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