Genome-wide association study of total starch and its components in common wheat

Wheat starch is closely related to yield and quality of wheat-based final products. This genome-wide association study focused on total starch content and its components using single nucleotide polymorphisms (SNPs) in a panel of 205 elite winter wheat accessions. Twenty-nine significant marker-trait associations (MTAs) were detected for total starch (TSC), amylose (AMS) and amylopectin (AMP) contents under four environmental regimes. Nine MTAs were detected for two traits, and eleven MTAs were found for all three traits. These SNPs were distributed across seven chromosomes, explaining 11.26–23.83% of the phenotypic variance (PVE). Furthermore, eighteen MTAs related to the ratio of AMS and AMP under four environmental conditions explained 5.92–17.2% of the phenotypic variance. One important multi-trait MTA on chromosome 3A at the 93 cM position was found for thousand kernel weight, AMP, AMS and TSC. A set of elite alleles was identified, including allele Kukri_c5615_1214-A, which increased AMS and AMP by 5.80% and 15.32%, respectively. The allele Excalibur_c16376_351-T increased AMP by 4.43%, and the T allele of marker BS00022255_51 and T allele of marker D_contig25392_201 had the most significant effects, increasing the ratio of AMS to AMP by 3.77%. Fourteen candidate genes associated with significant markers were identified. For example, TRIAE_CS42_2AL_TGACv1_093900_AA0288950 participated in carbohydrate metabolism and hydrolysed O-glycosyl compounds. The lines that carry these elite alleles could be used as genetic stock for breeding to improve these traits. These results could lay the foundation for molecular marker-assisted selection in improving wheat quality.