Intrapopulation genomics in a model mutualist: Population structure and candidate symbiosis genes under selection in Medicago truncatula

Michael A. Grillo, Stephane De Mita, Patricia V. Burke, Kathryn L.S. Solórzano-Lowell, Katy Denise Heath

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)2704-2717
Number of pages14
JournalEvolution
Volume70
Issue number12
DOIs
StatePublished - Dec 1 2016

Fingerprint

Medicago truncatula
Metagenomics
Symbiosis
Genomics
symbiosis
population structure
genomics
Mediterranean Region
outlier
Rhizobium
Bayes Theorem
gene
Genetic Structures
Linkage Disequilibrium
Population Genetics
linkage disequilibrium
Mediterranean region
Fabaceae
Population
Genes

Keywords

  • Coevolution
  • DMI1
  • legume-rhizobium, Medicago
  • mutualism
  • population genomics
  • population structure

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Agricultural and Biological Sciences(all)

Cite this

Intrapopulation genomics in a model mutualist : Population structure and candidate symbiosis genes under selection in Medicago truncatula. / Grillo, Michael A.; De Mita, Stephane; Burke, Patricia V.; Solórzano-Lowell, Kathryn L.S.; Heath, Katy Denise.

In: Evolution, Vol. 70, No. 12, 01.12.2016, p. 2704-2717.

Research output: Contribution to journalArticle

Grillo, Michael A. ; De Mita, Stephane ; Burke, Patricia V. ; Solórzano-Lowell, Kathryn L.S. ; Heath, Katy Denise. / Intrapopulation genomics in a model mutualist : Population structure and candidate symbiosis genes under selection in Medicago truncatula. In: Evolution. 2016 ; Vol. 70, No. 12. pp. 2704-2717.
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