Research
A centre of excellence for Plant and Crop Sciences
The University of Nottingham represents an International Centre of Excellence for Plant and Crop Science. Its researchers originally pioneered the use of transgenic technologies and gene silencing to create the first GM product for sale in Europe. Nottingham plant scientists have also been at the forefront of international research studying the model plants Arabidopsis thaliana and tomato, identifying several of the key genes that regulate their development, coordinating their genome sequencing efforts and, through the Nottingham Arabidopsis Stock Centre (NASC), providing underpinning resources to the international scientific community that have fuelled the recent impressive advances in our knowledge about fundamental plant processes.
The Division has always adopted an integrated approach to research extending from studies at the molecular and biochemical level to physiological analysis and agronomy of whole plants. This vision is enshrined in the new £9.2m Centre for Plant Integrative Biology (CPIB). CPIB builds on the world-class research strengths and collaborations across four RAE 5-rated schools (Schools of Biosciences, Computer Science and IT, Mathematical Sciences and Mechanical, Materials and Manufacturing Engineering). The BBSRC/EPSRC sponsored Centre aims to create a virtual Arabidopsis root which will serve as an exemplar for using integrative systems biology to model multi-cellular systems. Crop scientists within the Division are internationally recognised for their research and teaching programmes involving the analysis of physiological and genetic traits controlling important agronomic and quality traits in temperate and tropical crops. Modelling approaches to identify crop ideotypes and the integration of genomic techniques into crop breeding are also being used.
A world class research environment
The Plant and Crop Sciences Division at the University of Nottingham is one of the largest communities of plant and crop scientists in the UK with over 170 members of the division, including 26 academic staff, 20 post-doctoral staff, 29 technicians and 90 postgraduate research students. Plant and Crop scientists are accommodated in a custom designed £6.5M building containing an excellent research infrastructure which includes a genomics facility, advanced confocal microscopy equipment and the NASC Affymetrix expression profiling service. NASC is also the international repository for Arabidopsis expression data; and provide an integrated genome browser (AtEnsembl ) ; and, as one of two international stock centres, is the repository for over 550,000 Arabidopsis lines. The scale of our research and support activities demands state-of-the-art plant propagation facilities which include transgenic greenhouses and over 30 controlled environment rooms.
Crop-Plant Science research is structured into six thematic areas: Plant Development, Integrative Systems Biology, Crop Physiology, Biotic and Abiotic Stress, Breeding and Biotechnology, Genome Resources. There is extensive collaboration between these thematic areas, with other Divisions / Schools within the University and with external academic and commercial organizations.
Plant Development (Bennett, Gonzalez, Holdsworth, Murchie, Pyke, Robbins, Roberts, Seymour, Swarup, Wilson)
Crop-Plant researchers employ model species to identify key regulatory genes that control important agronomic traits such as seed germination, vegetative development, fruit ripening and reproductive biology.
Example highlights include:
Characterisation of the critical role of auxin and gibberellin in root growth and development - Bennett/Swarup
Receptor-kinase control of organ development and fusion - Gonzalez/Roberts
Determining the role of ABA in seed germination control - Holdsworth
Identifying and characterising rice mutants with a C4-like leaf morphology - Murchie/Pyke
Exploring the transcriptional regulation of ripening in fleshy fruits - Seymour
Dissection of the regulatory networks which control male reproductive development in Arabidopsis - Wilson
References:
1. Ugartechea-Chirino, Y., Swarup, R., Swarup, K., Peret, B., Whitworth, M., Bennett, M., and Bougourd, S. (2010) The AUX1 LAX family of auxin influx carriers is required for the establishment of embryonic root cell organization in Arabidopsis thaliana. Annals of Botany 105:277-289.
2. Ubeda-Tomas, S., Swarup, R., Coates, J., Swarup, K., Laplaze, L., Beemster, G.T.S., Hedden, P., Bhalerao, R., and Bennett, M.J. (2008) Root growth in Arabidopsis requires gibberellin/DELLA signalling in the endodermis. Nature Cell Biology 10:625-628.
