In:
Molecular Ecology Resources, Wiley, Vol. 13, No. 1 ( 2013-01), p. 84-95
Abstract:
Extensive genomic resources are available in the model legume M edicago truncatula . Here, we present the discovery and design of the first array of single‐nucleotide polymorphism ( SNP ) markers in M . truncatula through large‐scale S anger 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 I llumina's G olden G ate assay, genotyped on a collection of 192 inbred lines ( CC 192) representing the geographical range of the species and used to survey the diversity of two natural populations. Finally, 86% of the tested SNP s were of high quality and exhibited polymorphism in the CC 192 collection. Even at the population level, we detected polymorphism for more than 50% of the selected SNP s. Analysis of the allele frequency spectrum in the CC 192 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 M edicago truncatula .
Type of Medium:
Online Resource
ISSN:
1755-098X
,
1755-0998
DOI:
10.1111/men.2012.13.issue-1
DOI:
10.1111/1755-0998.12021
Language:
English
Publisher:
Wiley
Publication Date:
2013
detail.hit.zdb_id:
2406833-0
SSG:
12
