Rice (Oryza sativa) is a staple food for nearly half of the world’s population. It is susceptible to drought stress due to its shallow rooting relative to other cereal crops. Roots are the primary organs that perceive changes in soil, and hence play a vital role in the response of plants to drought. As an essential strategy to minimize the negative impact of drought stress, the manipulation of root structure towards wider and deeper distribution of roots in the soil may enable plants to avoid drought-induced stress by extracting water (and nutrients) from deep soil layers. The most important part of roots are the root tips, which encompass the root cap, apical meristem and elongation zones, as these regions determine the fate of root length, root diameter and root angle.
In this project, we are aiming to modify the root architecture of a commercial rice variety to transform shallow rooting plants into deeper rooting plants, while retaining commercially desirable characteristics such as grain yield. The project is built on three pillars: phenotyping, gene and protein discovery, and functional analysis. We profiled the proteome, transcriptome and epigenome of three zones of root tips from two different rice genotypes with contrasting root architecture phenotypes; a lowland rice with shallow roots (IR64) and an upland rice with deeper roots (Azucena), grown under control and water deficit stress conditions. Many of the expressed molecules exhibited zone/genotype/water regime-specific differential expression patterns. We also observed substantial differences in expression of isoforms and lncRNAs in different zones. This systems biology approach resulted in a short list of candidate genes for further characterisation. We are examining the function of these root structure associated genes by transferring them into shallow rooted plants, which will be screened for root phenotype, drought tolerance, and nutrient uptake.