Natural Variation in Wheat Homologs of the Rice Thermotolerance Gene QT12 Reveals Two Divergent Haplotypes of TaQT12-B1

The rice gene QT12, which encodes the β subunit of the Sec61 translocon complex, has previously been shown to negatively regulate grain thermotolerance, suggesting that variation in related cereal genes may contribute to heat responses. We characterized the natural sequence diversity of three QT12 homeologs located on homoeologous group 3 chromosomes in bread wheat using publicly available whole-genome assemblies and Oxford Nanopore amplicon sequencing. TaQT12-A1 and TaQT12-D1 were highly conserved in their transcribed regions, whereas TaQT12-B1 was represented by two strongly differentiated haplotype groups, Hap1 and Hap2, distinguished by 108 sequence variants across the gene and its 7-kb flanking regions. The protein-coding sequence of TaQT12-B1 was conserved between the two haplotype groups, while most differences occurred in non-coding and flanking regions. A KASP marker was developed to distinguish the two groups and used to genotype 200 winter wheat accessions, of which six carried Hap2. Comparisons of grain-related traits over 2018–2020 revealed differences between haplotypes, but none remained significant after false discovery rate correction. Seasonal temperature records provided environmental context but did not support a clear haplotype-specific heat-response pattern. These results identify TaQT12-B1 as a candidate locus with substantial non-coding sequence variation and provide a molecular marker for further functional investigation of its haplotypes.