Agropolis Resource Center for Crop Conservation, Adaptation and Diversity Jean-Louis Pham...
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Transcript of Agropolis Resource Center for Crop Conservation, Adaptation and Diversity Jean-Louis Pham...
Agropolis Resource Center for Crop Conservation, Adaptation and Diversity
Jean-Louis PhamJean-Pierre Labouisse
Research on plant genetic resources and agrobiodiversity in Montpellier
•Conservation•Evolution•Genetic diversity•Genomics•Information technology•Plant breeding•Social Sciences•Economics•Farming systems•Seed systems•...
Initiative oncrop biological resources
Financial support to new infrastructure/facilitiesfor the conservation and analysis of crop biological resources
Flagship scientific programme
Give Montpellier - Languedoc-Roussillon Regionworld-wide visibility in the field of agrobiodiversity,
plant genetics and genomics
Nurturing the future of crop biodiversity
•An open platform for genetic and genomic resource conservation, management and analysis
•A research programme addressing key challenges on Mediterranean and tropical crop diversity for agriculture and sustainable development
•A demand-oriented training platform for Southern scientific communities
Crop biodiversity research and resource center
• New facilities on the La Valette campus (> € 10M)(on-going decision process)– Conservation (PGR, genomic resources)– DNA analysis– Scientific exchanges, Training
• Scientific project (€ 3M, operational costs) 2009-2013– Agrobiodiversity preservation and exploration: going beyond the
freezer– Understand how human societies and environment have shaped plant
agrobiodiversity over time : Crop domestication and adaptation– Africa + Mediterranean regions
Crop biodiversity research and resource center
Crop domestication :
How a never-ending story started
Farmers’ practicesIndigenous and non-indigenous knowledge
Genetic content and structure of crop species
Wild forms
migration
cultivationhybridizations
selectionmigration
etc
cultivation
Selectively neutral
under selection
Allele diversityCrop history
Crop genetic diversity has been shaped by domestication and successive events
Courtesy of JC Glaszmann
SP1 Comparative crop population genomics
SP2 Crop Adaptation
SP3 Cereals in Africa
Conservation of biological resources
Mediterranean and tropical plant genetic resources(Vitis, Medicago, Zea, rice, millets, Coffea, …)
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ASTERIDS
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ANGIOSPERMS
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r in progress
domestication bottlenecks, LD evolution…
rate of divergenceselection footprints…
SP1. Comparative crop population genomics :a phylogenetic and genome-wide approach of crop adaptation
Identify genomic selective patterns within and across crops
•High throughput bulk cDNA sequencing of a wide range of crops and wild relatives
•Bioinformatics analysis
>>mechanisms governing genome evolution>>influence of life history traits>>detection of selection footprints>>identification of agronomical genes
crop
wild
ancestor
relative 1
relative 2
molecular evolution
Crop Phylogeny Units Domestication Cultivated taxon Mating Life form
African Rice Poaceae old Oryza glaberrima A self Herb
Banana Musacées old Musa acuminata P out Herb
Cocoa Malvaceae DAP old Theobroma cacao P mixed tree
Coffea Rubiaceae recent C. canephora P out tree
Einkorn wheat Poaceae old A self Herb
Grapevine Vitaceae DIAPC old P Herm vine
Medicago Fabaceae DIAPC old medicago sativa P out Herb
Palm Arecaceae unknown Elaeis guineenis P out tree
Pearl millet Poaceae DIAPC old A out Herb
Sorghum Poaceae DAP old A self Herb
Tomato Solanaceae UGAFL old A self Herb
Life span
GDP/DAP/ UR AIVADAP / BGPI / UR 75
DIAPC/RPB/DAP
DIAPC /ISEM
Triticum monococcum
Vitis vinifera ssp. sativa
UPR 28/ DAP/ DIAPC
Pennisetum glaucum
Sorghum bicolor ssp bicolor
Solanum lycopersicum
SP1. Comparative crop population genomics-Studied crops
Studying genetic and evolutionary processes of adaptation a focus on phenological responses
Spatial gradients: populations/varieties collected along climatic gradients.
• M. truncatula : Latitudinal variation around the Mediterranean basin• rice : altitudinal variation (Madagascar)• pearl millet and sorghum : latitudinal gradient in West Africa.
