Discovery and analysis of novel resistance genes in rice to the parasitic weed Striga hermonthica

Striga species are obligate hemi-parasitic plants that infect the roots of maize, sorghum, millet and upland rice in sub-Saharan Africa, causing reductions in yield that range from ~ 30 % to total crop failure. Improving the yields of cereals in the presence of Striga is difficult as the parasite begins to negatively affect the growth and development of the host immediately after attachment. By the time Striga emerges above ground, the crop is often severely damaged. The use of resistant cultivars would provide a low cost and effective form of control that would target the parasite before the impacts on growth and development of the host crop can occur. The aim of this thesis was to identify novel Striga hermonthica resistance Quantitative Trait Loci (QTL) and underlying resistance genes in rice, and to functionally validate their role in providing resistance using comparative and functional genomic approaches. A Recombinant Inbred Line population of rice derived from a cross between the resistant cultivar IR64 (Oryza sativa ssp. indica) and the susceptible cultivar Azucena (O. sativa ssp. japonica) was phenotyped for post-attachment resistance to S. hermonthica and a QTL analysis performed. A major QTL on chromosome 12 was identified. This QTL mapped to the same position as a previously identified QTL for S. hermonthica resistance in the temperate O. sativa spp japonica cultivar Nipponbare, suggesting that resistance to S. hermonthica in these two cultivars may be governed by the same (or similar) genes. Bioinformatics tools and gene prediction software were used to identify genes present within the IR64 QTL. These genes comprised transposable elements, expressed and hypothetical proteins and a cluster of genes predicted to encode cell surface receptor-like proteins (RLPs) annotated as orthologs of genes conferring resistance to Verticillium wilt in tomato. Verticillium wilts are xylem invading fungal pathogens with a remarkably similar infection strategy and lifestyle to Striga species, making these genes top candidates for S. hermonthica resistance genes. A cluster of highly similar RLP genes is also present in the Nipponbare S. hermonthica resistance QTL. RNAi lines where suites of these RLP genes had been down-regulated in Nipponbare were phenotyped for S. hermonthica resistance, and gene expression examined by qPCR. Increased susceptibility was associated with suppression of multiple RLP genes, and could not be associated with suppression of a single gene. Tos17 and T-DNA insertion lines targeting 4 of the genes independently showed no increase in susceptibility, suggesting that these genes did not underlie the resistance, that there was functional redundancy or that multiple RLP genes may act together to confer resistance to S. hermonthica in this cultivar. Finally, the genetic diversity of the candidate resistance genes in the QTL were examined across a range of diverse rice cultivars to determine if it was possible to exploit their diversity to reduce the number of candidate resistance genes. Cultivars were phenotyped for resistance to S. hermonthica and a correlation analysis performed for each gene between S. hermonthica resistance and similarity of the gene to the Nipponbare allele. A good correlation was observed for a number of candidate genes, and a region of the QTL was identified that was more likely to be involved in S. hermonthica resistance. These results compiled across experiments provide evidence for the involvement of the RLP resistance genes in contributing to the resistance to S. hermonthica seen in the rice cultivars IR64 and Nipponbare.