Identification of a novel major QTL and F-box candidate genes controlling seed dormancy in common wheat

A novel major locus (Qgi.245.ahau-4B.3) controlling seed dormancy, and its candidate genes (TaF-box-B1 and TaF-box-B2), were identified by integrating association and linkage mapping with expression and sequence variation analyses. Moderate seed dormancy is essential for reducing pre-harvest sprouting (PHS) and ensuring uniform germination in cereal crops. In this study, seed dormancy was evaluated in 245 wheat varieties with diverse genetic backgrounds across seven environments, and genotypes were obtained using the Wheat 90 K SNP array. A genome-wide association study (GWAS) identified 55 loci associated with seed dormancy, including a novel major locus (Qgi.245.ahau-4B.3) on chromosome 4B. This locus was validated by integrating molecular marker development, re-GWAS, linkage mapping, and expression analysis. Two candidate F-box protein-encoding genes underlying this locus were identified: TraesCS4B03G0269800 (TaF-box-B1) and TraesCS4B03G0270500 (TaF-box-B2). The expression levels of TaF-box-B1 and TaF-box-B2 were significantly lower in the moderate dormancy wheat variety Annong 1124 (AN1124) than in weak dormancy variety Annong 8455 (AN8455). Sequence and haplotype analyses showed that variations in TaF-box-B1 and TaF-box-B2 were completely linked, forming two haplotypes: TaF-box-Hap1 for strong dormancy and TaF-box-Hap2 for weak dormancy. Frequency analysis further revealed that the favorable haplotype TaF-box-Hap1 was predominantly distributed in the Middle and Lower Yangtze River winter wheat region, characterized by relatively high rainfall and humidity. These findings establish a robust foundation for molecular marker-assisted breeding of wheat varieties with enhanced climate resilience and stable PHS resistance, thereby contributing substantively to global food security.