title: Population Genomics Related to Adaptation in Elite Oat Germplasm.
abstract: Six hundred thirty five oat ( 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 = 1 to 20 model-based analyses suggested a structured population. However, the PC and = 2 model-based analyses supported clustering of lines on spring oat vs. southern United States origin, accounting for 16% of genetic variation ( < 0.0001). Single-locus -statistic () 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 = 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.
authors.forename: Kathy
authors.initials: K
authors.lastname: Esvelt Klos
authors.forename: Yung-Fen
authors.initials: YF
authors.lastname: Huang
authors.forename: Wubishet A
authors.initials: WA
authors.lastname: Bekele
authors.forename: Don E
authors.initials: DE
authors.lastname: Obert
authors.forename: Ebrahiem
authors.initials: E
authors.lastname: Babiker
authors.forename: Aaron D
authors.initials: AD
authors.lastname: Beattie
authors.forename: Åsmund
authors.initials: Å
authors.lastname: Bjørnstad
authors.forename: J Michael
authors.initials: JM
authors.lastname: Bonman
authors.forename: Martin L
authors.initials: ML
authors.lastname: Carson
authors.forename: Shiaoman
authors.initials: S
authors.lastname: Chao
authors.forename: Belaghihalli N
authors.initials: BN
authors.lastname: Gnanesh
authors.forename: Irene
authors.initials: I
authors.lastname: Griffiths
authors.forename: Stephen A
authors.initials: SA
authors.lastname: Harrison
authors.forename: Catherine J
authors.initials: CJ
authors.lastname: Howarth
authors.forename: Gongshe
authors.initials: G
authors.lastname: Hu
authors.forename: Amir
authors.initials: A
authors.lastname: Ibrahim
authors.forename: Emir
authors.initials: E
authors.lastname: Islamovic
authors.forename: Eric W
authors.initials: EW
authors.lastname: Jackson
authors.forename: Jean-Luc
authors.initials: JL
authors.lastname: Jannink
authors.forename: Frederic L
authors.initials: FL
authors.lastname: Kolb
authors.forename: Michael S
authors.initials: MS
authors.lastname: McMullen
authors.forename: Jennifer
authors.initials: J
authors.lastname: Mitchell Fetch
authors.forename: J Paul
authors.initials: JP
authors.lastname: Murphy
authors.forename: Herbert W
authors.initials: HW
authors.lastname: Ohm
authors.forename: Howard W
authors.initials: HW
authors.lastname: Rines
authors.forename: Brian G
authors.initials: BG
authors.lastname: Rossnagel
authors.forename: Jessica A
authors.initials: JA
authors.lastname: Schlueter
authors.forename: Mark E
authors.initials: ME
authors.lastname: Sorrells
authors.forename: Charlene P
authors.initials: CP
authors.lastname: Wight
authors.forename: Weikai
authors.initials: W
authors.lastname: Yan
authors.forename: Nicholas A
authors.initials: NA
authors.lastname: Tinker
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D018554:Avena / Q000235:genetics*; D056726:Genetic Association Studies; D014644:Genetic Variation; D015810:Linkage Disequilibrium; D056186:Metagenomics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics