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The evolution of extreme nitrogen uptake in plants

  • Full or part time
    Dr G Chomicki
  • Application Deadline
    Friday, January 10, 2020
  • Funded PhD Project (European/UK Students Only)
    Funded PhD Project (European/UK Students Only)

Project Description

We are seeking a highly motivated PhD student to join this exciting project on the macroevolution of mutualisms. Competence in molecular biology and/or bioinformatics are desirable (but not compulsory) for the project. The scope of the project can be modified in function of the students interests and skills.
Background The growing world population is expected to reach 10 billion by 2050, putting strong pressure on food security. Research to enhance crop yield have largely focused on two aspects: boosting photosynthetic efficiency and harnessing nitrogen more effectively [1]. Because most plants –including our crops– take up nitrogen from the soil, they are not naturally exposed to very high nitrogen concentrations. Thus, the speed at which plants can take up nitrogen is a key limitation to plant growth rate. Recently, a farming symbiosis involving ants that cultivate, fertilize, live in and defend epiphytic plants (Squamellaria) has been discovered in the Fiji Islands [2,3], raising new promise in the race to increase plant nitrogen uptake efficiency. For millions of years, farming ants have practised a form of ‘precision agriculture’ wherein have deposited nitrogen-rich faeces directly inside the plants, on structures that have evolved hyper-absorptive function [4]. This project proposes to decipher the evolution of such extreme nitrogen uptake in plants using a combination of genomics, molecular genetics and physiological experiments. The ultimate aim of this project will be to transfer the nitrogen uptake system of Squamellaria to our crops.

Aims The student will conduct gene expression analyses and comparative genomic analyses to identify candidate genes linked to nitrogen uptake in Squamellaria. Physiological assays will be used to determine the kinetics of nitrogen absorption in vivo, using greenhouse cultivated plants. Immunolocalisation will be used to determine the nitrogen transporter spatial expression pattern in planta and complement transcriptomic analyses. Nitrogen transporter genes from Squamellaria will be cloned and transformed in Arabidopsis thaliana with (i) the native Squamellaria promoter and (ii) a root-specific promoter (e.g. NTR2) in both a nitrogen mutant background (ntr2) and wild type to test whether ectopic expression of the Squamellaria domatium nitrogen uptake in roots can (i) complement the mutant – an essential step in its functional characterization and (ii) increase plant growth rate and yield. The project will thus bring about the fundamental biology of symbiotic nitrogen uptake and test whether it can increase plant crop yield. Following successful increase in nitrogen uptake in Arabidopsis, transformation in crops (e.g. wheat, rice) will be performed.

Methodology This project will use (i) transcriptomics and comparative genomic analysis, (ii) physiological assays to test the kinetics of nitrogen absorption in vivo, (iii) immunolocalization to determine the spatial expression pattern in vivo, (iv) reverse genetics using Arabidopsis thaliana and cross-species complementation and ectopic expression, (v) growth rate assays using distinct N fertilization levels and the multiple Arabidopsis transgenic lines generated and appropriate wild type controls.

Timetable of Activities Year 1: Complete transcriptomic and genomic analyses and physiological assays; clone nitrogen transporters from Squamellaria and make DNA constructs using directional cloning. Year 2: Transform the different constructs with Squamellaria nitrogen transporters in Arabidopsis plants. Start crossing transformants to obtain homozygous lines. Year 3: Finish selecting transformed Arabidopsis lines, perform nitrogen fertilization growth assays to compare growth rate and yield of the different transgenic lines and write up thesis.
Novelty The fast-growing world population jeopardize global food security, urging scientists to engineer plant growth rate and yield. The approach proposed here is innovative because: (i) it proposes to decipher a newly discovered symbiotic nitrogen mechanism and then transfer it to crop plant species; (ii) at the same time as investigating a new possible pathway to increase plant growth rate, it will unveil a unique mechanism that mediate plant nitrogen fertilization by ants; (iii) the discovery of this unique symbiosis has been highlighted in over 100 media and dozen of languages, and the original paper (Chomicki & Renner 2016 Nature Plants) is the top 2 most discussed paper in all papers published in Nature Plants in three years (https://www.nature.com/collections/dnshkjhpxx). As a result, I anticipate that this will result in high-profile publications and general public interest.

Student Training The student will receive training in (1) genomics; (2) physiological experiments; (3) reverse genetics using Arabidopsis.

Funding Notes

This project is in competition with others for funding. Success will depend on the quality of applications received, relative to those for competing projects. If you are interested in applying, in the first instance contact , with a CV and covering letter, detailing your reasons for applying for the project

References

1. Schroeder et al. (2013). Nature 497: 60-66. 2. Chomicki G. & Renner S.S. (2016). Nature Plants 2: 16181. 3. Chomicki G. & Renner S.S. (2017). PNAS 114: 3951-3956. 4. Chomicki G. et al. PNAS (In revision).



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