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Engineering more water-use efficient crops: functional genomics of high water use efficiency associated with Crassulacean acid metabolism

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  • Full or part time
    Dr Hartwell
    Prof Borland
  • Application Deadline
    Applications accepted all year round
  • Self-Funded PhD Students Only
    Self-Funded PhD Students Only

Project Description

Crassulacean acid metabolism (CAM) is an adaptation of photosynthesis found in a diverse range of plant species that inhabit arid and semi-arid environments. CAM plants can achieve water use efficiencies up to ten-times greater than C3 species. Our over-arching goal is to develop a systems-level view of CAM and the associated inverse stomatal control by achieving a detailed understanding of the genes, proteins and metabolites involved in these valuable adaptations. Comprehensive knowledge of the CAM and stomatal control ‘parts-list’ will permit forward engineering of CAM into C3 crops. In particular, we are collaborating with US scientists on a major plant synthetic biology project that aims to introduce CAM into poplar trees (http://cambiodesign.org).

We have performed whole genome and transcriptome sequencing (RNA-seq) for our model CAM systems, Kalanchoë fedtschenkoi and K. laxiflora, and the CAM-performing, biomass feedstock crop, Agave sisalana. Our gene discovery work is yielding candidate genes for engineering CAM into C3 crops, but we first need to understand which are the most critical genes for CAM and stomatal control within a CAM species, before forward engineering the minimal set of CAM and stomatal control genes into a C3 species. In particular, in the last year we have succeeded in obtaining a high quality RNA-seq dataset comparing gene regulation over the light dark cycle for both leaf epidermal peels (enriched for stomatal guard cells) and leaf mesophyll cells (where CAM photosynthesis proceeds).

We are now ready to use this dataset to discover the genes that control inverse stomatal opening for CAM (stomata open in the dark and close in the light during CAM).

This project will focus on the production and characterisation of transgenic Kalanchoë lines in which genes proposed to be essential for the inverse stomatal opening associated with CAM will be manipulated in a guard cell-specific manner either through gene silencing or over-expression approaches. Detailed phenotypic analysis of these transgenic lines in terms of their stomatal control, photosynthetic physiology, biochemistry and molecular biology will be undertaken thereby defining which genes are most critical for inverse stomatal opening for CAM. In the long term, this work will make a substantial contribution to the development of more drought tolerant, water use efficient bioenergy crops and new biofuel feedstock crops suitable for desert cultivation.

Training:
The student will be trained in the plant functional genomics techniques required to underpin novel gene discovery within our genome and transcriptome datasets. By the time a student would start work on this project, we will have published the draft whole genome sequence of both Kalanchoë fedtschenkoi and Kalanchoë laxiflora, plus we have very deep sequencing and de novo assembly of the leaf transcriptome of Agave sisalana. With these datasets in hand, we will be poised to exploit the goldmine of novel genes associated with high water use efficiency, inverse stomatal opening and CAM through transgenic approaches in our model CAM system, K. laxiflora. The student will become an accomplished and well-rounded plant biologist with training spanning from molecular biology (e.g. gene cloning/ binary construct generation, tissue culture-based plant transformation, real-time PCR, ChIP-Seq and traditional and high-throughput DNA sequencing) through biochemistry (metabolomics, enzyme assays, Western blotting) all the way to whole plant physiology (infra-red gas analysis of leaf and whole plant gas exchange characteristics).


References

Yang, Xiaohan , Cushman, John C. , Borland, Anne M. , Edwards, Erika J. , Wullschleger, Stan D. , Tuskan, Gerald A. , Owen, Nick A. , Griffiths , Howard , Smith, J. Andrew C. , De Paoli, Henrique C. , Weston, David J. , Cottingham, Robert , Hartwell, James , Davis, Sarah C. , Silvera, Katia , Ming, Ray , Schlauch, Karen , Abraham, Paul , Stewart, J. Ryan , Guo, Hao-Bo , Albion, Rebecca , Ha, Jungmin , Lim, Sung Don , Wone, Bernard W. M. , Yim, Won Cheol , Garcia, Travis , Mayer , Jesse A. , Petereit, Juli , Nair, Sujithkumar S. , Casey, Erin , Hettich, Robert L. , Ceusters, Johan , Ranjan, Priya , Palla, Kaitlin J. , Yin, Hengfu , Reyes-García, Casandra , Andrade, José Luis , Freschi, Luciano , Beltrán, Juan D. , Dever, Louisa , Boxall, Susanna , Waller, Jade , Davies, Jack , Bupphada, Phaitun , Kadu, Nirja , Winter, Klaus , Sage, Rowan F. , Aguilar, Cristobal N. , Schmutz , Jeremy , Jenkins, Jerry and Holtum, Joseph A. M. . A roadmap for research on crassulacean acid metabolism (CAM) to enhance sustainable food and bioenergy production in a hotter, drier world. (2015) New Phytologist, 207 (3). pp. 491-504.

Dever LV, Boxall SF, Knerova J, Hartwell J (2015) Transgenic perturbation of the decarboxylation phase of crassulacean acid metabolism alters physiology and metabolism but has only a small effect on growth. Plant Physiology. Vol. 167 pp. 44 - 59.

Borland AM, Wullschleger SD, Weston DJ, Hartwell J, Tuskan GA, Yang X, Cushman JC (2015) Climate-resilient agroforesty: physiological responses to climate change and engineering of crassulacean acid metabolism (CAM) as a mitigation strategy. Plant Cell and Environment. Vol. 38, pp. 1833 -1849.

Borland AM, Hartwell J, Weston DJ, Schlauch KA, Tschaplinski TJ, Tuskan GA, Yang X, Cushman JC (2014) Engineering crassulacean acid metabolism to improve water-use efficiency. Trends in Plants Sciences. vol. 19, pp. 327 - 338.

How good is research at University of Liverpool in Agriculture, Veterinary and Food Science?

FTE Category A staff submitted: 54.64

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