3. Swarup, R., Perry, P.J., Hagenbeek, D., Van Der Straeten, D., Beemster, G.T.S., Sandberg, G., Bhalerao, R., Ljung, K., and Bennett, M.J. (2007) Ethylene upregulates auxin biosynthesis in Arabidopsis seedlings to enhance inhibition of root cell elongation. Plant Cell 19: 2186-2196.
4. Gonzalez-Carranza, Z.H, Rompa, U., Peters, J.L., Bhatt, A.M., Wagstaff, C., Stead, A.D. and Roberts, J.A. (2007) HAWAIIAN SKIRT: an F-Box gene that regulates organ fusion and growth in Arabidopsis. Plant Physiology 144:1370-1382.
5. Holman, T.J., Jones, P.D., Russell, L., Medhurst, A., Tomas S.U'Beda, Tallojie, P., Marquez, J., Schmuths, H., Tung, S-A., Taylor, I., Footitt, S., Bachmaire, A., Theodouloua, F.L, Holdsworth, M.J. (2009) The N-end rule pathway promotes seed germination and establishment through removal of ABA sensitivity in Arabidopsis. Proceedings of the National Academy of Sciences USA. 106: 4549-4554.
6. Jaakola, L., Poole, M., Jones, M.O., Kämäräinen-Karppinen, T., Koskimäki, J.J., Hohtola, A., Häggman, H., Fraser, P.D., Manning, K., King, G.J., Thomson, H., and Seymour, G.B. (2010). A SQUAMOSA MADS-box gene involved in the regulation of anthocyanin accumulation in bilberry fruits. Plant Physiology 153:1619-1629.
7. Xu, J., Yang, C.Y., Yuan, Z., Zhang, D.S., Gondwe, M.Y., Ding, Z.W., Liang W.Q., Zhang, D.B., and Wilson, Z.A. (2010) The ABORTED MICROSPORES regulatory network is required for postmeiotic male reproductive development in Arabidopsis thaliana. Plant Cell 22:91-107.
Integrative Systems Biology (Bennett, Broadley, Holdsworth, May, Seymour, Swarup, Wilson)
Nottingham researchers are pioneering multidisciplinary and multiscale approaches to study plant development.
Example highlights include:
A systems biology approach to understanding the control networks of seed dormancy, after-ripening and germination as part of the vSEED consortium - Holdsworth
A £9.2m BBSRC / EPSRC Systems Biology Centre award to create the Centre for Plant Integrative Biology (CPIB) which will initially focus on modelling root development - Bennett, Broadley, Holdsworth, May
Integrating genetics and high throughput genomics to identify genes underlying tomato quantitative trait loci (QTL) for metabolites that influence fruit quality under the ERA-net Plant Genomics TomQML initiative - Seymour
References:
1. Carrera, E., Holman, T., Medhurst, A., Dietrich, D., Footitt, S., Theodoulou, F.L., Holdsworth M.J.(2007) Seed after-ripening is a discrete developmental pathway associated with specific gene networks in Arabidopsis. The Plant Journal, 53:214-224.
2. Massonett, C. et al (2010) Probing the reproducibility of leaf growth and molecular phenotypes: a comparison of three Arabidopsis accessions cultivated in ten laboratories. Plant Physiology 152:2142-57.
3. French, A., Ubeda-Tomas, S., Holman, T.J., Bennett, M.J. and Pridmore, T., (2009). High throughput quantification of root growth using a novel image analysis tool. Plant Physiology 10:1104.
4. Romero-Campero, F.J., Twycross, J., Camara, M., Bennett, M., Gheorghe, M., Krasnogor, N. (2009) Modular assembly of cell systems biology models using P systems. International Journal of Foundations of Computer Science 20:427-772.
5. Middleton, A.M., King, R.J., Bennett, M.J., and Owen, M.R. (2010) Mathematical modelling of the Aux/IAA negative feedback loop. Bulletin of Mathematical Biology 72:1383-1407.
