Dissecting the genetic basis for resistance to pre-harvest sprouting in a wheat line with strong seed dormancy

Pre-harvest sprouting (PHS) significantly reduces yield and quality in wheat (Triticum aestivum). One effective way to address this issue is to identify and deploy quantitative trait loci (QTL) for PHS resistance. In this study, we developed a recombinant inbred line (RIL) population derived from a cross between the PHS-resistant red wheat line ‘Shannong 0316’ (SN0316), which has strong seed dormancy, and the PHS-susceptible white wheat line ‘Gaoyou 9409’ (GY9409), which has weak seed dormancy, to map QTL for PHS resistance. We also mapped grain color, an important quality trait that is related to PHS. In five experiments, we identified thirteen QTL for PHS resistance, nine of which were detected in at least two experiments. QTL mapping identified seven QTL for grain color, three of which were also associated with PHS resistance. A comparison with previously reported QTL suggested that QPhs.sdau-1A, QPhs.sdau-5A, QPhs.sdau-6D, QPhs.sdau-7A, and QPhs.sdau-7B.1 are newly discovered QTL for PHS resistance, and that QGc.sdau-5A.1, QGc.sdau-5A.2, QGc.sdau-7A, and QGc.sdau-7B are newly discovered QTL for grain color. The three major QTL (QPhs.sdau-3A.1, QPhs.sdau-3D.1, and QPhs.sdau-1A) showed additive effects on PHS. We identified six elite lines with high PHS resistance, with three white wheat lines. We converted the single-nucleotide polymorphisms linked to the nine QTL into Kompetitive Allele-Specific PCR (KASP) markers and used them to genotype the RIL population and 192 elite breeding lines. QPhs.sdau-1A was associated with PHS resistance in the breeding lines, whereas the other QTL require further validation due to the low frequency of one genotype. Therefore, we dissected the genetic basis of the strong seed dormancy and PHS resistance of wheat line SN0316, identified QTL, obtained germplasm lines, and developed molecular markers for marker-assisted selection of PHS resistance, which should be valuable for breeding.