Genome-Wide Association Analysis Identifies Agronomic Trait Loci in Quinoa
2026
Zhike Xu | Fucai Ma | Jiedong Li | Jiansheng Yu | Chengkai Liu | Yun Li | Baolong Liu | Xu Su | Dong Cao | Yunlong Liang
Understanding the genetic basis of agronomic traits in quinoa adapted to the Qinghai&ndash:Tibet Plateau is essential for developing high-yield cultivars, as conventional breeding is constrained by limited molecular tools. In this study, 300 cultivated accessions were evaluated for five quantitative traits, and whole-genome resequencing generated 3.69 million high-quality SNPs. Population structure analysis and genome-wide association study (GWAS) were conducted, with integration of seed developmental transcriptomes to refine trait-associated loci. A highly admixed genetic background (K = 7) was revealed, and 11 significant QTLs across seven chromosomes were identified, involving genes related to metabolism, transport, and cell-wall formation. Among these, CesA4 (CQ042210) showed a strong association with thousand grain weight (TGW) and a distinct expression maximum at the early seed-filling stage. These results provide a genomic framework for understanding trait variation in plateau-adapted quinoa and highlight promising targets for marker-assisted breeding.
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