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Maintaining Plant Genetic Diversity in Agroecosystems
Tony BrownCSIRO Plant Industry
Canberra, Australia
Toby HodgkinIPGRI Rome, Italy
Maintaining diversity on farm
Durum wheat landrace, Iran
•Introduction•Perspectives on genetic diversity
Molecular diversitySingle nucleotide polymorphismsPhylogeny and coalescenceFunctional genomics
Landrace adaptedness•Research and development opportunities•Indicators for monitoring genetic diversity •Conclusions
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What is a gene?How do genes work?
E S DennisCSIRO Plant Industry
1) Single nucleotide polymorphisms (SNPs)
0.0013 RFLP probes, 6 loci
Adapted cultivars
Triticum aestivum
0.0160.014A
Adh3 – IntronsExons
0.0030.003A
Adh1 – IntronsExons
25 acc’nsIsrael-Afghan
Hordeum spontaneum
0.0110.0170.004
21 loci – InExon-Syn.Exon-Repl.
9 Inbreds, 16 landraces
Zea mays
Theta(per bp)
Gene(s)SampleSpecies
A About 2/3 synonymous; 1/3 amino acid replacements
2) Phylogeny & Coalescence
Alleles at the Adh3 locus from Hordeum
spontaneum (wild barley) belong to two
distinct lineages – east and west, diverging
3M years ago.
(Lin, Brown & Clegg)
3) Genomics - Microarrays for Gene Discovery
CDNA library / EST’s
DNA arrayedonto microscopeslide by robot
Robot
Microscope slide
mRNAs fromplant tissues
Expressionof all genes
E S DennisCSIRO Plant Industry
Robot for making Microarrays
Placement accurate to 1 micronE S Dennis
CSIRO Plant Industry
Expression profileTimeReference Gene Array Stress Response
Extent & Timing
Accession with goodstress response
Cultivar with poorstress response
Key indicator genes for markers in breeding
program
Genetic Resource
E S DennisCSIRO Plant Industry
Overlap of stress responses ?
188Low [O2]
Wounding
146
34
Drought
5
280
3522
• Screening of 3.5K Array• Number of Genes Up- or down-regulated:
- Low Oxygen : 249- Wounding : 220- Drought : 342
E S DennisCSIRO Plant Industry
Cereal & pulse landrace research
5122TOTAL(42 population & 31 genebank samples)
31Farmers’ selection criteria
82Abiotic stress at extremes: aridity, heat, cold salinity, water-logging
147Abiotic gradients and mosaics: altitude, climate soil, field size
70Biotic interactions: diseases and pests
1912Geographic separation:between countries, regions, farms
Morphological characters
Genetic markers
Kind of diversifying factor
Teshome, Brown & Hodgkin (2001) Plant Breeding Reviews: 21: 221-261.
Sorghum farmer, Ethiopia; photo by A.Teshome
Sorghum Landrace Diversity in Ethiopia(Teshome)
Total number of fields = 238 Total number of plants = 71041Total number of landraces = 64
__________________________________________Average number of plants per field sampled = 298
Range (40 - 1514)
Average number of landraces per field = 10.3Range (2 - 21)
Dimensions of data from 1993 sampling ofSorghum in Ethiopia
Relationships detected with landracerichness per field
The number of landraces in a field was related to -Environmental variables - Fields at intermediate
altitudes were more diverse.Edaphic variables - Soils with low ph and low clay
content were more diverse.Farmer decision making - Fields where farmers used more selection criteria were more diverse.
[Teshome et al (1999) Economic Botany: 53:79-88.]
