Fig. 7
A representation of the promoter region of Glyma.09G008400.1 and the differences in amplicons from three different soybean lines. The 1505 bp sequence shown is that of the Williams 82 reference genome. Bases in bold italics at the ends are the primers used. Green highlighting indicates the 5’UTR region in the gene model, blue highlighting denotes the first two exons. The box and yellow highlight mark the five different WAAAG elements in the promoter regions of both strands. The 50 bp in red font indicate the repetitive AT region in the promoter. Within this region are the observed differences of the three sequenced amplicons as clearly shown in the alignments of Additional file 10. Both UC7 (ii R T Mi g) and UC413 (ii R t mi G) are identical and both lack 26 nucleotides of the AT region that are in red small letters. Amplicon sequencing of the cultivar Williams, the recurrent parent of the reference genome Williams 82 lacks 4 of the bases in the AT rich region which are also underlined in red. The bases in blue font mark the site of indel variants called by the VCF file of the whole genome sequence (Additional file 9), but they do not indicate the exact size of the deletions found in the AT-rich region as determined definitively by amplicon sequencing (Additional files 10 and 11)