Evaluation and association analysis of quality traits in Chinese winter wheat landraces on the Qinghai-Tibet Plateau

Abstract

Wheat grain quality is a complex traits governed by both genetic and environmental factors. Chinese winter wheat landraces on the Qinghai–Tibet Plateau harbor valuable genetic diversity, yet the loci underlying their grain quality remain largely unexplored. This study aimed to identify stable SNP loci, favorable haplotypes, and candidate genes for grain quality traits. Eight quality traits—moisture content (MC), flour water absorption (WA), grain protein content (GPC), wet gluten content (WGC), dough stability time (ST), dough development time (FT), grain hardness (HD), and test weight (TW)—were assessed in 279 winter wheat landraces across four environments on the Qinghai–Tibet Plateau. A genome-wide association study (GWAS) was conducted using a 120 K SNP array. All eight traits showed wide phenotypic variation. In total, 62 stable SNP loci were detected across environments ( P < 0.001), explaining 3.86%–15.64% of the phenotypic variance; 19 of these showed pleiotropic effects. A pleiotropic locus on chromosome 1B ( 1B:610760001 ) was significantly associated with WA, GPC, ST and FT in all four environments. Haplotype analysis of a 488 kb linkage disequilibrium (LD) block identified four haplotypes (Hap1–Hap4). Hap2 and Hap3 had significantly higher WA than Hap1, and Hap2 had significantly higher GPC and longer ST than Hap1 and Hap4 ( P < 0.05); FT was significantly longer in Hap2 than in Hap1 and Hap4. Ten candidate genes were predicted, annotated with functions involving signal transduction, metabolic regulation, cell development and stress response. This study identified 62 stable SNP loci, 19 pleiotropic loci, and two favorable haplotypes (Hap2 and Hap3) relevant to wheat quality improvement. These findings highlight the breeding potential of Chinese winter wheat landraces on the Qinghai–Tibet Plateau and provide targets for marker-assisted selection.