•Population size change•Migration & gene flow
•Mating system
•Monitoring population numbers & sizes
•Population genetic analysis
•Seed supply•Landrace promotion
•Benefit sharing•Networking
Whole population processes
•Development experience guides
research needs
•Understanding genetic change
•Actions to improve farms & communities,
& stall erosion
Adaptive divergence
•Participatory PB & VT•Diversity deployment
among fields•Mutual information flow
•Technology transfer
•Gene action assay•Abiotic & biotic stress tests•Farmer diversifying criteria
•Use surveys
Selection
•Understanding genetic change
•Actions to improve farms & communities,
& stall erosion
•Development experience guides
research needs
•Population size change•Migration
•Mating system
Adaptive divergence
•Participatory PB & VT•Diversity deployment
among fields•Mutual information flow
•Technology transfer
•Monitoring population numbers & sizes
•Population genetic analysis
•Gene action assay•Abiotic & biotic stress tests•Farmer diversifying criteria
•Use surveys
•Seed supply•Landrace promotion
•Benefit sharing•Networking
Research & development opportunities
Research
Development
Genetic structure of Pyrenophora teresinfecting barley landraces in Sardinia
Domenico Rau, Giovanna Attene, Roberto PapaUniversity of Sassiri, Sardinia, Italy
Tony Brown, Curt BrubakerCanberra, Australia
Barley in Sardinia -•Widely cultivated cereal•Green fodder, grain and straw •Oldest traces: 4000 B.C. (Neolithic Period)•Today: some farmers grow modern varieties,many grow local populations of the six-row landrace called “S’orgiu sardu”
Collection sites in four agro-ecological areas
N urra
O gliastra
Trexenta
Sinis
Cam pidano
N
= both host and pathogen sampled
The pathogen
• Pyrenophora teres (anamorph: Drechslera teres) causes Net Blotch in barley and occurs world wide.
• Two formae speciales areknown:
P. teres f. sp. teres(the “Net form”) and
P. teres f. sp. maculata(the “Spot form”)
AFLP Fingerprint
18 isolates of P. teres from one population (Trexenta) produced with the primer combination E-GC/M-C.
Arrows indicate some polymorphic markers.
Coefficient0 .0 9 0 .3 2 0 .5 5 0 . 77 1 .0 0
sec1n sec32n sec52s sec21n t er17 s sec56n sec43ns erd20s ses30 s sir9s sec41s t er18 s sir18s sir10s ses18 s t er16 s sec4n erd19s sec7s sec8n sec24n pi r11 s erd15s erd24s sec49s sir5n ses23 s sec11n sec63n sec14n bp ir1 s sir27s ses12 s t er12 s sec45n sec61n t er14 s sir15n sir16n t er1s sir22n t er19 s t er20 ns sir20n sir2s sir23s ses6s ses13 s sec26n t er21 s sec3n t er22 s sec18s sec6n sec62n bt er1 s bt er1 2s t er6s bsir17n ses19 s t er9n s t er10 s bt er1 0s IT A5 IT A6 sec12s sec15s sir1s sec34n sir17s sir34s sec42s t er3s t er15 s sec23n erd18s erd24s sec48n sir7s sir13s sec51n t er5n s sir3s CAN2 t er8s sec16s ses16 s(2 ) pi r5n pi r6n bp ir7 n bp ir2 n bp ir3 ns pi r3n pi r14 n pi r8n ses11 n bp ir1 6s pi r22 s erd7s bp ir4 ns bp ir1 3n bp ir1 4n pi r23 n bsir2n ba c3n sir6n sir24n ba c29n bb ac1n ba c30 bb ac6n bb ac4n ba c4n bb ac14n ba c16n ses3n ses14 s ba c14n ba c18n ba c23n ba c10n ba c19n ba c26n ba c27n ba c1n ba c5n bb ac9n bb ac15n ba c21n ba c24n bb ac3n bb ac8n ba c2n ba c7n ba c8n bb ac13n ses16 s bb ac5n ba c9n ba c11n ba c17n ba c22n bb ac16n ba c25n AME 3 ba c20n AME 2 t er23 s AME 1 IT A1 IT A4 IT A3 IT A2 E URgr6 E URgr1 9 pi r12 n bt er4 n bt er3 n t er24 n bt er2 n t er11 s ab 9a ch ina CAN4 CAN5 CAN3 CAN6 CAN7 AME 4 sec57n CAN1 Grami n Dsork1 Dsork3 Dsork2 Ri nsc1 Ri nsc2 Ri nsc3 Outgroups
P. teres
Dendrogram (UPGMA) from Nei’sgenetic distance matrix of all P. teres
isolates and outgroupsSpot form
Net form
Isolates from a leaf lesion
Conclusions
• Isolates of P. teres from barley landraces in Sardinia are highly variable; more diverse than between isolates from advanced cultivars
• AFLP markers distinguish the two forms – this complex system involves three partners
• The net form has lower migration and astronger population genetic structure than the spot form
• Multilocus analysis showed that sexualreproduction is prevalent in both forms
Rice Landraces in 3 Nepal villages,
after Participatory Plant Breeding
pre -
1993
1995
1996
1997
Chhomr ongGha ndruk
Lumle
0
1
2
3
4
5
6
7
8
9
Sthapit& Joshi,
1998
Number of
landraces
Villages
Years
• PPB varieties have increased
farmers’ choices
“Indicators”
An indicator is a significant physical, chemical, biological, social or economic variable that is
measurable in a defined way for management purposes.
