Plant & Animal Genomes XI Conference

January 11-15, 2003
Town & Country Convention Center
San Diego, CA

Workshop: Arabidopsis
            

NESTED CORE COLLECTIONS IN ARABIDOPSIS THALIANA: A RESOURCE FOR EXPLOITING NATURAL GENETIC DIVERSITY.

¹ UMR Diversité et Génome des Plantes Cultivées, INRA Domaine de Melgueil, Mauguio, 34130 , France

² Station de Génétique et Amélioration des Plantes, INRA, Versailles, 78026 France

³ Unité de Malherbologie et Agronomie, INRA, Dijon, cedex 21065, France

⁴ Centre National de Recherche en Génomique, Evry, 91057 , France;

We are studying the natural genetic diversity present in Arabidopsis thaliana, since naturally occurring variation within a species can be exploited to identify quantitative trait loci (QTL), to perform genotype/phenotype association studies and to explore the ecological and evolutionary forces shaping currently observable genetic diversity. Our initial goal was to define a core collection, i.e., a subset of a larger germplasm collection that contains the maximum possible genetic diversity of the species with a minimum of repetitiveness. Such a collection would enhance the efficiency of SNP detection and facilitate phenotyping experiments. To allow flexibility particularly with respect to phenotyping we chose to build nested core collections. This permits the investigator to choose the appropriate size core collection to suit his needs. Ten gene fragments of ca. 600 bp (introns and exons), distributed throughout the genome, were sequenced on 95 or 265 Arabidopsis accessions from the different stock centers. SNP detection was performed using Genalys software, and the core collections chosen based on these results using the program MSTRAT. The core collections were validated on an independent set of morphological data, i.e., we verified that the core collections contained more morphological diversity that equivalent size random samples. This nested core collections will be used for SNP discovery by sequencing, following which the entire collection of Arabidopsis accessions will be genotyped for selected SNP markers. This resource will be available to the Arabidopsis community. Here we present the core collections, the expected efficiency of our sampling strategy and some of the features of the genetic diversity of Arabidopsis that we have remarked in generating this collection.