Population genomics of plant adaptation to rising atmospheric CO2

Project description
Atmospheric carbon dioxide (CO2) is predicted to rise over the next century and is known to induce physiological responses in plants, but whether or not CO2 can act as a selection pressure leading to adaptive changes remains open to speculation. Natural CO2 springs, where plants have been exposed to high CO2 over multiple generations, provide an opportunity to quantify the effect of CO2 as a selective agent. Using a spring in Italy producing mean daily CO2 concentrations ranging from 550 ppm to over 1000 ppm and an associated control site, we have employed next generation sequencing to complete the first transcriptome analysis of Plantago lanceolata originating inside the spring and compared this to a nearby control environment. The data reveal striking differences in phenotype and global gene expression, suggesting adaptation of photosynthesis and stomatal patterning and functioning in plants grown for multi-generations in high CO2. These data provide some of the very first insights into how rising CO2 may lead to altered function at the level of the gene with some evidence for genomic differentiation of populations from spring and control sites. The aim of this project will be to assess these responses in a wide range of calcareous plant species selected from the site.

Methodology
We will use population genomics and next generation sequencing. Our preliminary analysis has shown that RNA-Seq for non-model organisms for which no genomic resources are available, is tractable. We will extend this analysis for several of the co-existing spring species, representing different plant functional types within the CO2 spring (grasses and forbs; annual and perennial). We will test the hypothesis that spring plants are adapted to high CO2 and do not respond to CO2 at the level of gene, cell and whole plant. In these plants, photosynthesis is acclimated and stomatal numbers reduced (since CO2 uptake is optimized). We will identify a suite of genes linked to these changes. Using three approaches– (i) Plant phenotypes will be analyzed in the field, inside the spring and an adjacent control site and used for reciprocal transplant experiments to analyse long- and short-term impacts of the CO2 environment on plant function and transcriptomics, (ii) We will investigate population differentiation using population genomics and quantify diversifying selection in these plants (iii) Using eight controlled environments, seeds selected from spring and control plants will be used to quantify the responses of these plants to ambient (current) and elevated (future, 580-700 ppm CO2), for both geneotype and phenotype.

Training and wider implications
All doctoral candidates will be part of the University of Southampton SPITFIRE Doctoral Training Centre. In addition to the genetic and multi-disciplinary training opportunity that SPITFIRE provides, the project will enable the student to develop several skill-sets including an understanding of global climate change, current predictions and impacts on ecosystems. The student will gain molecular skills including DNA and RNA extraction, use of next generation sequencing to analyze the transcriptome using RNA-Seq and associated bioinformatics analysis of the large datasets that are generally > 1Tb. Global climate change threatens both semi-natural and managed vegetation in biomes across the globe. Since plants are necessary for maintenance of a number of ecosystem services, understanding impacts and resilience to change is important. Ecosystem services include provisioning services for energy and food, but very little information is available on CO2 as a selection pressure driving plant adaptation to the changing environment. This is an important omission since this information is of value for plant breeding to contribute to food and energy security but also in landscape scale conservation management that will ensure plants can survive in the face of future conditions.

Start Date: Available to start October 2014

Application Deadline: April 25th 2014 with interviews planned for early May 2014.