title: Single-nucleotide polymorphism discovery and diversity in the model legume Medicago truncatula.
abstract: Extensive genomic resources are available in the model legume Medicago truncatula. Here, we present the discovery and design of the first array of single-nucleotide polymorphism (SNP) markers in M. truncatula through large-scale Sanger resequencing of genomic fragments spanning the genome, in a diverse panel of 16 M. truncatula accessions. Both anonymous fragments and fragments targeting candidate genes for flowering phenology and symbiosis were surveyed for nucleotide variation in almost 230 kb of unique genomic regions. A set of 384 SNP markers was designed for an Illumina's GoldenGate assay, genotyped on a collection of 192 inbred lines (CC192) representing the geographical range of the species and used to survey the diversity of two natural populations. Finally, 86% of the tested SNPs were of high quality and exhibited polymorphism in the CC192 collection. Even at the population level, we detected polymorphism for more than 50% of the selected SNPs. Analysis of the allele frequency spectrum in the CC192 showed a reduced ascertainment bias, mostly limited to very rare alleles (frequency <0.01). The substantial polymorphism detected at the species and population levels, the high marker quality and the potential to survey large samples of individuals make this set of SNP markers a valuable tool to improve our understanding of the effect of demographic and selective factors that shape the natural genetic diversity within the selfing species Medicago truncatula.
authors.affiliation: INRA, UMR AGAP, 2 place Pierre Viala, F-34060, Montpellier Cedex 1, France. karine.loridon@supagro.inra.fr
authors.forename: Karine
authors.initials: K
authors.lastname: Loridon
authors.forename: Concetta
authors.initials: C
authors.lastname: Burgarella
authors.forename: Nathalie
authors.initials: N
authors.lastname: Chantret
authors.forename: Frédéric
authors.initials: F
authors.lastname: Martins
authors.forename: Jérôme
authors.initials: J
authors.lastname: Gouzy
authors.forename: Jean-Marie
authors.initials: JM
authors.lastname: Prospéri
authors.forename: Joëlle
authors.initials: J
authors.lastname: Ronfort
mesh_terms: D001483:Base Sequence; D017931:DNA Primers / Q000235:genetics; D003710:Demography; D005787:Gene Frequency; D014644:Genetic Variation; D018745:Genome, Plant / Q000235:genetics*; D005838:Genotype; D046913:Medicago truncatula / Q000235:genetics*; D019083:Mediterranean Region; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D017422:Sequence Analysis, DNA
chemical_list: D017931:DNA Primers