Genome‐Wide Association Study of Yield and Component Traits in Pacific Northwest Winter Wheat

Abstract

Grain yield and agronomic traits, key breeding goals for most crops, are under complex genetic control and subject to environmental interactions. Plant breeders require that the genetic architecture of agronomic traits be identified in locally relevant germplasm. Our goal was to conduct a genome‐wide association study to identify quantitative trait loci for eight agronomic traits in a diversity panel containing 402 Pacific Northwest winter wheat (Triticum aestivum L.) lines. Phenotypic evaluations of yield, yield components, phenology, and plant height were conducted under drought, rainfed, and irrigated conditions in 2012, 2013, and 2014. Linkage disequilibrium analysis, using 6492 single nucleotide polymorphism (SNP) markers from the 9K SNP array, determined that 70% of markers were in significant LD with other markers and formed 539 LD blocks with an average distance of 3.5 cM. Population structure analysis was conducted using 719 SNP tags that represent marker distribution. Three genetic subgroups were identified in the population, explaining 3 to 38% of the total phenotypic variation. A mixed linear model with 3653 SNP markers of known genetic position, the first two membership coefficients (Q = 2) of population structure and a compressed kinship (Kc = 192) was used in the association analysis. In this study, a total of 94 marker‐trait associations that were significant (false discovery rate < 0.05) were identified. Multiple trait associations for yield and component traits were identified on chromosomes 2B, 4B, 5A, 5B, 6A, and 7B. These findings highlight the possibility of using historical recombination in northern latitude winter wheat to identify genomic regions associated with desired agronomic traits.

Genetic Improvement of Wheat for Drought Tolerance: Progress, Challenges and Opportunities

“…Genome-wide association study (GWAS) and/or marker–trait association (MTA) approach overcomes several QTL mapping limitations by producing higher resolution, based on linkage disequilibrium across the genome, exploiting/employing data from diverse genetic backgrounds, making these approaches more efficient [ 81 , 143 , 260 , 261 ]. With GWAS/MTAs, an extensive collection of wheat germplasm is genotyped with SNPs or DArT markers throughout the genome to identify associations with the phenotypic trait(s) of interest [ 49 , 143 , 262 , 263 , 264 ].…”

Agroecological Advantages of Early-Sown Winter Wheat in Semi-Arid Environments: A Comparative Case Study From Southern Australia and Pacific Northwest United States

“…During the OFP, the risk of yield reductions caused by frost, heat, or drought is balanced and, on average, yield damage is minimized. Less work has been done defining an OFP for growing regions in the PNW, but there are certain yield penalties for wheat that encounters freezing air temperatures during flowering in mid-to-late May or has not finished reproductive growth by the onset of hot, dry weather in late June (Gizaw et al, 2018). In temperate regions, OFPs tend to be broad, meaning wheat can flower across a wider range of dates and still maximize yield.…”

Genome-wide association mapping for component traits of drought tolerance in dry beans (Phaseolus vulgaris L.)

“…It is based on linkage LD and historical recombination events of alleles of detected quantitative trait loci (QTL) at relatively high level of genetic resolution [43,44]. The high level of genetic or mapping resolution is due to high genetic variability and high number of recombination events in diverse natural population such as landraces, elite breeding lines and improved cultivars [43][44][45]. The historical recombination events would have naturally occurred during the evolution and domestication of the crop, and crop improvement (several generations) [33].…”