Host-induced adaptation of Xanthomonas oryzae pv. oryzae

Host-induced adaptation of Xanthomonas oryzae pv. oryzae

This dissertation reports research on the adaptation mechanisms of the Bacterial Blight (BB) pathogen Xanthomonas oryzae pv. oryzae (Xoo) in response to its growth in rice, as well as developing a tool for monitoring this pathogen intended to facilitate the specific deployment of resistance genes for breeding. BB is one of the major diseases of rice. The negative impact of virulent forms of this pathogen on rice production has been widely reported. It has a range of adaptations which contribute to its virulence. One of the less studied aspects of the rice-Xoo interaction is the biofilm forming capability of the pathogen in the rice xylem. In this research, the genetic diversity of biofilm-related proteins in Xoo was investigated. The results show both conservation of majority of the genes, but variability in a smaller subset. This variation could be part of the adaption of the pathogen to new rice varieties or geographic locations. To determine the incremental steps in Xoo adaptation to rice, a serial passage experiment was conducted using the Philippine Xoo strain PXO61, and subsequent experiments were performed comparing the wild-type strain (designated in this study as PXO61-0) and its derivative, PXO61-4. Characterization of both PXO61-0 and PXO61-4 revealed that PXO61-4 exhibited an increase in fitness during in vitro and in planta growth. A SNP was detected by genomic comparison of both variants, which was confirmed in RNA-sequencing reads. Finally, a prototype of a single nucleotide polymorphism (SNP)-based monitoring system was developed and tested on simulated populations of Xoo. The detection pipeline successfully detected target populations in samples prepared or collected from artificial and field conditions.

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