title: Intrapopulation genomics in a model mutualist: Population structure and candidate symbiosis genes under selection in Medicago truncatula.
abstract: Bottom-up evolutionary approaches, including geographically explicit population genomic analyses, have the power to reveal the mechanistic basis of adaptation. Here, we conduct a population genomic analysis in the model legume, Medicago truncatula, to characterize population genetic structure and identify symbiosis-related genes showing evidence of spatially variable selection. Using RAD-seq, we generated over 26,000 SNPs from 191 accessions from within three regions of the native range in Europe. Results from STRUCTURE analysis identify five distinct genetic clusters with divisions that separate east and west regions in the Mediterranean basin. Much of the genetic variation is maintained within sampling sites, and there is evidence for isolation by distance. Extensive linkage disequilibrium was identified, particularly within populations. We conducted genetic outlier analysis with FST-based genome scans and a Bayesian modeling approach (PCAdapt). There were 70 core outlier loci shared between these distinct methods with one clear candidate symbiosis related gene, DMI1. This work sets that stage for functional experiments to determine the important phenotypes that selection has acted upon and complementary efforts in rhizobium populations.
authors.affiliation: Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801.
authors.forename: Michael A
authors.initials: MA
authors.lastname: Grillo
authors.affiliation: INRA Nancy-Lorraine, UMR 1136 Interactions Arbres Microorganismes, Route d'Amance, 54280, Champenoux, France.
authors.forename: Stephane
authors.initials: S
authors.lastname: De Mita
authors.affiliation: Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801.
authors.forename: Patricia V
authors.initials: PV
authors.lastname: Burke
authors.affiliation: Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801.
authors.forename: Kathryn L S
authors.initials: KL
authors.lastname: Solórzano-Lowell
authors.affiliation: Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801.
authors.forename: Katy D
authors.initials: KD
authors.lastname: Heath
mesh_terms: D005602:France; D018745:Genome, Plant; D005843:Geography; D015810:Linkage Disequilibrium; D046913:Medicago truncatula / Q000235:genetics* / Q000382:microbiology; D020641:Polymorphism, Single Nucleotide; D012231:Rhizobium / Q000502:physiology; D013030:Spain; D013559:Symbiosis
keywords: Coevolution; DMI1; legume-rhizobium, Medicago; mutualism; population genomics; population structure