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Cis-acting regulatory elements in the rice genome

A novel source of alleles for rice breeding

Contact: Dr David Lee

A central challenge for the 21st century is to expand the reductionist ‘molecular view of biology’ into a more predictive science that embraces the need to create translatable outputs. This work aims to elucidate how plants regulate gene expression in a globally relevant crop, rice and use this knowledge to devise innovative plant breeding solutions based on mechanistically functional alleles that can directly impact rice improvement programmes in the developing world. A compendium of genetic variants that affect gene regulation will be a key resource for rice breeders and will complement studies on variation in coding regions of the rice genome.

Heritable differences in gene expression are now considered to be the primary mechanism responsible for determining the genetic control of complex traits. 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. In contrast to identifying variation in coding regions of the genome, characterising the extent of cis-acting regulatory variation presents a much greater challenge since it is not possible to discern even for fully sequenced genomes, whether a particular gene harbours a polymorphism that regulates its expression.

Therefore, the overall goal of this work is to develop a robust, streamlined, expression based assay (based on allelic imbalance) to identify and quantify the amplitude of imbalance, the frequency, inheritance and tissue specificity of cis-acting regulatory variation in rice. The allelic imbalance assay will be used to identify polymorphisms and haplotypes that are surrogate markers for high or low levels of transcript expression. A particular strength of the approach is that it does not require a priori knowledge of specific regulatory polymorphism and is therefore an efficient method for both discovering and elucidating mechanisms controlling cis-acting regulatory elements. The identification of regulatory SNPs will provide a completely novel class of molecular marker that connect genotype to phenotype based on changes in gene expression rather than on changes in the encoded protein.

In addition, asymmetric allelic differences in gene expression observed across the genome of F1 hybrids may provide a scientific explanation for overdominance or heterozygote superiority, as the biological determinant of heterosis. This is of special significance to rice breeding in the developing world where hybrid rice varieties generally outperform inbred lines under water-stressed environments.

Funding: Biotechnology and Biological Sciences Research Council (BBSRC) and Department for International Development (DFID).

Collaborating Organizations: International Rice Research Institute (IRRI)