A novel 33-bp insertion in the promoter of TaMFT-3A is associated with pre-harvest sprouting resistance in common wheat

TaMFT-3A on wheat chromosome 3AS, encoding a phosphatidyl ethanolamine-binding protein, was previously determined to be a candidate gene underlying the major quantitative trait locus (QTL) for pre-harvest sprouting (PHS) resistance. Three single nucleotide polymorphisms (SNPs) (−222, +646, and +666) and one insertion/deletion (InDel) variation at TaMFT-3A locus are associated with PHS resistance. In the present study, we detected a novel 33-bp InDel in the promoter (−194) of TaMFT-3A and developed a gene-specific marker (MFT-A2). Linkage mapping indicated that MFT-A2 co-segregated with a major QTL on chromosome 3AS for PHS resistance in the recombinant inbred line population from the cross of Annong 0711 × Henong 825, explaining 17.79 and 14.22% of phenotypic variations in 2016 and 2017, respectively. Association analysis also showed that the InDel was significantly associated with PHS resistance using 260 current wheat varieties (lines) and 183 Chinese mini-core wheat collections across environments. TaMFT-3A expression levels in genotypes with the resistance allele TaMFT-3Aa were significantly higher than those in varieties with the susceptible allele TaMFT-3Ab. Moreover, TaMFT-3A transcription was up-regulated in high-temperature and abscisic acid treatments, but down-regulated in low-temperature and gibberellic acid treatments. Notably, PHS resistance of varieties simultaneously carrying favorable haplotypes of SNP-222, SNP646/666, TaMFT-A1, and TaMFT-3A (designated Hap-11) was significantly higher than that of other haplotypes across environments. This study provides useful information for the use of the MFT-A2 marker for improvement of PHS resistance in wheat breeding, and for our better understanding of TaMFT-3A regulatory mechanism for PHS resistance.