Cis-acting regulatory elements in the rice genome: a novel source of alleles for rice breeding

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In recent years analysis of genetic variation has focused on the study of changes in DNA coding for proteins. It is now becoming increasingly clear that this only accounts for one aspect of heritable variation and for many traits, notably complex, quantitative traits, the level of gene expression is also likely to be of great importance. If changes in gene expression underlie many evolutionary changes in phenotype, then identifying the genetic variants that regulate gene expression is a significant and important endeavour. A key problem in genetics is how to identify this type of variation. We propose a robust, quantitative approach to efficiently identify plant genes that harbour such regulatory variants. The approach is novel and particularly amenable to plants since it is based on monitoring gene expression in experimentally created hybrids. A successful outcome will provide a new mechanism to connect genotype to phenotype based on changes in gene expression rather than changes in the structure of an encoded protein. This approach will be used to characterize a series of genes with the objective of identifying potential candidates for tolerance to drought and blast resistance in rice. Through this knowledge, we will develop new breeding tools for application in rice breeding for Asia and Africa. The approach is generic and widely applicable with the potential to reveal new sources of genetic variability for deployment in plant breeding and biotechnology programmes.