Population Genomics Related to Adaptation in Elite Oat Germplasm

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 genotypephenotype 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 (F ST ) 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 r 2 = 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. Core Ideas• An oat association-mapping panel contributed by active breeding programs worldwide.• Characterized population structure and found subdivisions related to adaptation• Characterized genome-wide and chromosomespecific linkage disequilibrium• Performed association-mapping and post hoc modeling of heading date• Found several consistently associated QTL

Haplotype‐based genotyping‐by‐sequencing in oat genome research

“…FST‐based analysis by Esvelt Klos et al . () failed to identify these major translocation regions, and this may further demonstrate the improved sensitivity of the pcadapt method. These two chromosome representations were assigned by Oliver et al .…”

“…As haplotype structure is related to LD, these differences are consistent with differences in LD decay observed by Esvelt Klos et al . () and may indicate footprints of adaptive QTL. These differences could have resulted from natural or artificial selection during breeding for different agro‐climatic conditions (e.g., northern vs. southern or spring vs. winter production).…”

“…Genome‐wide genotype–phenotype associations were identified using two marker systems (SNP and TL haplotype) on the same set of CORE diversity lines ( n = 635) reported by Esvelt Klos et al . (). The TL haplotype data were converted to HapMap format using the four nucleotides plus the presence/absence codes (+/−) to recode the first six haplotypes per locus.…”

Genetic variation and associations involving Fusarium head blight and deoxynivalenol accumulation in cultivated oat (Avena sativa L.)

“…A strong DTF QTL on Mrg02/9D coincides with FHB in TASSEL. Furthermore, the Mrg12/13A DTF QTL, the strongest in Norwegian conditions (Esvelt Klos et al., ), coincides with FHB in TASSEL and FHB and DON in PLSR. We hypothesize that due to photoperiod sensitivity, lines from the Midwest may have a precocious flowering in very long days and possibly immature cell walls, making them very susceptible.…”

“…In recent studies, this SNP marker platform has been expanded to utilize a 6k Illumina chip (Tinker et al., ), and these markers have been supplemented using a genotyping‐by‐sequencing (GBS) platform (Huang, Poland, Wight, Jackson, & Tinker, ). Combining these resources, two foundation studies were developed: a consensus map based on the larger set of markers mapped in 12 populations (Chaffin et al., ), and a study of diversity and population structure, including a GWAS analysis of heading date in 635 oat lines (Esvelt Klos et al., ). As this prior analysis confirmed that the primary population structure present in oat is related to spring vs. winter habit, the current work is focused on a set of spring oat varieties that are a subset of the 635 oat lines used in the aforementioned work.…”