Genome-wide association study and genomic prediction reveal key genomic regions for sharp eyespot resistance at adult stage in Chinese wheat germplasm

Sharp eyespot, caused by the soil-borne fungus Rhizoctonia cerealis, is becoming a major disease affecting wheat production in China. To dissect the genetic basis of adult stage resistance and accelerate breeding, a genome-wide association study (GWAS) and genomic prediction were performed using 427 Chinese wheat accessions including released varieties and advanced breeding lines evaluated across five environments. Phenotypic analysis revealed extensive variation in sharp eyespot resistance with significant inter-environment correlations. Disease index was negatively correlated with phenology but positively correlated with plant height. Thirty-five accessions (8.2%) showed stable moderate resistance across the environments. GWAS using 159,248 markers identified 35 significant SNPs associated with sharp eyespot resistance on chromosomes 1B (583–586 Mb), 5D (464–470 Mb), 6B (191–207 Mb), and 6D (385 Mb). QTL pyramiding demonstrated additive effects, and combining four favorable QTLs reduced disease index by 29%. Genomic prediction using 35 significant SNPs achieved over 90% of the predictive power of a full-genome marker set, with the Bayes B model (accuracy: 0.52–0.57) demonstrating higher accuracy than GBLUP (0.46–0.50). These findings provide key genomic resources, including stable resistant germplasm, QTLs with favorable haplotypes, and predictive models, would be valuable for improving sharp eyespot resistance in wheat breeding programs.