Maintaining Plant Genetic Diversity in Agroecosystems Tony Brown Toby Hodgkin
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Maintaining Plant Genetic Diversity in Agroecosystems Tony Brown CSIRO Plant Industry Canberra, Australia Toby Hodgkin IPGRI Rome, Italy Maintaining diversity on farm •Introduction •Perspectives on genetic diversity Molecular diversity Single nucleotide polymorphisms Phylogeny and coalescence Functional genomics Landrace adaptedness •Research and development opportunities •Indicators for monitoring genetic diversity •Conclusions Durum wheat landrace, Iran What is a gene? How do genes work? 7,0( 48$17,7< 3/$&( 3527(,1 E S Dennis CSIRO Plant Industry 67$%,/,7< (175< 1(;7 *(1( 1(;7 *(1( 67$57 6723 1) Single nucleotide polymorphisms (SNPs) Species Sample Gene(s) Theta (per bp) Zea mays 9 Inbreds, 16 landraces 21 loci – In Exon-Syn. Exon-Repl. 0.011 0.017 0.004 Hordeum spontaneum 25 acc’ns Israel-Afghan Adh1 – Introns Exons 0.003 0.003A Adh3 – Introns Exons 0.016 0.014A 3 RFLP probes, 6 loci 0.001 Triticum aestivum Adapted cultivars 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 Robot mRNAs from plant tissues Microscope slide E S Dennis CSIRO Plant Industry DNA arrayed onto microscope slide by robot Expression of all genes Robot for making Microarrays Placement accurate to 1 micron E S Dennis CSIRO Plant Industry Expression profile Reference Gene Array Time Stress Response Extent & Timing Genetic Resource Accession with good stress response Cultivar with poor stress response Key indicator genes for markers in breeding program E S Dennis CSIRO Plant Industry Overlap of stress responses ? • Screening of 3.5K Array • Number of Genes Up- or down-regulated: - Low Oxygen : 249 - Wounding : 220 - Drought : 342 188 34 Low [O2] 22 5 35 146 280 Wounding Drought E S Dennis CSIRO Plant Industry Cereal & pulse landrace research Kind of diversifying factor Genetic markers Morphological characters 12 19 Biotic interactions: diseases and pests 0 7 Abiotic gradients and mosaics: altitude, climate soil, field size 7 14 Abiotic stress at extremes: aridity, heat, cold salinity, water-logging 2 8 Farmers’ selection criteria 1 3 22 51 Geographic separation: between countries, regions, farms TOTAL (42 population & 31 genebank samples) Teshome, Brown & Hodgkin (2001) Plant Breeding Reviews: 21: 221-261. Sorghum Landrace Diversity in Ethiopia (Teshome) Sorghum farmer, Ethiopia; photo by A.Teshome Dimensions of data from 1993 sampling of Sorghum in Ethiopia Total number of fields = 238 Total number of plants = 71041 Total number of landraces = 64 __________________________________________ Average number of plants per field sampled = 298 Range (40 - 1514) Average number of landraces per field = 10.3 Range (2 - 21) Relationships detected with landrace richness 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.] Whole population processes •Monitoring population numbers & sizes •Population genetic analysis •Development experience guides research needs •Understanding genetic change •Population size change •Migration & gene flow •Mating system •Seed supply •Landrace promotion •Benefit sharing •Networking •Actions to improve farms & communities, & stall erosion Selection •Understanding genetic change •Gene action assay •Abiotic & biotic stress tests •Farmer diversifying criteria •Use surveys Adaptive divergence •Actions to improve farms & communities, & stall erosion •Participatory PB & VT •Diversity deployment among fields •Mutual information flow •Technology transfer •Development experience guides research needs Research & development opportunities •Monitoring population numbers & sizes •Population genetic analysis Research •Population size change •Migration •Mating system •Seed supply •Landrace promotion •Benefit sharing •Networking •Gene action assay •Abiotic & biotic stress tests •Farmer diversifying criteria •Use surveys Adaptive divergence Development •Participatory PB & VT •Diversity deployment among fields •Mutual information flow •Technology transfer Genetic structure of Pyrenophora teres infecting barley landraces in Sardinia Domenico Rau, Giovanna Attene, Roberto Papa University of Sassiri, Sardinia, Italy Tony Brown, Curt Brubaker Canberra, 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 N urra O gliastra Sinis T rexenta = both host and pathogen sampled C a m pidano The pathogen • Pyrenophora teres (anamorph: Drechslera teres) causes Net Blotch in barley and occurs world wide. • Two formae speciales are known: 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. 