institutionalframework of FAO, where – while they are both inincluded in the Multi-year Programme of Work(MYPOW) – the process for plants is very different,being mostly contained in the framework of theITPGRFA.

Lessons that can be learned

In light of rapid change and genetic erosion, theremay be need for international regulation andcross-border controls to improve cooperation anddevelopment in the AnGR field. If you decide to gothat way in this Conference, there are lessonswhich, I think, might be learned from the ITPGRFAand its negotiations. These lessons include theimportance of multilateralism in designingappropriate policy and legal frameworks for geneticresources for food and agriculture. This is soimportant in agricultural genetic resources becauseof the millennia of open exchange of geneticresources in agriculture, both in both plant andanimal kingdoms, which makes a bilateralapproach very difficult to implement.

Another important consideration is the need fora Funding Strategy. The paper recommends that “aninitial step” of a “conservation strategy to capture thediversity of breeds” could be for funding institutionsto “require project proposals to identify conservationneeds and to supply costed and timebound plans for suchneeds”. I am pleased to inform you that an Ad HocAdvisory Committee on the Funding Strategy of theTreaty has just identified some key priorities andeligibility for funding under the Funding Strategy ofthe Treaty. It has identified “on-farm conservation ofPGRFA” in particular those listed in Annex I of theTreaty as one of the key priorities for funding ofdevelopment projects. The Funding Strategy of theTreaty foresees all sorts of actors working together,including through other institutions.

Some concrete suggestions:• The process following up from this Conference

and the monitoring of the possible Global Planof Action for Animal Genetic Resources candraw upon the Treaty process for support alongthe lines of the linkages outlined above.This would mean:

• Coordinating the processes of the Global Plan ofAction for Animal Genetic Resources and theprocess of the ITPGRFA as far as their respectivework on forages and pastures go.

• In a possible future revision of Annex I of theTreaty – which is done according to criteria offood security and interdependence – the needs oflivestock production systems and theircontribution to food security should be takeninto account. This should take into account theimportance of grasses and forages for livestockproduction systems and thereby for foodsecurity. This should apply especially tolow- and medium-input livestock productionsystems.

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• One target for the priorities under the FundingStrategy could be fodders and feeds – grasses(Africa) and legumes (South America).

Summary of plenary discussionThe meeting was then opened for generaldiscussion and interventions from the floor. Keyissues raised during this discussion included:• The need to identify forces that drive breeds to

extinction.• The need for guidelines to ensure that

inappropriate restocking measures are avoidedin the aftermath of catastrophes.

• The need to consider policy and legalframeworks for conservation programmes.

• The need to identify priorities for immediateaction in the field of conservation.Responses and final comments of the authors

included the following points:• In general, action is most urgently required

where the livestock sector is undergoing rapidchanges.

• In situ and ex situ conservation measures arecomplementary, but need to be coordinated toensure that they achieve their objectiveseffectively.

• Cooperation with conservation organizationsinterested in specific animal genetic resources isrequired.

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