Utility of promoter sequence variation in plant breeding

DNA-based markers such as SNP and SSR, rely on the variations in DNA sequence, which in coding sequences can be determined by comparing EST sequences. The public availability of EST sequence data has supported the mining and discovery of a larger number of SNP-based markers. The advent of next generation sequencing (NGS) has accelerated the production of whole genome sequences providing sequence data of coding sequences but also of promoter sequences. The sequence variation within promoter sequences can now be harnessed to develop DNA-based markers for plant breeding. Promoter sequences are crucial for functional genomics where controlled expression of a transgene is desired to determine or confirm its function in transgenic plants. In addition, well characterised homologous and heterogonous promoters would be a valuable tool for successful gene stacking to impart multiple traits. We are interested in altering gene expression in the seed to manipulate grain quality. Several promoters from rice, wheat and barley that control the expression of genes in the grain were investigated to determine their utility to drive gene expression in the grain across these cereals for quality manipulation. Included in our study are the barley B- and D-hordein gene and the bifunctional alpha-amylase and subtilisin gene promoters, the rice glutelin-B1 and globulin gene promoters, and the wheat high molecular weight glutenin and the Early maturing gene promoters. Our data demonstrates that seed-specificity of these cereal promoters is not always maintained in other heterologous cereal suggesting adequate testing of promoters in the desired cereal. We also report the strength of these promoters and their potential to drive high levels of transgene expression in the cereal grain.