A natural allelic variation of TaIAA10-6A confers pre-harvest sprouting resistance in wheat.

Pre-harvest sprouting (PHS) severely impacts white-grain wheat production. To uncover its genetic basis, we conducted a genome-wide association study (GWAS) across 273 wheat varieties and identified 41 quantitative trait loci (QTLs) for PHS resistance. Among these, a major and stable QTL on chromosome 6A, designated QTL15, was detected across all tested environments and accounted for up to 19.12% of the phenotypic variance. Integrated analysis of RNA-seq data and sequence variation within the QTL15 interval pinpointed TaIAA10-6A, an auxin-responsive Aux/IAA family gene, as the candidate. An elite haplotype, TaIAA10-6A-M, featuring an 18-bp deletion and a 21-bp substitution in its coding sequence, was strongly correlated with enhanced PHS resistance. Intriguingly, overexpressing TaIAA10-6A-M allele significantly increased PHS susceptibility, demonstrating that TaIAA10-6A encodes a dose-dependent PHS-promoting protein. Therefore, the TaIAA10-6A-M haplotype confers resistance by acting as a functionally attenuated allele that reduces PHS-promoting signal. A co-dominant CAPS marker, phs-TaIAA10-6A-M, was also developed and validated for its tight association with PHS resistance. Overall, this study not only elucidates a novel auxin-mediated regulatory mechanism for PHS in wheat but also provides a valuable gene resource for marker-assisted breeding of PHS-resistant white-grain wheat varieties.