A genome-wide association study of wheat yield and quality-related traits in southwest China

Wheat (Triticum aestivum L.) is one of the most productive and important crops and its yield potential and quality characteristics are tightly linked with the global food security. In this study, genome-wide association study (GWAS) was conducted for yield and quality-related traits. Based on the high-density wheat 90K Illumina iSelect SNP Array, 192 bread wheat lines from southwest China, including 25 synthetic hexaploid wheat lines, 80 landraces, and 87 cultivars were analyzed. Association analysis results indicated that there were 57, 27, 30, and 34 SNPs associated with plant height (PH), grain protein content (GPC), thousand kernel weight (TKW), and SDS sedimentation volume (SSV) have been detected, respectively. Then, integrating RNA-Seq with bioinformatics analysis, 246 candidate genes (102 for GPC, 52 for TKW, and 92 for SSV) were found. Further analysis indicated that one up-regulated and two down-regulated expression genes affect GPC. Additionally, two haplotypes significantly affecting PH were detected in a 2.2-Mb genome region encompassing a gene which encoded an ubiquitin-specific protease, TaUBP24. The functional markers of TaUBP24 have been developed, which could be used for marker-assisted selection to improve wheat quality and yield.