Genomics-based exploitation of germplasm diversity in major tropical crops

Germplasm is the substrate used by plant breeders to create novel plant gene combinations and select crop varieties more suited to the needs of diverse agricultural systems. Crop germplasm diversity has been shaped by domestication, a complex anthropogenic process caused by a multitude of human populations with specific habits and needs. Genome analysis tools now provide access to thousands of polymorphisms, thus considerably enriching our approaches to the evaluation of diversity. This involves describing global diversity patterns, monitoring variations along the genome and investigating local sequence variation in regions of interest. The past few years have seen major progress in unravelling the drivers of crop evolution, including foundations, introgression, admixture, mutations, translocations, in a background of drift and selection. Results on rice, sorghum, banana, cacao, rubber tree, groundnut, among others, provide a range of situations which highlight targeted approaches to access the diversity conserved in ex situ germplasm collections and help build strategies for further germplasm collections. Soon it will be possible to determine and compare the whole sequence of hundreds of accessions. We therefore advocate identification for each important species of a common core set of reference materials to help R.E.A.D. (Represent existing diversity - Enter the whole collection - Assess phenotypic variation - Dissect trait-gene associations) germplasm through concerted efforts within the research community. This is being implemented by the Generation Challenge Programme (www.generationcp.org) of the CGIAR for the major food crops. The process of crop domestication is being analysed for a range of tropical crops by the Agropolis Resource Center for Crop Conservation, Adaptation and Diversity (www.arcad-project.fr) through a multidisciplinary approach associating ethnological studies to genomic surveys in search for selection signatures. This will help focus on specific germplasm compartments that enable high resolution genetic analyses in support for breeding as well as deploy renewed efforts for under-utilised species. (Resume d'auteur)