To detect polymorphisms in the putative TaFlo2 sequences between high and low TGW accessions, three conserved primers that covered scaffold segments from 793 to 6332 bp were used (Table 1). Polymorphism in TaFlo2-A1 sequences between high and low TGW accessions was observed between 1396 to 1791 bp, while no sequence variation was observed between high and low TGW accessions in TaFlo2-B1 and TaFlo2-D1 (Fig. 2b; Additional file 1: Figure S1). The conserved sequences of TaFlo2-B1 and TaFlo2-D1 in all the higher and lower TGW accessions implicated non-functional nature of these genes. An 8-bp InDel was identified in TaFlo2-A1 sequences from 1396 to 1403 bp which was −17 to −10 bp upstream of the first coding sequence (ATG) at position 1417–1419 bp (Fig. 2b). Five SNPs (G/C, A/G, C/T, C/G and −/T) were observed at 1514, 1538, 1545, 1727 and 1791 bp. From the start codon (ATG), the positions of these five SNPs (G/C, A/G, C/T, C/G and −/T) were in the first intron at 98, 122, 128, 311 and 375 bp, respectively (Fig. 2b). The 8-bp InDel and the five SNPs together formed the two haplotypes designated TaFlo2-A1a and TaFlo2-A1b (Fig. 2b). From the position 1792 to 6332 bp, no polymorphism was observed in the TaFlo2-A1 sequence.