Exploring the molecular-genetic and epigenetic basis of resistance in rice to the parasitic weed Striga

Striga is an obligate, root hemi-parasitic weed that infects cereal crops such as rice across Africa, causing 30-100% yield losses. Mitigating this effect is difficult, as most of the damage occurs underground before the parasite emerges. Harnessing Striga-resistant rice plants is arguably the most effective strategy to achieve this goal but relies on obtaining a better understanding of resistance mechanisms against this parasite. The aim of this thesis is to explore different forms of resistance in rice against Striga. Firstly, this PhD study aimed to characterise innate immunity against Striga by characterising the expression profiles of genes correlating with cultivar-specific resistance of rice against S. hermonthica and identifying genes that are co-expressed with the candidate resistance gene, which in previous work was identified within the S. hermonthica resistance Quantitative Trait Locus (QTL) of two resistant rice cultivars (Nipponbare and IR64) and validated by CRISPR knockout of this gene in IR64. This PhD study also aimed to explore a potential epigenetic basis of Striga resistance by quantifying the resistance phenotypes of rice mutants affected in DNA methylation. Finally, this thesis has investigated the potential of induced resistance by comparing the effects of silicon on resistance against S. hermonthica relative to silicon-induced resistance against the generalist herbivore Spodoptera littoralis. In Chapter 2, a transcriptome analysis was performed to investigate the immune response to S. hermonthica in rice roots of Nipponbare and IR64 and one susceptible rice cultivar (Azucena) at 2, 4 and 8 days post infection (dpi). The response of Pattern- Triggered Immunity (PTI)-, Effector-Triggered Immunity (ETI)- and the downstream immunity-related genes was vastly different in the resistant cultivars compared to the susceptible cultivar, Azucena. PTI- and ETI-related genes were strongly up-regulated at 2 dpi in the resistant cultivars, while such a response was absent in Azucena. These results show that Azucena is affected in its ability to mount an early innate immune response. In Chapter 3, a Weighted Gene Correlation Network Analysis was performed using the transcriptome dataset to identify genes that are co-expressed with the candidate resistance gene within the resistance QTL of Nipponbare and the resistance gene within that of IR64. The identified genes correlated strongly in expression with PTI- and ETI- related genes and many of the identified genes featured as highly connected ‘hub’ genes in the network. This expression profile is consistent with a signalling role in the regulation of innate immunity by the candidate resistance gene and the resistance gene. In Chapter 4, the role of DNA methylation in resistance to Striga was investigated, based on the observed transcriptional repression of genes encoding DNA methylation machinery during Striga infection. Rice mutants impaired in RNA-directed DNA methylation (RdDM) and Decrease in DNA Methylation 1 (DDM1)-mediated DNA methylation, which are mostly affected in DNA methylation of transposons, displayed increased resistance to S. asiatica. Although rice mutants impaired in the DNA demethylase ROS1c did not show a statistically significant change in the average number of S. asiatica or S. hermonthica attachments, the highest numbers of attachments by S. hermonthica were observed on ros1c roots, and there was statistically increased variation in the number of S. hermonthica attachments by the ros1c mutation. Together, these results suggest that reduced DNA methylation of transposons increases Striga resistance. In Chapter 5, Azucena was treated with silicon (silicic acid) and challenged with S. hermonthica and S. littoralis. While silicon induced strong resistance in the leaves against feeding by S. littoralis, it had no effect resistance against S. hermonthica. Together, the findings presented in this thesis demonstrate that rice resistance to S. hermonthica involves PTI-, ETI-, and downstream immunity-related genes, many of which were co-expressed with the candidate resistance gene and the resistance gene against S. hermonthica. Moreover, this thesis has provided first evidence for a role of decreased DNA methylation, and lack of evidence for a role of silicon, in rice resistance to Striga.