Animal genetic resource conservation and biotechnology

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Conservation of animal genetic resources and

Biotechnology

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Outline

1. Definitions – Biodiversity, Animal genetic resources, Domestic animal diversity

2. Loss of genetic diversity in domestic animals

3. Reasons and criteria for selecting breeds for conservation

4. Methods for conservation of animal genetic diversity

5. Status of breeds

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Definitions

BiodiversityBiological diversity inherent variability of life forms – animals, plants, microbes

–Levels:•Ecosystem•Species•genes

Agrobiodiversity:–Diversity of life forms used in food and agriculture (including the management of agric landscapes)

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DefinitionsAnimal genetic resources:

– All animal species, breeds and strains that are of economic, scientific and cultural interest to humankind in terms of food and agricultural production, both now and in the future.

– Distinct populations within a species are usually referred to as breeds.

– A breed is defined as a subspecific group of domestic livestock with definable and identifiable external characteristics that enable it to be separated by visual appraisal from other similarly defined groups within the same species.

– Some define a breed as a group for which geographical and/or cultural separation from phenotypically similar groups had led to acceptance of its separate identity.

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– Common agricultural species include sheep, goats, cattle, horses, pigs, buffalo and chickens, but there are many other domesticated animals such as camels, donkeys, elephants, reindeer, rabbits, guinea pigs, ducks, turkey, and guinea fowls species that are important to different cultures and regions of the world.

– Globally there are about 40 species of domestic animals which have been domesticated over the last 12,000 years.

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Definitions

Domestic animal diversity:

- The spectrum of genetic variation existing among species, breeds and individuals, of all animal species which have been domesticated and their immediate relatives.

- Globally, there are about 6300 breeds of domestic animals

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List of animal species used for food and agriculture

Widespread species

Species No. of breeds

Pig 350

Goat 320

Sheep 850

Cattle 815

Buffalo 70

Horse 350

Donkey/Ass 70

Dromedary 50

Bactrian Camel 6

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List of animal species used for food and agriculture

Widespread species

Species No. of breeds

Llama 2

Alpaka 2

Chicken >300

Turkey >30

Duck >65

Muscovy Duck None

Domestic goose >60

Guinea Fowl 10 varieties

Japanese Quail >6

Pigeon 150

Ostrich 4 races

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• The breeds and strains of domestic animals are referred to as the global animal genetic resources and the genetic variation both within and between the breeds/strains is described as the genetic diversity within the species of domestic animals.

• Genetic diversity:– Heritable variation between and within

populations of organisms

• A population:– entire species– collection of individuals within a species

• examples: landraces, breed, strain, herd/flock, etc

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• For conservation purpose, it is the diversity between breeds, rather than between species, which is of crucial importance.

• Genetic variation at the population level consists of the differences in the types of alleles present and their frequencies across all members of a population considered together.

• Genetic variation is caused by change in allele frequencies over time due to selection (environmental- and human-directed), random genetic drift, gene flow, demographic bottlenecks, founder effects and mutation.

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Loss of genetic diversity in domestic animals

• It is estimated that 30 to 40% of all animal genetic resources are at risk of extinction.

• Adequate breed records do not exist, thus the existing data on the number of endangered breeds may be an underestimate.

• The factors that diminish genetic diversity are: - genetic bottlenecks – severe reduction in size

due to environmental or human made catastrophes - drought, floods, disease outbreak and war.

- random genetic drift – random change in gene frequencies in small populations attributable to sampling error

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- Inbreeding – mating of close relatives results in inbreeding depression

- human activities - habitat destruction and degradation, pollution, over-exploitation, introduction of exotic breeds and crossbreeding.

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Definition

Conservation of animal genetic resources: Is the sum of all actions involved in the

management of the animal genetic resources, such that these resources are best utilised and developed to meet immediate and short term requirements for food and agriculture, while maintaining the diversity they harbour to meet possible longer term needs for future generations.

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Management of Animal Genetic Resources - Is the combined set of actions by which a sample, or the whole, of a genetic resource is subjected to a process of genetic manipulation with the aim of sustaining, utilizing, restoring and enhancing the quality and/or quantity of the resource and its products

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• Strategies for effective management of domestic animal genetic resources

- Identifying and listing all breeds - Describing and characterising breeds in order to

understand their unique qualities and potential contributions at present and in future

- Monitoring the population statistics for each breed and regularly reporting those populations at risk of extinction

- Defining utilisation and improvement strategies for available breeds

- Storing adequate samples of as many breeds as possible, in the from of frozen semen, ova and embryos to enable future regeneration of lost populations.

