Genome-wide association analysis for grain amylose content in a diverse panel of hexaploid bread wheat (Triticum aestivum L.)

Starch consisting of amylose and amylopectin is a major storage compound of the mature wheat kernel, where Grain amylose content (AC) is one of the key determinants which affects the end-use quality and nutritional value of bread wheat. In this study, we conducted a comprehensive GWAS study in a diverse panel of 1499 wheat accessions genotyped with 35K SNP array to identify loci associated with AC. By applying multiple GWAS approaches, six robust marker trait associations (MTAs) were identified on 1D, 3A, 3D, 4B, 5D, and 6B contributing to phenotypic variation in AC. Subsequent post-hoc statistical confirmation identified three MTAs with robust genotypic effects, while favourable alleles analysis identified five alleles consistently associated with increased AC. Candidate gene mining within the six MTA intervals identified 181 annotated genes, including a RING-type E3 ubiquitin ligase, a phosphate transporter, an AP2/ERF transcription factor and glycosyltransferases, all previously implicated in pathways related to starch metabolism or its regulation. Tissue-specific expression analysis revealed seed-preferential expression of several candidate genes (e.g. RING-type E3 ubiquitin ligase and glycosyltransferases), whereas photosynthetic and stress-responsive genes (e.g. RUBISCO, ABC transporters and protein kinases) showed higher expression in leaf tissues. Collectively, these findings refine the AC locus landscape in bread wheat identifying robust genomic loci, favorable alleles and putative candidate genes. These results provide valuable genomic resources for future functional validation and may facilitate the development of marker-assisted breeding strategies aimed at improving wheat grain quality.