For example: Mean annual average global temperature
between 90°N and 90°S
Properties of the ideal Indicator
Desirable properties
•scientifically valid•accepted and known methods•simple and cheap•adaptable to a range of scales•clear-cut meaning •shows trend over time
Saunders, Margules and Hill 1998 -“Environmental indicators for ... reporting
- Biodiversity ”
Lowest unit
Validity? Interpretation?Proposed Indicator
Admin. district
Relation of knowledge to diversity? Community involvement?
�Security of traditional knowledge
FarmDo diverse criteria & uses lead to genetic diversity?
�Number, durability & evolution of farmer management & selection criteria
RegionDoes genetic diversity relate to environmental diversity – on what scale & how productive?
�Environmental amplitude of area devoted to each crop
Field or parcel
Are names reliable?Variation within a name in time & space?
�Number, frequency & area of distinct landraces
Indicators for in situ crop populations
0.001.002.003.004.005.006.007.008.009.00
1 9 17 25 33 41 49 57 65 73
Landrace Overall Frequencies - 1993
Percent of fields
•About half of the landraces have frequencies of occurrence of at least 1% of fields
•Data of Teshome (1996)
Frequency of occurrence of sorghum landraces in Ethiopia
Indirect:• Field size• Population or sample size
Landrace richness:• Number of landraces in
sample• Number of landraces in a
sample of constant size (30)Landrace evenness:
• Simpson index of diversity• Shannon information index
Measures of Genetic Diversity
Landrace richness & population size
y = 0.7563Ln(x) + 4.5716
R2 = 0.0273
0.00
2.00
4.00
6.00
8.00
10.00
12.00
14.00
16.00
10 100 1000 10000
Total plants scored
# o
f la
nd
race
s in
sam
ple
of
30
• Landrace richness- the number in a sample of 30 - is related to the logarithm of the sample (population or field) size
Nepal – rice landraces
Farms:Few
Farms:Many
Fields:Small
Fields:Large
0 20 40 60 80
Number of rice landraces
1
2
3
Nep
al s
tud
y si
te
Jumla
Kaski
Bara
Khatiwada et al (2000) in IPGRI In situ Training Guide
2 x 2 Classification by acreage and
frequency
Landrace Use SurveyLatin American Maize Project
(Taba, 1999)
31
2413
Argentina (16)
8
55
5
4 2
Chile (13)5
11 3
Mexico (12)
PrimarySecondaryTertiary
No. specific uses:
Bolivia (42)
(No. of maize landraces)
Indicators for wild species in situLowest UnitValidity? Interpretation?Proposed Indicator
PopulationRelation between genetic information and strategy?
�Gene diversity, population divergence & distribution
Metapopulation (valley)
Does census size relate to durability? Minimum viable size?
�Population numbers & sizes
Natural resource administrative
district
Relative location of reserves versus agroecosystems?
�Species in protected areas in populations that cover its range
Gene Management ZoneAntalya, Turkey
Wild barley beside a field, Israel
Extra indicators for complementary strategies
Lowest Unit
Validity? Interpretation?
Proposed Indicator
National programs
Information & seed exchange protocols, benefit sharing, & technology transfer
�Cooperative links between ex situgenebanks & farming communities
Single collection
Sampling scale? Replenishment & use strategies?
�Ex situ samples that back up vulnerable in situ populations; �Secure in situ sites for recalcitrant species
Conclusions
•Genetic diversity is an important focus of agrobiodiversity management•Levels of genetic diversity reflect recent history(bottlenecks, inadequate seed supply) and the general sustainability of the system•Infraspecific diversity of function (variation in adaptation & uses) enables crop populations to cope with variable stress environments•Indicators for monitoring the management of genetic diversity should track both population genetic structureand functional diversity