The pyramiding effect of seed germination genes confers resistance to preharvest sprouting in wheat

Abstract Preharvest sprouting (PHS) is the germination of mature grains on the mother plant before harvest, which negatively impacts both the yield and baking/brewing quality of wheat ( Triticum aestivum ). PHS resistance is a complex quantitative trait influenced by numerous genes. Although gene pyramiding has effectively increased resistance, the combined effects of multiple genes have not been systematically analyzed. We shortlisted 35 germination‐related genes through homology searches and transcript profiling, then mined 16 public wheat genomes to locate functional single nucleotide polymorphisms and insertion/deletions. Kompetitive allele‐specific PCR assays were designed for 69 non‐synonymous candidate variants, and 11 reliably genotyped a panel of 113 cultivars and landraces. Four known functional markers were also verified, giving a 15‐marker set. Every assay was significantly associated with germination percentage (%G, p < 0.05), and favorable alleles acted additively: varieties carrying 10 or more resistant alleles germinated at less than 20%. The core haplotype TaOCO1_D_121 / TaPHS1_3A_222 (T:C) was especially stable, with mean %G falling from below 50% in F 4 progeny to below 20% in F 6 . Key three‐locus combinations including TaOCO1_D_121 / TaDFR_B_‐282 / TaMKK3_A_660 (T:C:G) and TaOCO1_D_121 / TaDFR_B_282 / TaDOG1_A_740 (T:C:C) reduced %G by up to 80% relative to the population mean. Using extreme‐phenotype subsets, the 20 lowest %G and 20 highest %G lines per population from two biparental recombinant inbred line populations (Huaqixiaomai × Yanfeng 168 and Huaqixiaomai × Chuanmai 23), we found that the tested marker combinations identify low‐germination lines across genetic backgrounds. These results clarify the genetic architecture of PHS resistance and provide a practical marker toolkit for pyramiding alleles in wheat breeding.