Out of Africa: Exploring the African germplasm for the sustainable production of rice in future climates

Asian rice (Oryza sativa) is a staple food for billions of people worldwide. There has been increasing focus on the introgression of diverse material to develop productive rice cultivars that are resilient to a changing climate. African rice (Oryza glaberrima) evolved independently to Asian rice and demonstrates exceptional abiotic stress resilience. O. glaberrima has been recognised as a potential source for crop improvement for over two decades but the heritable variation in the species remains relatively uncharacterised. The research described here uses a new genomic resource of 155 re-sequenced accessions to explore the diversity O. glaberrima has to offer. O. glaberrima accessions were grown to late tillering stage in an agronomy glasshouse and measured for traits that contribute to water use efficiency and productivity. Photosynthetic traits were measured by gas exchange and chlorophyll fluorescence, along with root and shoot biomass, stomatal density and leaf area. Photosynthetic steady state and kinetic responses were modelled. Using this phenotypic data, a genome wide association study (GWAS) was completed using four different algorithms to identify significant trait related candidate genes and genomic regions. Multi-variate analyses were used to explore the ecological and environmental factors that contribute to trait and genetic adaption in the O. glaberrima collection used here. This study identified broad heritable variation and candidate genes in a range of useful morphological, steady-state and dynamic photosynthetic traits, including genes known for mitigating drought and heat stress, alongside regulators of key phytohormones. This thesis highlights the importance of O. glaberrima as a source of heritable variation. The information compiled here provides a solid base for future elucidation of physiological processes and the functional validation of candidate genes to support future crop improvement efforts