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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.