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 tsec45n er12 s 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 ITer1 A5 0s 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 bb ac6n ac4n ba c4n bb ac14n ba c16n ses3n ses14 s ba c14n ba c23n c18n ba ba c10n ba c19n ba c27n c26n ba 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 A2 A3 IT E URgr6 E URgr1 9 pi er4 r12 nn bt bt er3 n t er24 n bt er2 ns t er11 ab 9a ch ina CAN4 CAN5 CAN3 CAN6 CAN7 AME 4 sec57n CAN1 Grami n Dsork1 Dsork3 Dsork2 Ri nsc1 Ri nsc2 Ri nsc3 Dendrogram (UPGMA) from Nei’s genetic distance matrix of all P. teres isolates and outgroups Isolates from a leaf lesion 0 .0 9 0 .3 2 0 .5 5 Coefficient 0 . 77 1 .0 0 Spot form P. teres Net form Outgroups 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 a stronger population genetic structure than the spot form • Multilocus analysis showed that sexual reproduction is prevalent in both forms Rice Landraces in 3 Nepal villages, after Participatory Plant Breeding 9 Number 8 of landraces 7 6 • PPB varieties have increased farmers’ choices 5 4 Sthapit & Joshi, 1998 3 2 1 1997 0 1996 1995 Lumle Gha ndruk Chhomr ong Villages pre 1993 Years “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 ” Indicators for in situ crop populations Proposed Indicator Number, frequency & area of distinct landraces Environmental amplitude of area devoted to each crop Number, durability & evolution of farmer management & selection criteria Security of traditional knowledge Validity? Interpretation? Lowest unit Are names reliable? Variation within a name in time & space? Field or parcel Does genetic diversity relate to environmental diversity – on what scale & how productive? Region Do diverse criteria & uses lead to genetic diversity? Farm Relation of knowledge to diversity? Community involvement? Admin. district Frequency of occurrence of sorghum landraces in Ethiopia •About half of the landraces have frequencies of occurrence of at least 1% of fields 73 65 57 49 41 33 25 17 9 Percent of fields 9.00 8.00 7.00 6.00 5.00 4.00 3.00 2.00 1.00 0.00 1 Landrace Overall Frequencies - 1993 •Data of Teshome (1996) Measures of Genetic Diversity 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 # of landraces in sam ple of 30 Landrace richness & population size y = 0.7563Ln(x) + 4.5716 16.00 2 R = 0.0273 14.00 12.00 • Landrace 10.00 8.00 6.00 4.00 2.00 0.00 10 100 1000 Total plants scored 10000 richness - the number in a sample of 30 - is related to the logarithm of the sample (population or field) size Nepal – rice landraces Jumla 3 Nepal study site 2 x 2 Classification by acreage and frequency Fields: Large Kaski 2 Farms: Many Bara 1 0 20 Farms: Few 40 60 80 Number of rice landraces Khatiwada et al (2000) in IPGRI In situ Training Guide Fields: Small Landrace Use Survey Latin American Maize Project Argentina (16) 31 Bolivia (42) No. specific uses: Primary Secondary Tertiary 8 5 13 24 5 (No. of maize landraces) Chile (13) Mexico (12) 5 4 5 2 (Taba, 1999) 11 3 Indicators for wild species in situ Proposed Indicator Species in protected areas in Relative location of reserves populations that cover its range versus agroecosystems? Population numbers & sizes Does census size relate to durability? Minimum viable size? Gene diversity, population Relation between genetic information and strategy? divergence & distribution Lowest Unit Validity? Interpretation? Natural resource administrative district Wild barley beside a field, Israel Gene Management Zone Antalya, Turkey Metapopulation (valley) Population Extra indicators for complementary strategies Proposed Indicator Ex situ samples that back up vulnerable in situ populations; Secure in situ sites for recalcitrant species Cooperative links between ex situ genebanks & farming communities Validity? Interpretation? Lowest Unit Sampling scale? Replenishment & use strategies? Single collection Information & seed exchange protocols, benefit sharing, & technology transfer National programs 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 structure and functional diversity
