Unraveling Allelic Impacts on Pre-Harvest Sprouting Resistance in TaVP1-B of Chinese Wheat Accessions Using Pan-Genome

The <i>TaVP1-B</i> gene, located on the 3B chromosome of wheat, is a homolog of the <i>Viviparous-1</i> (<i>VP-1</i>) gene of maize and was reported to confer resistance to pre-harvest sprouting (PHS) in wheat. In this study, the structure of the <i>TaVP1-B</i> gene was analyzed using the wheat pan-genome consisting of 20 released cultivars (19 wheat are from China), and 3 single nucleotide polymorphisms (SNPs), which were identified at the 496 bp, 524 bp, and 1548 bp of the <i>TaVP1-B</i> CDS region, respectively. Haplotypes analysis showed that these SNPs were in complete linkage disequilibrium and that only two haplotypes designated as hap1 (TGG) and hap2 (GAA) were present. Association analysis between <i>TaVP1-B</i> haplotypes and PHS resistance of the 20 wheat cultivars in four experiment environments revealed that the average PHS resistance of accessions with hap1 was significantly better than that of accessions with hap2, which infers the effects of <i>TaVP1-B</i> on wheat PHS resistance. To further investigate the impacts of alleles at the <i>TaVP1-B</i> locus on PHS resistance, the SNP at 1548 bp of the <i>TaVP1-B</i> CDS region was converted to a KASP marker, which was used for genotyping 304 Chinese wheat cultivars, whose PHS resistance was evaluated in three environments. The average sprouting rates (SRs) of 135 wheat cultivars with the hap1 were significantly lower than the 169 cultivars with the hap2, validating the impacts of <i>TaVP1-B</i> on PHS resistance in Chinese wheat. The present study provided the breeding-friendly marker for functional variants in the <i>TaVP1-B</i> gene, which can be used for genetic improvement of PHS resistance in wheat.