Temporal gradients : comparing current populations/varieties and populations collected 20-30 years ago in the same sites • M. truncatula• pearl millet• rice
>>> Develop statistical and methodological tools to detect selection footprints along environmental gradients and over time.>>> Ecogeographical distribution of alleles of agronomical interest
SP2. Crop adaptation to climate change
1976 germplasm collection 2003 Sampling in the same locations
Changes in pearl millet diversity in Niger (1976-2003)
Conservation at 4ºCfor 27 years
DNA markeranalysis
Morphological and phenological analysis
Conservation at 4ºCfor 27 years
Passeport dataon landraceaccessions
Bezancon et al. 2008, Vigouroux et al. submitted .
1976 2003
Pluviometry isohyetes from 1950 to 1976 Pluviometry isohyetes from 1977 to 2003
cycle duration
Rapid changes in phenology of pearl millet landraces in Niger
Flowering time of Pearl millet in Niger
1976
2003
50-55 days55-60 days60-65 days65-70 days70-75 days
75-80 days
80+ days
Saidou et al. 2009, Vigouroux et al, submitted
2005 field trial
2004 field trial
F=7.4, P<0.001 F=10.4, P<0.001
F=11.8, P<0.001 F=7.8, P<0.001
C/C C/G G/G
66
68
70
72 a
bab
C/C C/G G/G
58
60
62
64
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a
C/C C/G G/G50
60
70a
bb
C/C C/G G/G50
60
70a
b b
Flowering time Panicle length
Phytochrome C gene -- SNP 101
candidate gene, association analysis (pearl millet)
Association between PhyC and flowering time
Flowering in Arabidopsis, Komeda, 2004. Ann. Rev. Plant Biol.
Rice
Pearl Millet
Sorghum
Corn
SP3. Cereals in Africa
• Rice, Millet, Sorghum, Corn, Durum Wheat
•Domestication history•Diffusion, Adoption
•Impact of cultural and socioeconomic factors on crop diversity
>>> In situ diversity of crops and wild relatives>>> Diffusion of innovation>>> From advanced to underutilized crops
Guinea, 2007
Durum wheat
media-2.web.britannica.com
SP8 Training
Conservation of biological resources
- PGR - passeport data - New entries and data - Conservation strategies
SP7 CryopreservationSP6 DNA bank- samples conservation- traceability- transferable technology
Methods for detection of selection
Additional data on crop adaptation
Comparative crop population genomics
SP2 Crop Adaptation
SP3 Cereals in Africa
Genome wide SNP Knowledge on genome evolution
Intra-specific effects of selectionSP4
Bioinformatics
- Databases- Assembling- Sequence annotation- SNP detection- Web interfaces - Methodology
- Methodology- Population structure- Validation
SP5Linkage
Disequilibrium
SP8. Training
• Already planned– Bioinformatics
– Molecular evolution
– Cryopreservation
– Agrobiodiversity analysis (multidisciplinary approach)
• Involve South and international partners– International course on Agrobiodiversity
• 2008: Montpellier• 2010: Morocco (IAV Hassan II)
AgrobiodiversitAgrobiodiversitéé : des Hommes et des Plantes: des Hommes et des PlantesOutils et MOutils et Mééthodes dthodes d’’analyseanalyse
Montpellier-Carnon17-28 novembre 2008
Ecole thématique internationale
AgrobiodiversitAgrobiodiversitéé : des Hommes et des Plantes: des Hommes et des PlantesOutils et MOutils et Mééthodes dthodes d’’analyseanalyse
Montpellier-Carnon17-28 novembre 2008
Ecole thématique internationale
AgrobiodiversitAgrobiodiversitéé : des Hommes et des Plantes: des Hommes et des PlantesOutils et MOutils et Mééthodes dthodes d’’analyseanalyse
Montpellier-Carnon17-28 novembre 2008
Ecole thématique internationale
• Data– Germplasm collections, DNA collections– Genotypes (SSR, SNPs, sequences), Phenotypes– Environmental data– Indigenous knowledge
• Technical and legal issues– Data management– Data access/sharing
• Plant, DNA, society and data explorers,“cross-disciplinary pollinators”, …
• Ontologists• Data quality managers• Information disseminators• …
Information: a key issue for ARCAD