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.