Single‐nucleotide polymorphism discovery and diversity in the model legume Medicago truncatula. (27th September 2012)

• Record Type: Journal Article
• Authors: Loridon, Karine; Burgarella, Concetta; Chantret, Nathalie; Martins, Frédéric; Gouzy, Jérôme; Prospéri, Jean‐Marie; Ronfort, Joëlle
• Is Part Of: Molecular ecology resources. Volume 13:Number 1(2013:Jan.)
• Page Start: 84
• Page End: 95
• Publication Date: 2012-09-27
• Subjects: Molecular ecology -- Periodicals; 572.8
• DOI: 10.1111/1755-0998.12021
• Languages: English
• ISSNs: 1755-098X

Abstract

<abstract abstract-type="main" id="men12021-abs-0001"> <title>Abstract</title> <p>Extensive genomic resources are available in the model legume <italic>Medicago truncatula</italic>. Here, we present the discovery and design of the first array of single‐nucleotide polymorphism (SNP) markers in <italic>M. truncatula</italic> through large‐scale Sanger resequencing of genomic fragments spanning the genome, in a diverse panel of 16 <italic>M. truncatula</italic> 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 <italic>Medicago truncatula</italic>.</p> </abstract>