The genes encoding granule-bound starch synthases at the waxy loci of the A, B, and D progenitors of common wheat

Three genes encoding granule-bound starch synthase (wx-TmA, wx-TsB, and wx- TtD) have been isolated from Triticum monococcum (AA), and Triticum speltoi des (BB), by the polymerase chain reaction (PCR) approach, and from Triticu m tauschii (DD), by screening a genomic DNA library. Multiple sequence alig nment indicated that the wx-TmA, wx-TsB, and wx-TtD genes had the same extr on and (or) intron structure as the previously reported waxy gene from barl ey. The lengths of the three wx-TmA, wx-TsB, and wx-TtD genes were 2834 bp, 2826 bp, and 2893 bp, respectively, each covering 31 bp in the untranslate d leader and the entire coding region consisting of 11 exons and 10 introns . The three genes had identical lengths of exons, except exon1, and shared over 95% identity with each other within the exon regions. The majority of introns were significantly variable in length and sequence, differing mainl y in length (1-57 bp) as a result of insertion and (or) deletion events. Th e deduced amino acid sequence from these three genes indicated that the mat ure WX-TMA, -TSB, and -TTD proteins contained the same number of amino acid s, but differed in predicted molecular weight and isoelectric point (pI) du e to amino acid substitutions (13-18). The predicted physical characteristi cs of the WX proteins matched the respective proteins in wheat very closely , but the match was not perfect. Furthermore the exon5 sequences of the wx- TmA, wx-TsB, and wx-TtD genes were different from a cDNA encoding a waxy ge ne of common wheat previously reported. The striking difference was that an insertion of 11 amino acids occurred in the cDNA sequence that could not b e observed in the exons of the A, B, and D genes. It was noted, however, th at the 3' end of intron4 of these genes could account for the additional 11 amino acids. The sequence information from the available waxy genes identi fied the intron4-exon5-intron5 region as being diagnostic for sequence vari ation in waxy. The sequence variation in the waxy genes provides the basis for primer design to distinguish the respective genes in common wheat, and its progenitors, using PCR.