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

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.

Heritable differences in gene expression are considered to be a fundamental mechanism responsible for determining the genetic control of complex, multifactorial traits. Identifying naturally occurring genetic variants that regulate gene expression is an important route for connecting genotype to phenotype based on changes in gene expression. It is predicted that such mechanisms are pervasive and a common cause of both normal and disease related variation in humans and provide the evolutionary substrate for organismal diversity in the plant and animal kingdom. Reliable identification of sequence polymorphisms that affect gene regulation and are causatively associated with important traits will allow the identification and isolation of mechanistically functional alleles that can directly impact breeding programs. Recently methods have been developed that allow the identification of sequence polymorphisms that are linked in cis to regulatory variants and to predict which nucleotide differences are responsible for changes in gene expression. The principle of the approach is based on the hypothesis that the relative abundance of allelic transcripts when estimated for individuals in the heterozygous condition will be devoid of trans-acting influences and environmental factors. The approach is robust, scalable and particularly well suited to crop plants where the ability to produce sexually derived heterozygous hybrids is not rate limiting. We will develop a streamlined assay to detect and quantify allele specific expression in rice and use this methodology to quantify the frequency and tissue specificity of putative cis-acting regulatory factors. This approach will evolve from the detection of allelic imbalances to the mapping of functional variants in well characterised recombinant inbred lines of rice.