Genomics of local adaptation in wild rice

Abstract

Oryza rufipogon is the wild progenitor of cultivated rice (Oryza sativa) and exhibits high levels of genetic diversity across its native range, making it a useful resource for the identification of abiotic stress–tolerant populations and causal genes that could advance future rice breeding and limit climate-change–induced yield losses. The goal of this thesis is to explore the genetics of environmental adaptation through the analysis of current literature, a meta-analysis and three experimental investigations. These aimed to provide insight into the methodology of environmental association analyses (EAAs) and potential genetic adaptation of O. rufipogon across broad environmental conditions and to a specific environmental stress (water stress), as well as reveal genetic changes in wild rice populations over the last century.

An analysis of 102 EAA studies revealed a large diversity in the methodology at each stage of the analyses and, via a comparison of four models, revealed the effect of model selection on detection of significant environmentally associated single nucleotide polymorphisms (SNPs). It also showed that the results of these studies are not being effectively used for crop improvement. This meta-analysis informed an EAA of 286 O. rufipogon accessions, identifying 15 genomic regions associated with temperature and/or precipitation factors and revealing genes that are candidates for underlying local adaptation across the population. Through a differential expression analysis of 15 O. rufipogon accessions, grouped in four populations, transcriptional changes that occur during water stress were identified, as well as differences in gene expression between populations. Whole-genome sequencing of 17 herbarium specimens and comparisons to modern populations revealed genetic differences between these populations, potentially related to changes in the abiotic and biotic environment over the last century.

Reflecting on the findings of EAA meta-analysis, during each experimental investigation we sought to analyse the overlap of results between methods, resulting in the identification of 34 genes that were detected with multiple analyses. Candidate genes such as these are a good starting point for future studies and are potential targets for rice breeding, or other crop species, in the future.

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Identifiers

ORCID for Mark Chapman: orcid.org/0000-0002-7151-723X

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