Interrogating the multi-stress tolerance of Oryza australiensis using novel genomic and phenomic strategies

Abstract

Elite high-yielding rice cultivars are, by necessity, grown under high-input scenarios, requiring substantial nitrogen and water inputs to achieve their yield potential. As a result of intensive breeding for performance in the relatively benign conditions of the tropics, they are also susceptible to a number of abiotic stresses including heat wave events and drought. To keep pace with increasing food demand, domestic rice will need to be augmented such that its realised yield is close to its potential yield. Recently there has been great interest in exploring novel germplasm for traits associated with increased nitrogen use efficiency (NUE), water use efficiency (WUE), and stress tolerance. Part of this exploration includes the exploitation of wild Oryza species. There are ~24 recognised wild Oryza species, each occupying and adapted to different ecological niches. Amongst them, O. australiensis has received attention because of its tolerance to leaf brown hopper and extreme heat and its hypothesised tolerance to drought conditions. Native to the northern savannahs of Australia, this species has evolved in a relatively hot and seasonally dry environment, with high rainfall variability and poor soil nutrition. Because of this, we hypothesised that this species might also possess both high WUE and high NUE. However, knowledge of the mechanisms behind its tolerance to extreme heat are lacking, and no reliable experiments have been performed to substantiate claims of drought tolerance in O. australiensis. Further, the International Oryza Map Alignment Project, an initiative that aimed to sequence Oryza genomes for the benefit of domestic rice breeding, called for the genome of O. australiensis to be sequenced in 2003. However, there has been no publicly available O. australiensis genome since. This thesis presents the results of several novel phenotyping techniques including RACiR gas exchange and state of the art imaging techniques to resolve questions of both heat and drought tolerance in the wild rice. I also present the first long-read assembly of the O. australiensis genome, and a novel tool, CLAW (Chloroplast Long-read Assembly Workflow), developed for the assembly of chloroplast genomes derived from larger long-read libraries. Having identified several traits of interest in O. australiensis under stress conditions and having provided significant tools (the genome assembly and a tool for the assembly of chloroplast genomes), this thesis sets the stage for future studies hoping to identify candidate genes for the improvement of domestic rice performance under stress conditions.