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Why should animal genetic resources be conserved

• Reasons for conservation:– Opportunities to meet future market demands– Insurance against future changes in

production circumstances– Present socio-economic value– Sustainable crossbreeding schemes requires

different viable populations– Opportunities for research– Cultural and historical reasons– Ecological value

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Criteria for selecting breeds for conservation

• Degree of endangerment

• Adaptation to a specific environment

• Traits of economic importance

• Unique traits

• Cultural or historical value

• Genetic uniqueness

• Species a breed belongs to

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Conservation methods1. In-situ conservation – refers to conservation of

livestock through continued use by livestock keepers in the production system in which the livestock evolved or are now normally found and bred (i.e. maintenance of breeds within their normal environment) .

- operations for in-situ conservation include performance recording and breeding programmes, ecosystem management for sustainable production of food and agriculture

- Minimum number of animals to be maintained 150 – 1500 breeding females in developed countries, but in developing countries the number should not be below 5000

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Enhancing the importance and use of a genetic resource

Options for enhanced usea. Demonstrating value

b. Continuous use in breeding programs

c. Incorporation of genes into other populations

d. Selection within the same population

e. Explore potential for niche markets/novel products

f. Incentive payments

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Key operational components

• Performance monitoring/recording• Design of appropriate breeding programmes

• Applying and sustaining breeding programmes

• Capacity building: training & infrastructure development

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Advantages of in-situ conservation - Animals are still being utilized- The performance characteristics can be properly

recorded and evaluated- Breeds have the opportunity to evolveDisadvantages- Animals are at risk from diseases and other natural

disasters.- Genetic drift may result in unfavourable genetic

changes if the population is small,- There is a risk of increasing inbreeding and hence

homozygosity, which is associated with reduced fitness.

- The animals may be less productive and so more costly to maintain.

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2. Ex situ in vivo conservation

- Refers to conservation through maintenance of live animal populations in farm or zoological parks or other collections including government farms.

- It involves the preservation of a sample of a breed in a situation removed from its normal production environment or habitat.

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3. Ex situ in vitro conservation:- refers to conservation external to the living animal in artificial environment, under cryogenic conditions including the cryoconservation of embryos, semen, oocytes, somatic cells or tissues having the potential to reconstitute live animals at a later date.

- Cryopreservation – involves frozen storage of

rare breeds in the form of living semen, ova, embryos, somatic cells or tissues and DNA, which can be used to regenerate animals.

- This is necessary when there is a critical threat of a breed becoming extinct to ensure that an adequate gene pool is retained for future improvement programmes.

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Cryopreservation of semen

• Semen from all mammalian livestock species as well as poultry species can be successfully frozen.

• Freezing procedures for semen cryopreservation are species-specific, but the general procedures are as follows:

- Following collection, semen is diluted in a suitable ionic (salt) or non-ionic (sugar) solution adjusted to near physiological osmolarity.

- Suitable cryoprotectant is added, glycerol is mostly used, but dimethyl sulfoxide (DMSO), dimethylacetamide (DMA) or dimethylformamide (DMF) are also used especially in avian species.

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- Diluted semen is cooled, sampled and then frozen in liquid nitrogen (-196oC).

- Individual semen doses are generally frozen in straws rather than pellets to guarantee optimal sanitary conditions and permanent identification of each dose.

- the number of semen doses that need to be stored is a function of the number of doses required per parturition or hatching, the expected lifetime production of fertile refounder females and the number of males and females desired in the reconstructed population.

- Where semen is used to reconstruct breeds by backcrossing, sufficient semen must be stored to produce the number of backcross generations required.

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Cryopreservation of oocytes

• Viable oocytes can be recovered after freezing and thawing in a great number of species.

• Live-born young from embryos produced from cyopreserved oocytes have been reported in many mammalian species and humans.

• However, in birds hatched chicks have not yet been successfully obtained from eggs that were frozen and thawed, because of large size, high lipid content and polar organization of the bird ova.

• Embryos from mammalian livestock species can be produced in vitro from matured oocytes collected at slaughter or from live females by ovum pick-up.

