Agropolis Resource Center for Crop Conservation, Adaptation and Diversity Jean-Louis Pham Jean-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 on crop biological resources Financial support to new infrastructure/facilities for the conservation and analysis of crop biological resources Flagship scientific programme Give Montpellier - Languedoc-Roussillon Region world-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) –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

Why so much focus on crop domestication ? BPTDWG 2009 Agriculture Crop domestication

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

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

Association genetics : linking genotype and phenotype History of crop populations

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, …)

domestication bottlenecks, LD evolution … rate of divergence selection 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

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 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 collection2003 Sampling in the same locations Changes in pearl millet diversity in Niger ( ) Conservation at 4ºC for 27 years DNA marker analysis Morphological and phenological analysis Conservation at 4ºC for 27 years Passeport data on landrace accessions

Bezancon et al. 2008, Vigouroux et al. submitted 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 days days days days days days 80+ days

Saidou et al. 2009, Vigouroux et al, submitted 2005 field trial 2004 field trial F=7.4, P<0.001F=10.4, P<0.001 F=11.8, P<0.001F=7.8, P<0.001 Flowering timePanicle length Phytochrome C gene -- SNP 101 candidate gene, association analysis (pearl millet) Association between PhyC and flowering time Flowering in Arabidopsis, Komeda, 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 Cryopreservation SP6 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 selection SP4 Bioinformatics - Databases - Assembling - Sequence annotation - SNP detection - Web interfaces - Methodology - Population structure - Validation SP5 Linkage 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)

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

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

Thank you