Genetic dissection and candidate gene prediction for pre-harvest sprouting resistance in wheat

Pre-harvest sprouting (PHS) can severely compromise yield and quality in wheat ( Triticum aestivum L.). In this study, we performed quantitative trait locus (QTL) mapping to identify PHS resistance loci in two recombinant inbred line (RIL) populations genotyped using the Wheat 55 K SNP array and assessed for sprouting rate (SR) across multiple environments. We identified seven QTL in the P82/Luomai 21 and Cunmai 1/Jimai 22 RIL populations. Notably, QPhs.zknu-2D was mapped to a 5.02-Mb interval (627.96–632.97 Mb) in both populations and identified as a stable, background-independent major locus that explained 8.4%–21.3% of the phenotypic variance. Another QTL, QPhs.zknu-5D , exhibited the strongest effect, explaining up to 28.9% of the phenotypic variance. We developed KASP markers for these loci and validated them in a natural panel of 329 accessions across six environments. The favorable alleles significantly lowered the SR, and the combination of both favorable alleles demonstrated a strong additive effect, with the mean SR falling to 44.8%, compared to 82.0% with the two alternative alleles. We identified ten elite accessions with stable PHS resistance (SR < 10%), and performed transcriptomic profiling to help identify potential candidate genes for QPhs.zknu-2D , QPhs.zknu-5D , and QPhs.zknu-7A . This work provides robust markers, elite germplasm, and mechanistic insights to accelerate the breeding of PHS-resistant wheat.