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• The oocytes can be frozen for prolonged periods prior to in vitro fertilization (IVF) to produce embryos.

• Two methods of freezing are available: slow-freezing and ultra-rapid freezing procedures.

• Most protocols use high concentrations of cryoprotectants and sugars to remove water from the cells. This limits intracelluar ice formation and thus prevents injuries to the oocytes.

• However, working procedures which would make the cryopreservation of oocytes useful for conservation of AnGR on a large scale remain to be validated

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Cryopreservation of embryos

• Embryos of virtually all mammals can be successfully frozen, thawed and then transferred into recipient females to produce progeny.

• A variety of protocols to freeze and thaw embryos from livestock have been developed, they can be classified into two major categories: slow freezing and fast freezing (vitrification) techniques.

• Embryo preservation techniques are useful because they allow full recovery of the initial genome.

• Currently the use of embryo cryoconservation is limited to cattle, sheep and goats..

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Artificial insemination and embryo transfer technologies can provide support for cryopreservation.

The ability to rapidly recreate living purebreds is a key issue. If frozen semen is used as the only method of conservation, then several generations of backcrossing are needed to reinstate the breed concerned. Breeds can be reinstated rapidly from frozen embryos.

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• Frozen storage of semen and embryos have advantage that the breed being conserved is free from unintended genetic change.

• During storage,frozen genetic material is at less risk from diseases and natural disasters.

• The disadvantages are that reproductive technologies are not uniformly successful or presently available for all species and the expertise is not always available in the places where it is need most.

• Breeds conserved through cryopreservation of semen and embryos are not able to adapt to changes in the production environment . Semen or embyos frozen now may as well be unable to meet future production requirements.

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Conservation methods (cont’d)

In situ and ex situ are complementary, not mutually exclusive

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In situ or ex situ conservation?

Making the decision:

–Decision will depend on• Risk status• (Commitment to) CBD priority – incl.

sustainability issues• Costs – long- and short-term• Technical difficulty• Risk of failure

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Options for using cryo-preserved material

–Re-establishing extinct populations–Developing new lines – e..g

varieties–Supporting in vivo populations–Research – e.g. identification of

major genes–DNA-level studies

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Conservation methods (cont’d)

Gene bank– A physical repository where

samples of a genetic resource which are being preserved (e.g.live animals, embryos, oocytes, semen, tissues, DNA) are kept.

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Conservation methods (cont’d)

• Data bank

A collection of information on characteristics (including production system, production levels, adaptive traits and physical characteristics), status, husbandry, users and uses, etc, of genetic resources, stored in a systematic manner (usually electronic) and with provisions for editing and retrieval for viewing and analyses.

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Establishing the status

• Understanding the diversity

• Sources of information–Characterization

»Field/On-farm surveys – snap (baseline)

»Field/On-farm monitoring»On-station studies»Molecular diversity assessments

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Determining levels of threat

– Ranked levels – used in AnGR1. Extinct – A breed is categorized as

extinct if is no longer possible to recreate the breed population. This situation becomes absolute when there are no breeding males or breeding females remaining.

2. Critical – the total number of breeding females is less than or equal to 100 or the total number of breeding males is less or equal to five OR

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The overall population size is less than or equal to 120 and decreasing and the percentage of females being bred to males of the same breed is below 80%.

3. Endangered – the total number of breeding females is greater than 100 and less than or equal to 1000 or the total number of breeding males is less than or equal to 20 and greater than five.

OR

The overall population size is greater than 80 and less 100 ad increasing and the percentage of females being bred to males of the same breed is above 80%.

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OR

The overall population size is greater than 1000 and less than or equal to 1200 and decreasing and the percentage of females being bred to males of the same breed is below 80%.

Breeds may be further categorized as critical maintained or endangered maintained – these are endangered populations for which active conservation programmes are in place or populations are maintained by commercial companies or research institutions.

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• Breed at risk – a breed that has been classified as either critical, critical-maintained, endergered or endangered-maintained

• Not at risk – the total number of breeding females and males are greater than 1000 and 20, respectively.

• OR• If the population size is greater than 1200 and

the overall population size is increasing

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Proportion of the world’s breeds by risk status

Critical

Critical-maintained

Endagered

Endagered-maintained

Extinct

Not at risk

Unknown