Identification and validation of the superior alleles for wheat kernel traits detected by genome-wide association study under different nitrogen environments

Increasing kernel weight is a major driven force for high yield breeding. Dissecting the genetic basis of kernel traits and their response to nitrogen are essential for improving wheat yield and nitrogen use efficiency (NUE). In this study, genome-wide association studies were carried out based on Wheat55K SNP array genotyping data of 132 common wheat accessions. And phenotype values of four kernel traits were acquired from eight environments across both high nitrogen (HN) and low nitrogen (LN) environments. Twenty-four significant marker-trait associations grouped into 20 loci for thousand kernel weight (TKW), kernel length (KL), kernel width (KW) and kernel diameter ratio (KDR) were repetitively detected in three or more environments. Of these, AX - 111690659 - 7B was a novel locus for KL, and four loci AX - 110556510 - 1D , AX - 109775854 - 2D , AX - 109303193 - 3B and AX - 110468887 - 4A were validated in two recombinant inbred line populations and/or the Chinese wheat mini core collection. Ten loci for KL, KW and KDR were stably identified in HN and LN environments. The six KASP markers related to TKW, KL and KW would benefit the kernel weight, yield potential and NUE improvement in wheat breeding. Evaluation of the additive effects, distribution and frequency of the superior alleles that were significantly associated with kernel traits suggested that the loci for KW are with the most promising in elevating kernel weight.