Diversification of the promoter sequences of wheat Mother of FT and TFL1 on chromosome 3A

Mother of FT and TFL1 ( MFT ) participates in the regulation of seed dormancy in wheat. A single-nucleotide polymorphism (SNP) in the promoter of MFT on chromosome 3A ( MFT - 3A ) can explain the difference in the levels of MFT - 3A expression, and the difference in seed dormancy, between Chinese Spring (CS) and the CS line with a substituted chromosome 3A from Zenkoujikomugi (Zen) (CS(Zen3A)). Using a cleaved amplified polymorphic sequence (CAPS) marker for this SNP, we analyzed the distribution of the SNP in 694 cultivars, including 117 Japanese cultivars and 551 cultivars from a wheat core collection. The Zen-type SNP predominantly occurs in cultivars used in Japan, where the rainy season overlaps with the wheat harvest season. We also sequenced the ~800 bp genomic fragment amplified by the CAPS marker and categorized the sequences into 16 groups, G1–G16. Only G11 has the Zen-type SNP; all the others have the CS-type SNP. This indicates that the CS-type allele (T) is ancestral, and during cultivation, nucleotide substitution occurred to give the Zen-type allele (C), which has been adopted to improve pre-harvest sprouting tolerance. Phylogenetic analysis indicates that G11 is derived from G3, which occurs worldwide. Our results suggest that the CAPS marker provides a valuable tool to select the Zen-type MFT - 3A allele in wheat breeding programs for improving pre-harvest sprouting tolerance.