Population Genomics Related to Adaptation in Elite Oat Germplasm

Authors Organisations
  • Kathy Esvelt Klos(Author)
    USDA–ARS Small Grains and Potato Germplasm Research Unit
  • Yung-fen Huang(Author)
    National Taiwan University
  • Wubishet A. Bekele(Author)
    Eastern Cereal and Oilseed Research Centre (ECROC)
  • Don E. Obert(Author)
    Limagrain Cereal Seeds
  • Ebrahiem Babiker(Author)
    USDA–ARS Small Grains and Potato Germplasm Research Unit
  • Aaron D. Beattie(Author)
    University of Saskatchewan
  • Åsmund Bjørnstad(Author)
    Norwegian University of Life Sciences
  • J. Michael Bonman(Author)
    USDA–ARS Small Grains and Potato Germplasm Research Unit
  • Martin L. Carson(Author)
    USDA-ARS Cereal Disease Laboratory
  • Shiaoman Chao(Author)
    USDA-ARS Cereal Crops Research Unit
  • Belaghihalli N. Gnanesh(Author)
    Agriculture and Agri-Food Canada
  • Irene Griffiths(Author)
  • Stephen A. Harrison(Author)
    Louisiana State University
  • Catherine Howarth(Author)
  • Gongshe Hu(Author)
    USDA–ARS Small Grains and Potato Germplasm Research Unit
  • Amir Ibrahim(Author)
    USDA–ARS Small Grains and Potato Germplasm Research Unit
  • Emir Islamovic(Author)
  • Eric W. Jackson(Author)
    General Mills Crop Biosciences
  • Jean-luc Jannink(Author)
    USDA-ARS Plant, Soil and Nutrition Research
  • Frederic L. Kolb(Author)
    University of Illinois at Chicago
  • Michael S. Mcmullen(Author)
    North Dakota State University
  • Jennifer Mitchell Fetch(Author)
    Agriculture and Agri-Food Canada
  • J. Paul Murphy(Author)
    North Carolina State University
  • Herbert W. Ohm(Author)
    Purdue University
  • Howard W. Rines(Author)
    University of Minnesota
  • Brian G. Rossnagel(Author)
    University of Saskatchewan
  • Jessica A. Schlueter(Author)
    University of North Carolina
  • Mark E. Sorrells(Author)
    Cornell University
  • Charlene P. Wight(Author)
    Eastern Cereal and Oilseed Research Centre (ECROC)
  • Weikai Yan(Author)
    Eastern Cereal and Oilseed Research Centre (ECROC)
  • Nicholas A. Tinker(Author)
    Eastern Cereal and Oilseed Research Centre (ECROC)
Type Article
Original languageEnglish
Article number0103
Number of pages12
JournalThe Plant Genome
Volume9
Issue number2
DOI
Publication statusPublished - 13 May 2016
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Abstract

Six hundred thirty five oat (Avena sativa L.) lines and 4561 single-nucleotide polymorphism (SNP) loci were used to evaluate population structure, linkage disequilibrium (LD), and genotype–phenotype association with heading date. The first five principal components (PCs) accounted for 25.3% of genetic variation. Neither the eigenvalues of the first 25 PCs nor the cross-validation errors from K = 1 to 20 model-based analyses suggested a structured population. However, the PC and K = 2 model-based analyses supported clustering of lines on spring oat vs. southern United States origin, accounting for 16% of genetic variation (p < 0.0001). Single-locus F-statistic (FST) in the highest 1% of the distribution suggested linkage groups that may be differentiated between the two population subgroups. Population structure and kinship-corrected LD of r2 = 0.10 was observed at an average pairwise distance of 0.44 cM (0.71 and 2.64 cM within spring and southern oat, respectively). On most linkage groups LD decay was slower within southern lines than within the spring lines. A notable exception was found on linkage group Mrg28, where LD decay was substantially slower in the spring subpopulation. It is speculated that this may be caused by a heterogeneous translocation event on this chromosome. Association with heading date was most consistent across location-years on linkage groups Mrg02, Mrg12, Mrg13, and Mrg24