Targeted Mapping of Oryza sativa Chilling Tolerance Candidate Genes Using Multiple Stress-Relevant Quantitative Traits
Date of Award
Doctor of Philosophy (PhD)
Developing chilling tolerant accessions of domesticated Asian rice is a potential source of significant crop improvement to address the needs of a growing global population. The uniquely chilling sensitive nature of the tropically originating Oryza sativa make it the most important staple crop that could gain the maximum benefit from improved tolerance to low temperature stress. However, mechanisms underlying this complex trait are not fully understood. Oryza sativa has two major varietal groups with different levels of chilling tolerance, JAPONICA and INDICA, providing an ideal tool to investigate mechanistic differences in the chilling stress tolerance responses within this important crop species. By understanding the mechanistic differences between these groups, methods for improving the chilling tolerance of all domesticated rice can be studied.The Rice Diversity Panel 1 (RDP1) was used to investigate a representative set of Oryza sativa accessions. The bioinformatics tools available for this panel allowed for genomic analysis of chilling tolerance traits at multiple temperatures across a 354-cultivar subset of the RDP1. Chilling tolerance trait values were distributed as mostly subpopulation specific clusters of Tolerant, Intermediate, and Sensitive accessions. Genome-wide association study (GWAS) mapping approaches yielded a total of 245 quantitative trait loci (QTL), containing 178 unique QTL while 40 QTL were identified by multiple traits. The genes within these QTL were filtered and investigated for pathway enrichments by analyzing Gene Ontology (GO) term enrichment, gene expression profiles, and annotated protein-protein interactions (PPI). Enriched GO terms related to Golgi apparatus, stress response, transmembrane transport, signal transduction, and ubiquitination were identified. Alternative gene filtering was also conducted using publicly available expression and PPI data to identify candidate genes that are members of functional pathways involved in rice chilling tolerance. A smaller subset the panel was used to conduct a GWAS on an assay of chilling-induced lipid peroxidation. The results assay generally followed the chilling tolerance clustering previously seen in EL and LTSS. The mapping analysis resulted several genomic regions that overlapped with several QTL from the 5-temperature mappings. The resulting gene list was enriched with terms associated with the Shikimate pathway of aromatic amino acid biosynthesis.