Crop Physiology (Black, Broadley, Foulkes, Murchie, Pyke, Holdsworth, Sparkes)
Tools and approaches generated in the thematic areas of Plant Development and Integrative Biology are being actively applied within a Crop Physiology context.
Example highlights include:
A DEFRA-LINK funded programme on seed dormancy with British Wheat Breeders, based on fundamental research in Arabidopsis, has identified key factors underlying pre-harvest sprouting and uniformity of germination in barley and wheat - Holdsworth, Foulkes
A DEFRA-LINK and other funding to optimise crop selenium biofortification through agronomic and genetic approaches - Broadley
Characterising altered photosynthetic capacity traits in rice - Murchie/Pyke
Research on the physiology of lodging in wheat has developed a mathematical model that is widely applied in cereals - Sparkes
References:
1. Gerjets, T., Scholefield, D., Foulkes, M.J., Lenton, J.R., and Holdsworth, M.J. (2010) An analysis of dormancy, ABA responsiveness, after-ripening and pre-harvest sprouting in hexaploid wheat (Triticum aestivum L.) caryopses. Journal of Experimental Botany 61:597-607
2. Broadley, M.R., Alcock, J., Alford, J., Cartwright, P., Fairweather-Tait, S.J., Foot, I., Hart, D.J., Hurst, R., Knott, P., McGrath, S.P., Meacham, M.C., Norman, K., Mowat, H., Scott, P., Stroud, J.L., Tovey, M., Tucker, M., White, P.J., Young, S.D., and Zhao, F-J. (2010) Selenium biofortification of high-yielding winter wheat (Triticum aestivum L.) by liquid or granular Se fertilisation. Plant and Soil 332: 31-40.
3. Sparkes, D.L., Berry, P., and King, M. (2008) Effects of shade on root characters associated with lodging in wheat (Triticum aestivum). Annals of Applied Biology 152:389-395.
Biotic and abiotic stress (Black, Dickinson, Ray, Foulkes, Fray, Rossall, Taylor)
Understanding the basis for plant/crop responses to biotic and abiotic stresses is fundamental to protecting and improving crop yields.
Example highlights include:
A major project SAFEmalt (Strategies against Fusarium effective in malting barley) - Ray
A major DEFRA LINK programme focused on manipulating tissue levels of the plant hormone abscisic acid, for significantly improved water use efficiency in tomato - Taylor
This is complemented by work on classical and marker-assisted approaches to water-use efficiency approaches - Foulkes
Joint research with the World Agroforestry Centre (ICRAF) and Jomo Kenyatta University continues to develop technologies for improving the efficiency of resource capture and biomass production in semi-arid agroforestry systems - Black
The development of techniques to identify the causative organism of Lethal Yellowing in Coconut has led to an important tool for diagnosis and a DIFD-BBSRC grant with CSIR (Ghana) which will identify sources of resistant germplasm - Dickinson
References:
1. Thompson A.J., Andrews, J., Mullholland, B.J., McKee, J.M.T., Hilton, H.W., Horridge, J.S., Farquhar, G.D., Smeeton, R.C., Smillie, I.R.A., Black, C.R., Taylor, I.B. (2007) Over-production of abscisic acid in tomato increases transpiration efficiency and root hydraulic conductivity and influences leaf expansion. Plant Physiology 143: 1905-1917.
2. Siriri, D., Ong, C.K., Wilson, J., Boffa, J.M., Black, C.R. (2010). Tree species and pruning regime affect crop yield on bench terraces in SW Uganda. Agroforestry Systems, 78, 65-77.
3. Hodgetts, J., Boonham, N., Mumford, Dickinson, M., 2009. A panel of real-time PCR assays for improved universal and group specific detection of phytoplasmas, based on the 23S rRNA gene. Applied and Environmental Microbiology, 75, 2945-2950.
Breeding and Biotechnology (Davey, Foulkes, Fray, King I, King J, Lycett, Mayes, Murchie, Robbins, Seymour, Wilson)
In this theme, developing the tools and approaches needed to allow basic plant and crop science to make an impact in the real world is the central goal. Coupling basic research with marker-assisted breeding is one strategy to make this bridge.
