title: Whole-genome nucleotide diversity, recombination, and linkage disequilibrium in the model legume Medicago truncatula.
abstract: Medicago truncatula is a model for investigating legume genetics, including the genetics and evolution of legume-rhizobia symbiosis. We used whole-genome sequence data to identify and characterize sequence polymorphisms and linkage disequilibrium (LD) in a diverse collection of 26 M. truncatula accessions. Our analyses reveal that M. truncatula harbors both higher diversity and less LD than soybean (Glycine max) and exhibits patterns of LD and recombination similar to Arabidopsis thaliana. The population-scaled recombination rate is approximately one-third of the mutation rate, consistent with expectations for a species with a high selfing rate. Linkage disequilibrium, however, is not extensive, and therefore, the low recombination rate is likely not a major constraint to adaptation. Nucleotide diversity in 100-kb windows was negatively correlated with gene density, which is expected if diversity is shaped by selection acting against slightly deleterious mutations. Among putative coding regions, members of four gene families harbor significantly higher diversity than the genome-wide average. Three of these families are involved in resistance against pathogens; one of these families, the nodule-specific, cysteine-rich gene family, is specific to the galegoid legumes and is involved in control of rhizobial differentiation. The more than 3 million SNPs that we detected, approximately one-half of which are present in more than one accession, are a valuable resource for genome-wide association mapping of genes responsible for phenotypic diversity in legumes, especially traits associated with symbiosis and nodulation.
authors.affiliation: Department of Plant Biology, University of Minnesota, Saint Paul, MN 55108, USA.
authors.forename: Antoine
authors.initials: A
authors.lastname: Branca
authors.forename: Timothy D
authors.initials: TD
authors.lastname: Paape
authors.forename: Peng
authors.initials: P
authors.lastname: Zhou
authors.forename: Roman
authors.initials: R
authors.lastname: Briskine
authors.forename: Andrew D
authors.initials: AD
authors.lastname: Farmer
authors.forename: Joann
authors.initials: J
authors.lastname: Mudge
authors.forename: Arvind K
authors.initials: AK
authors.lastname: Bharti
authors.forename: Jimmy E
authors.initials: JE
authors.lastname: Woodward
authors.forename: Gregory D
authors.initials: GD
authors.lastname: May
authors.forename: Laurent
authors.initials: L
authors.lastname: Gentzbittel
authors.forename: Cécile
authors.initials: C
authors.lastname: Ben
authors.forename: Roxanne
authors.initials: R
authors.lastname: Denny
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Sadowsky
authors.forename: Joëlle
authors.initials: J
authors.lastname: Ronfort
authors.forename: Thomas
authors.initials: T
authors.lastname: Bataillon
authors.forename: Nevin D
authors.initials: ND
authors.lastname: Young
authors.forename: Peter
authors.initials: P
authors.lastname: Tiffin
mesh_terms: D018744:DNA, Plant / Q000235:genetics; D007887:Fabaceae / Q000235:genetics; D014644:Genetic Variation; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D015810:Linkage Disequilibrium; D046913:Medicago truncatula / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D011995:Recombination, Genetic
chemical_list: D018744:DNA, Plant