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Agropolis Resource Center for Crop Conservation, Adaptation and Diversity

Agropolis Resource Center for Crop Conservation, Adaptation and Diversity. Jean-Louis Pham Jean-Pierre Labouisse arcad@agropolis.fr. Research on plant genetic resources and agrobiodiversity in Montpellier Conservation Evolution Genetic diversity Genomics Information technology

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Agropolis Resource Center for Crop Conservation, Adaptation and Diversity

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  1. Agropolis Resource Center for Crop Conservation, Adaptation and Diversity Jean-Louis Pham Jean-Pierre Labouisse arcad@agropolis.fr

  2. 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 • ...

  3. Flagship scientific programme Financial support to new infrastructure/facilitiesfor the conservation and analysis of crop biological resources Initiative oncrop biological resources Give Montpellier - Languedoc-Roussillon Region world-wide visibility in the field of agrobiodiversity, plant genetics and genomics

  4. Crop biodiversity research and resource center • 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

  5. 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

  6. Why so much focuson crop domestication ? 12 000 BP TDWG 2009 AgricultureCrop domestication

  7. Genetic content and structure of crop species Farmers’ practices Indigenous and non-indigenous knowledge Crop domestication : How a never-ending story started

  8. cultivation hybridizations selection migration etc cultivation Wild forms migration under selection Selectively neutral Crop genetic diversity has been shaped by domestication and successive events Allele diversity Crop history Courtesy of JC Glaszmann

  9. Association genetics : linking genotype and phenotype History ofcrop populations

  10. 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, …)

  11. SP1. Comparative crop population genomics :a phylogenetic and genome-wide approach of crop adaptation domestication bottlenecks, LD evolution … • 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 rate of divergence selection footprints …

  12. SP1. Comparative crop population genomics-Studied crops

  13. SP2. Crop adaptation to climate change • 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

  14. Passeport dataon landraceaccessions Conservation at 4ºC for 27 years Conservation at 4ºC for 27 years DNA markeranalysis Morphological and phenological analysis Changes in pearl millet diversity in Niger (1976-2003) 1976 germplasm collection 2003 Sampling in the same locations

  15. Pluviometry isohyetes from 1950 to 1976 Pluviometry isohyetes from 1977 to 2003 2003 1976 cycle duration Rapid changes in phenology of pearl millet landraces in Niger Flowering time of Pearl millet in Niger 1976 50-55 days 55-60 days 60-65 days 65-70 days 70-75 days 75-80 days 80+ days 2003 Bezancon et al. 2008, Vigouroux et al. submitted .

  16. Flowering in Arabidopsis, Komeda, 2004. Ann. Rev. Plant Biol. Phytochrome C gene -- SNP 101 Flowering time Panicle length 2004 field trial F=7.4, P<0.001 F=10.4, P<0.001 2005 field trial F=11.8, P<0.001 F=7.8, P<0.001 candidate gene, association analysis (pearl millet) Association between PhyC and flowering time Saidou et al. 2009, Vigouroux et al, submitted

  17. 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 Rice Pearl Millet Durum wheat Sorghum Corn media-2.web.britannica.com Guinea, 2007

  18. Conservation of biological resources • -PGR • passeport data • New entries and data • Conservation strategies SP7 Cryopreservation SP6 DNA bank • samples conservation • traceability • transferable technology SP4Bioinformatics • Databases • Assembling • Sequence annotation • SNP detection • Web interfaces • Methodology Comparative crop population genomics • Methodology • Population structure • - Validation Intra-specific effects of selection SP5LinkageDisequilibrium Genome wide SNP Knowledge on genome evolution Methods for detection of selection SP2 Crop Adaptation SP3 Cereals in Africa Additional data on crop adaptation SP8 Training

  19. 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)

  20. ARCAD : study countries (2009) As an open platform, ARCAD will continuously seek new partnerships

  21. Information: a key issue for ARCAD • 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 • …

  22. Thank you

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