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.

Wheat grains contain various bioactive substances, of which, condensed tannins (CT) are polymeric flavan-3-ols that accumulate in wheat seed coat influencing the end-use quality and nutritional value. However, the genetic architecture underlying CT biosynthesis in wheat grain remains unclear. Here, we studied the deposition and genetic regulation of CT in wheat grains, and found that CT deposited specifically in the testa layer of red-grained wheat as catechin- and epicatechin-formed polymers. Genome-wide association study identified 22 genetic loci affecting CT content, one of which, TaTAN, a single dominant gene controlling CT presence, was mapped to chromosome 3A in a segregation population. Further pan-genome analysis, transcriptome profiling and ethyl methanesulfonate induced mutants sequencing revealed a R2R3-MYB transcription factor, TaMYB10-3A, as the causal gene. Three loss-of-function alleles in TaMYB10-3A caused by large fragment inversion-deletion and insertion were identified which abolish both CT deposition and red pigmentation, demonstrating the pleiotropic effect of TaMYB10-3A on CT presence and grain color. TaMYB10-3A directly trans-activates core flavonoid genes such as chalcone synthase and dihydroflavonol 4-reductase to initiate CT biosynthesis. Our investigation provides a comprehensive understanding of CT presence in wheat grains and lays a solid foundation for manipulating CT metabolites to improve wheat grain end-use quality and nutrition values in wheat.

Spike length (SL) is an important factor affecting yield in wheat (Triticum aestivum L.). Here, a recombinant inbred line (RIL) population derived from a cross between Shannong 4155 (SN4155) and Shimai 12 (SM12) was used to map quantitative trait loci (QTL) controlling SL. A QTL, qSL2B, on chromosome 2B was identified in all experiments and explained 9.92%–12.71% of the phenotypic variation. Through transcriptome and gene expression analysis, we identified a gene encoding Elongation Factor 1-alpha (TaeEF1A) as the candidate gene for qSL2B. Genome editing of TaeEF1A demonstrated that TaeEF1A positively regulates SL, spikelet number per spike (SNS), and grain number per spike (GN). Transcriptome analysis showed that TaeEF1A may affect the protein translation process and photosynthesis to regulate spike development. We used haplotype analysis of wheat germplasm to identify seven types of genetic variations in TaeEF1A, with Type Ⅰ, Type Ⅱ, and Type Ⅲ being the major haplotypes. Screening of 428 cultivars and breeding lines identified 225 and 203 accessions as Type Ⅰ and Type Ⅱ haplotypes, respectively, with Type Ⅲ not detected. Comparison of SL, SNS, and GN between the Type Ⅰ and Type Ⅱ haplotypes revealed that the Type Ⅰ allele can increase SL, SNS, and GN simultaneously, and is thus preferred for use in wheat molecular breeding efforts to increase SL, SNS, and GN.

Pre-harvest sprouting (PHS) influences yield and end-use quality of bread wheat. Developing varieties with PHS resistance is the most effective way to reduce this problem. In this study, a panel of 725 Chinese wheat accessions were evaluated for PHS resistance in three environments. There was abundant variation in PHS resistance and 63 accessions showing high resistance had germination rates of less than 10% across three experiments. The distribution of three causal single nucleotide polymorphisms in TaPHS1 at bases −222, +646, and +666 were assessed and frequencies were determined. Favorable alleles conferring PHS resistance were identified for each locus. Haplotype analysis showed that bases C, G, and A at each of the three loci comprised the best haplotype for PHS resistance, whereas TAT showed the highest sprouting rate. Accessions with the superior TaPHS1 haplotypes proved to be resistant to PHS providing a basis to develop varieties with PHS resistance through marker assisted breeding.