Genome-wide association study for grain yield and related traits in an elite spring wheat population grown in temperate irrigated environments

Key message Through genome-wide association study, loci for grain yield and yield components were identified in chromosomes 5A and 6A in spring wheat (Triticum aestivum) . Abstract Genome-wide association study (GWAS) was conducted for grain yield (YLD) and yield components on a wheat association mapping initiative (WAMI) population of 287 elite, spring wheat lines grown under temperate irrigated high-yield potential condition in Ciudad Obregón, Mexico, during four crop cycles (from 2009–2010 to 2012–2013). The population was genotyped with high-density Illumina iSelect 90K single nucleotide polymorphisms (SNPs) assay. An analysis of traits across subpopulations indicated that lines with 1B/1R translocation had higher YLD, grain weight, and taller plants than lines without the translocation. GWAS using 18,704 SNPs identified 31 loci that explained 5–14 % of the variation in individual traits. We identified SNPs in chromosome 5A and 6A that were significantly associated with yield and yield components. Four loci were detected for YLD in chromosomes 3B, 5A, 5B, and 6A and the locus in 5A explained 5 % of the variation for grain number/m 2 . The locus for YLD in chromosome 6A also explained 6 % of the variation in grain weight. Loci significantly associated with maturity were identified in chromosomes 2B, 3B, 4B, 4D, and 6A and for plant height in 1A and 6A. Loci were also detected for canopy temperature at grain filling (2D, 4D, 6A), chlorophyll index at grain filling (3B and 6A), biomass (3D and 6A) and harvest index (1D, 1B, and 3B) that explained 5–10 % variation. These markers will be further validated.