Mining QTLs and candidate genes in bread wheat associated with kernel hardness through GWAS.

key message35 candidate quantitative trait loci (QTLs) and 12 key candidate genes have been identified as associated with kernel hardness in wheat. They encode γ-gliadins, Avenin-3, glutenin subunits, β-glucosidase, α-galactosidase, 1,4-α-glucan-branching enzyme. Kernel hardness constitutes a core indicator of wheat quality, reflecting endosperm texture characteristics and playing a decisive role in milling performance. This study employed 189 genetically diverse bread wheat accessions, integrating genome-wide association studies (GWAS) with genomic prediction techniques to elucidate the genetic mechanisms underlying kernel hardness. Kernel hardness index (KHI) exhibited significant phenotypic variation across four environments and best linear unbiased estimation (BLUE) values within the test population. GWAS conducted using wheat 660 K SNP chip genotyping data identified 67 quantitative trait locis (QTLs) consistently associated with KHI in at least two environments (includes BLUE values). Among these, 35 QTLs showed significant KHI differences across environments based on their different haplotypes. Functional annotation of genes within QTL regions identified 12 key candidate genes encoding γ-amylopectin, Avenin-3, glutenin sub-units, β-glucosidase, α-galactosidase, 1,4-α-glucan-branching enzyme, which are presumed to be closely associated with KHI. Genomic prediction using Bayesian ridge regression achieved over 75% accuracy across all three SNP matrices. These findings provide theoretical and technical support for understanding the genetic basis of wheat KHI and for screening innovative wheat germplasm resources with distinct kernel hardness.