Research article

Microsatellite diversity and broad scale geographic structure in a model legume: building a set of nested core collection for studying naturally occurring variation in Medicago truncatula

Joëlle Ronfort^1*†, Thomas Bataillon^1,2†, Sylvain Santoni¹, Magalie Delalande¹, Jacques L David¹ and Jean-Marie Prosperi¹

• * Corresponding author: Joëlle Ronfort Joelle.Ronfort@ensam.inra.fr

• † Equal contributors

Author Affiliations

¹ UMR 1097 « Diversité et Adaptation des Plantes Cultivées », INRA Montpellier, Domaine de Melgueil 34130 Mauguio, France

² Department of Genetics and Ecology, Bioinformatics Research Center, University of Aarhus, Høgh-Guldbergs Gade 10, Building 1090, DK-8000 Århus C, Denmark

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BMC Plant Biology 2006, 6:28 doi:10.1186/1471-2229-6-28

Published: 13 December 2006

Abstract

Background

Exploiting genetic diversity requires previous knowledge of the extent and structure of the variation occurring in a species. Such knowledge can in turn be used to build a core-collection, i.e. a subset of accessions that aim at representing the genetic diversity of this species with a minimum of repetitiveness. We investigate the patterns of genetic diversity and population structure in a collection of 346 inbred lines representing the breadth of naturally occurring diversity in the Legume plant model Medicago truncatula using 13 microsatellite loci distributed throughout the genome.

Results

We confirm the uniqueness of all these genotypes and reveal a large amount of genetic diversity and allelic variation within this autogamous species. Spatial genetic correlation was found only for individuals originating from the same population and between neighbouring populations. Using a model-based clustering algorithm, we identified four main genetic clusters in the set of individuals analyzed. This stratification matches broad geographic regions. We also identified a set of "admixed" individuals that do not fit with this population structure scheme.

Conclusion

The stratification inferred is discussed considering potential historical events like expansion, refuge history and admixture between neighbouring groups. Information on the allelic richness and the inferred population structure are used to build a nested core-collection. The set of inbred lines and the core collections are publicly available and will help coordinating efforts for the study of naturally occurring variation in the growing Medicago truncatula community.