Increased grain yield (GY) is the primary breeding target of wheat breeders. We performed the genome-wide association study (GWAS) on 168 elite winter wheat lines from an ongoing breeding program to identify the main determinants of grain yield. Sequencing of Diversity Array Technology fragments (DArTseq) resulted in 19,350 single-nucleotide polymorphism (SNP) and presence-absence variation (PAV) markers. We identified 15 main genomic regions located in ten wheat chromosomes (1B, 2B, 2D, 3A, 3D, 5A, 5B, 6A, 6B, and 7B) that explained from 7.9 to 20.3% of the variation in grain yield and 13.3% of the yield stability. Loci identified in the reduced genepool are important for wheat improvement using marker-assisted selection. We found marker-trait associations between three genes involved in starch biosynthesis and grain yield. Two starch synthase genes (TraesCS2B03G1238800 and TraesCS2D03G1048800) and a sucrose synthase gene (TraesCS3D03G0024300) were found in regions of QGy.rut-2B.2, QGy.rut-2D.1, and QGy.rut-3D, respectively. These loci and other significantly associated SNP markers found in this study can be used for pyramiding favorable alleles in high-yielding varieties or to improve the accuracy of prediction in genomic selection.

Increased grain yield (GY) is the primary breeding purpose of wheat. In order to identify the main determinants of grain yield we used Genome-Wide Association Study (GWAS) on 168 elite lines of winter wheat from an ongoing breeding program. Sequencing of Diversity Array Technology fragments (DArTseq) resulted in 19,350 Single Nucleotide Polymorphism (SNP) and Presence Absence Variation (PAV) markers. We identified 15 main regions involving ten wheat chromosomes (1B, 2B, 2D, 3A, 3D, 5A, 5B, 6A, 6B, and 7B) that explain from 7.9 to 20.3% of the variation in grain yield and 13.3% of the yield stability. Loci identified in the reduced genepool are important for wheat improvement using marker assisted selection. We first found marker-trait associations of three genes involved in starch biosynthesis with grain yield. Two starch synthase genes, TraesCS2B03G1238800, TraesCS2D03G1048800, and sucrose synthase (TraesCS3D03G0024300) were located in regions of QGY3, QGY6, and QGY9, respectively. The loci and significantly associated SNP markers found in this study can be used for pyramiding favourable alleles in high-yielding varieties or to improve the accuracy of prediction in genomic selection.