Genetic dissection of gluten characteristics based on single- and multi-locus genome-wide association studies in wheat (Triticum aestivum L.)

Gluten protein quantity and quality, crucial factors determining the baking quality of wheat-based foods, are primary targets for wheat breeding. To elucidate their genetic basis, five key gluten traits were investigated utilizing a genome-wide association study (GWAS) approach: wet gluten content (WGC), residual gluten content (RGC), dry gluten content (DGC), water-holding capacity (WHC), and gluten index (GI). Using 48,057 SNPs across 200 wheat accessions, analyses employed one single-locus (SL) model and five multi-locus (ML) models. Genotype primarily influenced these gluten traits, with broad-sense heritability (H²) ranging from 0.85 (DGC) to 0.97 (GI). The SL-GWAS and ML-GWAS models identified 143 and 203 significant marker-trait associations (MTAs), respectively. Of these, 15 stable quantitative trait loci (QTL) were detected in at least three environments using multiple GWAS models. Most notably, qGI·1D for GI, which integrated from 138 significant MTAs, was identified in multi-environments and recognized by all five ML-GWAS models across all environments. This QTL was shown to be co-localized with qWGC·1D, qRGC·1D, and qWHC·1D. Furthermore, five candidate genes related to wheat gluten including <i>TraesCS1A02G317500</i>, <i>TraesCS1A02G466400LC</i>, <i>TraesCS1A02G466500LC</i>, <i>TraesCS1B02G330000</i>, and <i>TraesCS1D02G317300</i> were indentified. Interestingly, <i>TraesCS1B02G330000</i> has the PF13016 domain related to gliadins and has collinearity with two other genes, suggesting the genes in the first homologous group encoding gliadins may play an important role in GI. Additionally, four kompetitive allele-specific PCR (KASP) markers (<i>K_AX-108</i>,<i>999</i>,<i>948</i>, <i>K_AX-110</i>,<i>940</i>,<i>435</i>, <i>K_AX-111</i>,<i>216</i>,<i>618</i> and <i>K_AX-94</i>,<i>670</i>,<i>671</i>) for GI were developed successfully and validated in the natural population. This work elucidates the genetic basis of wheat gluten traits and provides both valuable germplasm and robust molecular tools for breeding applications.