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GrainGenes Reference Report: TPG-9-103

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Population Genomics Related to Adaptation in Elite Oat Germplasm
The Plant Genome
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Esvelt Klos K
Huang YF
Bekele WA
Obert DE
Babiker E
Beattie AD
Bjornstad A
Bonman JM
Carson ML
Chao SM
Gnanesh BN
Griffiths I
Harrison SA
Howarth CJ
Hu G
Ibrahim A
Isamovic E
Jackson EW
Jannink JL
Kolb FL
McMullen MS
Mitchell Fetch J
Murphy JP
Ohm HW
Rines HW
Rossnagel BG
Schleuter JA
Sorrells ME
Wight CP
Yan W
Tinker NA
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.
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