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ARS Home » Pacific West Area » Pullman, Washington » WHGQ » Research » Publications at this Location » Publication #343247
Title: Using spectral reflectance indices as proxy phenotypes for genome-wide association studies of yield and yield stability in Pacific Northwest winter wheat

Author
item GIZAW, SHIFERAW - Washington State University
item GODOY, JAYFRED GRAHAM - Washington State University
item Garland-Campbell, Kimberly
item CARTER, AARON - Washington State University

Submitted to: Crop Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/30/2018
Publication Date: 3/22/2018
Citation: Gizaw, S.A., Godoy, J.V., Garland Campbell, K.A., Carter, A.H. 2018. Using spectral reflectance indices as proxy phenotypes for genome-wide association studies of yield and yield stability in Pacific Northwest winter wheat. Crop Science. https://doi:10.2135/cropsci2017.11.0710.
DOI: https://doi.org/10.2135/cropsci2017.11.0710

Interpretive Summary: The problem to be addressed is that improvement in grains yields by wheat breeding efforts is complicated because the varied environments of the Pacific Northwest favor different traits depending on the timing and duration of drought. We examined grain yield and other important plant growth characteristics in a set of regionally adapted wheat breeding lines and cultivars under a range of irrigated and rainfed conditions over three years and we conducted genomic analysis to associate specific regions of the wheat genome with improved performance in specific environments. Our results showed that specific regions of the genome can be selected to improve grain yield in specific environments and that a few of those regions showed improvements across a wide range of environments. This research enables wheat breeders to select for favorable genes using DNA markers, prior to evaluation in the field which should increase their ability to develop better performing wheat varieties for the region.

Technical Abstract: Grain yield and agronomic traits, key breeding goals for most crops, are under complex genetic control 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 (GWAS) to identify quantitative trait loci (QTL) for various agronomic traits in a Pacific Northwest (PNW) winter wheat diversity panel. Phenotypic evaluation of yield, yield components, phenology, and plant stature was conducted under rain-fed and irrigated conditions in 2012, 2013, and 2014. A total of 3564 single nucleotide polymorphism (SNP) markers were used to determine linkage disequilibrium (LD), population structure, and marker-trait associations. More than 70 % of markers were in significant LD with other markers and formed 539 LD blocks with an average distance of 3.5 cM. Three genetic subgroups were identified in the population, explaining 3 to 38 % of the total phenotypic variation. A mixed linear model with two membership coefficients (Q) of population structure and a compressed kinship (Kc = 192) was used to identify 103 QTLs (FDR < 0.05) for agronomic traits. Pleotropic loci for yield and component traits were identified on chromosomes 1A, 2A, 2B, 3B, 4B, 5A, and 6B. Kompetitive Allele Specific PCR (KASP) markers were used to validate known loci for photoperiod sensitivity (Ppd-D1), vernalization response (Vrn-A1), and plant height (Rht-B1 and Rht-D1). These findings highlight the possibility of using historical recombination in northern latitude winter wheat to identify genomic regions associated with desired agronomic traits.