To clone the full-length genomic sequence of TaFlo2 in Chinese Spring, six conserved primer pairs were used (Table 1). The assembly of sequences with the six conserved primer pairs yielded three fragments, 14,009, 14,078 and 13,814 bp. Based on alignment with wheat scaffolds in the database and genome-specific primers, the fragments were designated TaFlo2-A1, TaFlo2-B1 and TaFlo2-D1. The open reading frames of TaFlo2-A1, TaFlo2-B1 and TaFlo2-D1 were 12,183 bp, 12,270 bp and 12,022 bp in length, respectively. The TaFlo2 mRNA of 4902 bp was cloned with three primer pairs (Table 1). Based on the prediction and alignment with cloned mRNA, the cloned genomic sequences from 2AL, 2BL and 2DL consisted of 23, 23 and 24 exons, respectively (Fig. 2a). Among the three homoeologs, the sequence and size of the first four exons were conserved, whereas the size and sequence of the other exons varied.Fig. 2Polymorphism, molecular marker and ORF structure of TaFlo2 homoeologs. a Exon and intron pattern in the ORFs of TaFlo2-A1, TaFlo2-B1 and TaFlo2-D1. The length of each ORF (between the start and stop codons) is shown to the right of the graph. The number of nucleotides in each exon or intron is indicated. CDSf: First coding sequence, CDSi: Internal coding sequence, CDSl: Last coding sequence. b Alignment of the part of cloned TaFlo2 orthologs. Polymorphism both in the promoter and first intron is indicated by stars. c PCR product of molecular marker TaFlo2-InDel8 discriminated by PAGE in 60 MCC accessions