Engineering more water-use efficient crops: functional genomics of CO2 fixation during Crassulacean acid metabolism

Description

The world is getting hotter and drier due to climate change, and the human population is growing rapidly to the extent that it has been predicted that we will need to increase crop yields by 50 - 70 % by 2050 in order to feed the predicted 9 - 10 billion people. This extra food production has to be achieved using the same land and the same or less fresh water relative to the water used by agriculture today. Achieving such dramatic advances in crop productivity to underpin human food security this century is widely regarded as a key global grand challenge that requires ground-breaking, innovative approaches that "think outside the box". Our research aims to leverage a naturally occurring super-charged adaptation of photosynthesis called Crassulacean acid metabolism (CAM). This adaptation can enhance plant water use efficiency well beyond that of any of today's major food crop species such as rice, wheat or maize. Through decoding the genomes and transcriptomes of model CAM species and undertaking functional genomics research in model CAM species in the genus Kalanchoë, our work is establishing the minimal parts list for engineering CAM into C3 crops to enhance water use efficiency and photosynthesis. This project will leverage our recent discoveries by exploring the genes involved in CAM using transgenic approaches to switch genes off or on. In particular, we seek to understand how the endogenous circadian clock (the internal timekeeper that organisms use to optimise their biochemistry relative to the daily light/ dark cycle) signals to the CAM system in order to optimize the steps that occur separately both in the dark and the light. This PhD will allow the student to make a key contribution to our understanding of the genetic elements associated with CAM and its optimal temporal regulation. The student will also become accomplished in plant transformation and the techniques required for the detailed molecular, biochemical and physiological characterisation of the generated transgenic lines.

The student will be trained in the plant functional genomics techniques required to underpin novel gene discovery within our genome and transcriptome datasets. We have decoded whole genomes for Kalanchoë fedtschenkoi (strong CAM), K. laxiflora (strong CAM) and K. gracilipes (weak inducible CAM). With these datasets in hand, we are poised to exploit the goldmine of novel genes associated with high water use efficiency and CAM through transgenic approaches in our model CAM system, Kalanchoë. The student will become an accomplished and well-rounded plant biologist with training spanning from molecular biology (e.g. gene cloning/ Agrobacterium binary construct generation, tissue culture-based plant transformation, real-time quantitative PCR, ChIP-Seq and traditional and high-throughput DNA sequencing) through biochemistry (metabolomics, enzyme assays, immunoblotting) all the way to whole plant physiology (infra-red gas analyser analysis of whole plant gas exchange characteristics).

For any enquiries or if you are interested in applying please contact Dr James Hartwell at .

Availability

Open to students worldwide

Funding information

Self-funded project

This is a self funded opportunity.  

Supervisors

References

Susanna F Boxall, Nirja Kadu, Louisa V Dever, Jana Kneřová, Jade L Waller, Peter J D Gould and James Hartwell (2020) Kalanchoë PPC1 is Essential for Crassulacean Acid Metabolism and the Regulation of Core Circadian Clock and Guard Cell Signaling Genes. The Plant Cell, 32, 1136 – 1160.

Cecile Lefoulon, Susanna F. Boxall, James Hartwell and Michael R. Blatt (2020) Crassulacean acid metabolism guard cell anion channel activity follows transcript abundance and is suppressed by apoplastic malate. New Phytologist, 227: 1847-1857. 

Renata C. Ferrari, Priscila P. Bittencourt, Maria A. Rodrigues, Jose J. Moreno‐Villena, Frederico R.R. Alves, Vinícius D. Gastaldi, Susanna F. Boxall, Louisa V. Dever, Diego Demarco, Sónia C. Andrade, Erika J. Edwards, James Hartwell and Luciano Freschi (2020) C4 and crassulacean acid metabolism within a single leaf: deciphering key components behind a rare photosynthetic adaptation. New Phytologist, 225: 1699-1714. 

Susanna F Boxall, Louisa V Dever, Jana Kneřová, Peter D. Gould and James Hartwell (2017) Phosphorylation of Phosphoenolpyruvate Carboxylase Is Essential for Maximal and Sustained Dark CO2 Fixation and Core Circadian Clock Operation in the Obligate Crassulacean Acid Metabolism Species Kalanchoë fedtschenkoi. The Plant Cell 29, 2519-2536

Xiaohan Yang, Rongbin Hu, Hengfu Yin, Jerry Jenkins, Shengqiang Shu, Haibao Tang, Degao Liu, Deborah A. Weighill, Won Cheol Yim, Jungmin Ha, Karolina Heyduk, David M. Goodstein, Hao-Bo Guo, Robert C. Moseley, Elisabeth Fitzek, Sara Jawdy, Zhihao Zhang, Meng Xie, James Hartwell, Jane Grimwood, Paul E. Abraham, Ritesh Mewalal, Juan D. Beltrán, Susanna F. Boxall, Louisa V. Dever, Kaitlin J. Palla, Rebecca Albion, Travis Garcia, Jesse A. Mayer, Sung Don Lim, Ching Man Wai, Paul Peluso, Robert Van Buren, Henrique Cestari De Paoli, Anne M. Borland, Hong Guo, Jin-Gui Chen, Wellington Muchero, Yanbin Yin, Daniel A. Jacobson, Timothy J. Tschaplinski, Robert L. Hettich, Ray Ming, Klaus Winter, James H. Leebens-Mack, J. Andrew C. Smith, John C. Cushman, Jeremy Schmutz and Gerald A. Tuskan (2017) The Kalanchoë genome provides insights in convergent evolution and building blocks of crassulacean acid metabolism. Nature Communications. 8, Art. No. 1899. DOI: 10.1038/s41467-017-01491-7.

James Hartwell, Louisa V Dever, Susanna F Boxall (2016) Emerging model systems for functional genomics analysis of Crassulacean acid metabolism. Current Opinion in Plant Biology 31, 100-108.

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. 19, 327 - 338.