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Background  Sucrose phosphate synthase (SPS) is an important component of the plant sucrose biosynthesis pathway. In the monocotyledonous Poaceae, five  SPS  genes have been identified. Here we present a detailed analysis of the wheat  SPSII  family in wheat. A set of homoeologue-specific primers was developed in order to permit both the detection of sequence variation, and the dissection of the individual contribution of each homoeologue to the global expression of  SPSII .    Results  The expression in bread wheat over the course of development of various sucrose biosynthesis genes monitored on an Affymetrix array showed that the  SPS  genes were regulated over time and space.  SPSII  homoeologue-specific assays were used to show that the three homoeologues contributed differentially to the global expression of  SPSII . Genetic mapping placed the set of homoeoloci on the short arms of the homoeologous group 3 chromosomes. A resequencing of the A and B genome copies allowed the detection of four haplotypes at each locus. The 3B copy includes an unspliced intron. A comparison of the sequences of the wheat  SPSII  orthologues present in the diploid progenitors einkorn, goatgrass and  Triticum speltoides , as well as in the more distantly related species barley, rice, sorghum and purple false brome demonstrated that intronic sequence was less well conserved than exonic. Comparative sequence and phylogenetic analysis of  SPSII  gene showed that false purple brome was more similar to  Triticeae  than to rice. Wheat - rice synteny was found to be perturbed at the SPS region.    Conclusion  The homoeologue-specific assays will be suitable to derive associations between SPS functionality and key phenotypic traits. The amplicon sequences derived from the homoeologue-specific primers are informative regarding the evolution of  SPSII  in a polyploid context.

Delineating the structural, functional and evolutionary relationships of sucrose phosphate synthase gene family II in wheat and related grasses