Genome-Wide Association Study of Agricultural and Biochemical Traits in Radiation-Induced Colored Wheat

Colored wheat lines, which feature elevated anthocyanin content and associated traits, represent valuable genetic resources for enhancing the plant’s nutritional and aesthetic properties. This genome-wide association study (GWAS) utilized a set of radiation-induced mutant lines to identify genetic loci linked to agricultural and biochemical traits. The GWAS models Fixed and Random Model Circulating Probability Unification, and the Bayesian-information and Linkage-Disequilibrium Iteratively Nested Keyway were employed to increase the reliability of marker–trait associations (MTAs). In total, 35 significant MTAs were identified, and seven single-nucleotide polymorphisms (SNPs) were commonly detected by both models. To explore candidate genes, a ± 1.5-Mb window around each significant SNP was analyzed according to the estimated linkage disequilibrium decay, revealing 635 genes. Among these, several genes were annotated as transcription factors and enzymes associated with flavonoid biosynthesis and modification, including MYB, WD-repeat proteins, and UDP-glycosyltransferases. Expression profiling and RT-qPCR further supported the functional relevance of selected SNP–gene pairs, particularly for anthocyanin accumulation and seed color variation. In summary, the integration of GWAS, gene annotation, and expression data could provide valuable insights into the genetic basis of complex traits in wheat, providing data for future molecular studies and marker-assisted breeding of colored wheat mutant cultivars.