Genomics of Adaption to Climate Change in Rice

Project Rationale:

Feeding a growing population sustainably in the face of climate change requires us to resolve the genetic basis of crop tolerance to stress (especially temperature, precipitation and edaphic factors). Crops have reduced genetic diversity for stress tolerances compared to wild species; the analysis of crop-wild relatives can lead to the identification of adaptive genetic variation that can be bred into commercial cultivars.

In this project, the student will use genome-scale data for wild rice to identify genes involved in environmental adaptation, confirm the role of these genes, and determine if the distributions of adaptive alleles have changed over time.
Rice is a staple for almost half of the world population, therefore plentiful genomic data and seed material exists. Yet the data has not been exhaustively analysed, and we have identified a novel cutting-edge way to identify adaptive genetic variation. The three key stages are:

• Genomes of locally-adapted wild rice and locally important cultivars will be analysed to identify genes involved in adaptation to soil and climate.
• Candidate genes will be functionally tested using transgenics
• Sequencing of adaptive alleles from 20-100 year old herbarium samples will assess how allele frequencies change over time, with implications for climate change resilience.

Methodology:

The student will have access to genome sequences from 2000 wild rice varieties. These will be analysed for population structure and subsequently Environmental Association Analysis will infer correlations between polymorphisms and environmental variables (precipitation, temperature, soil chemistry), aided by access to the Iridis supercomputer. The output from this phase will be novel gene candidates underlying adaptation to these conditions.

To determine the role of these candidates, a subset of genes will be functionally analysed by identifying their effect on adaptive phenotypes under stress. Native alleles will be knocked out using gene-editing technology, recently optimised at UoS, and putatively adaptive alleles inserted. The resulting plants will be tested by growing under a range of stress conditions in state-of-the-art growth rooms, to infer the phenotypic and fitness effects of these alleles.

Herbarium accessions of wild rice (ca. 20 to >100 years old) will be identified and ancient DNA extracted in the purpose-built aDNA lab at UoS. Using PCR and sequencing, polymorphisms in the candidate genes will be identified. Distributions of adaptive alleles in space and time will then be correlated to longitudinal climate data to assess if frequencies of adaptive alleles have been affected by recent climate change.

Training:

The INSPIRE DTP programme provides comprehensive personal and professional development training alongside extensive opportunities for students to expand their multi-disciplinary outlook through interactions with a wide network of academic, research and industrial/policy partners. The student will be registered at the University of Southampton and hosted at Biological Sciences, University of Southampton. Specific training will include:

Bioinformatics: Genome sequence data QC, population genomics, Environmental Association Analysis;
Molecular plant biology: Generation of transgenic/gene-edited rice; plant growth and phenotypic analysis;
Ancient DNA: DNA extraction from herbarium DNA, PCR and sequencing using world-class facilities.

The student will be encouraged to attend a NERC bioinformatics course, and have the opportunity to visit the International Rice Research Institute in the Philippines.

By the end of this PhD the student will be skilled in a range of modern molecular and bioinformatic techniques in relation to crop manipulation and environmental tolerances of relevance to climate change.