Example highlights include:
A major BBSRC-funded programme to breed grasses and cereals with greater resistance to abiotic stresses - King, King
In collaboration with colleagues in Chemistry (Hayes), the tomato carotenoid pathway has been diverted for the production of high levels of previously inaccessible taxanes and this has lead to EMDA funding to aid commercial development - Fray
In collaboration with colleagues from Food Sciences, work is further our understanding of fruit softening in tomato - Lycett
The effect of novel wheat ear fertility genes on crop yields is being investigated in collaboration with UK wheat breeders, CPB-Twyford - Foulkes, Mayes, Wilson
An integrated approach to crop improvement through a molecular, environmental and nutritional evaluation of bambara groundnut (Vigna subterranea L.Verdc.) for food production in semi-arid Africa and India, coordinated by Nottingham - Mayes, Murchie, Roberts
A major programme funded by BBSRC-INRA is focused on the identification of traits and genetic markers to improve the nitrogen-use efficiency and grain protein concentration in wheat - Foulkes
References:
1. Tamura K, et al. (2009) Development of intron-flanking EST markers for the Lolium/Festuca complex using rice genomic information Theoretical and Applied Genetics 118, 1549-1560.
2. Kovacs et al. (2007) Redirection of carotenoid metabolism for the efficient production of taxadiene [taxa-4(5),11(12)-diene] in transgenic tomato fruit. Transgenic Research, 16: 121-6.
3. Phan, T.D., Bo, W., West, G., Lycett, G.W. and Tucker, G.A. (2007) Silencing of the major salt-dependent isoform of pectinesterase in tomato alters fruit softening. Plant Physiology, 144: 1960-1967.
4. Basu et al. (2007) Inheritance of domestication traits in bambara groundnut (Vigna subterranea L.) Verdc.). Euphytica, 157:59-68.
5. Foulkes, M.J., Hawkesford, M.J., Barraclough, P.B., Holdsworth, M.J., Kerr, S., Kightley, S., and Shewry, P.R. (2009) Identifying traits to improve the nitrogen economy of wheat: recent advances and future prospects. Field Crops Research 114:329-342.
Genome Resources (Bennett, May, Mayes, Seymour)
Nottingham scientists have been at the forefront of applying genomic technologies in UK and International Plant and Crop research.
Example highlights include:
The European Arabidopsis Stock Centre (NASC; http://arabidopsis.info ) which has secured over £10m competitive funding since 2001. This facility provides germplasm, genomics and bioinformatics resources (AtEnsembl and NASC Arrays; http://affy.arabidopsis.info ) to the International Arabidopsis and crop science communities - May
NASC also collaborates with Crop-Plant researchers, Nutritional Biochemistry, Food Sciences, Animal Physiology the Vet School and the School of Biology all at Nottingham developing native and cross-species transcriptomic techniques in species as diverse as Elephants and Oil-palm passing through honey bees and yeast - May, Mayes
The International Tomato Genome Sequencing Programme, the UK portion of which is being spearheaded by Nottingham and colleagues from Imperial, Sanger and SCRI, with funding from BBSRC, Defra and SEERAD - Seymour
A £1.6m JIF Nutritional Genomics Award to Bennett, Grierson, Tucker with members of Food Science, Nutritional Science, Pharmaceutical Sciences and Biomedical Sciences has provided state-of-the-art -omics equipment to facilitate research between these disciplines uniting activities across the University
References:
1. Craigon et al. (2004) NASCArrays: a repository for microarray data generated by NASC's transcriptomics service. Nucleic Acids Research, 32:(Database issue), D575-D577
2. Gibson BR, Graham NS, Boulton CA, Box WG, Lawrence SJ, Linforth RST, May ST, and Smart KA (2010). Differential Yeast Gene Transcription During Brewery Propagation. Journal of the American Society of Brewing Chemists. 68: 21-29
3. Davey MW, Graham NS, Vanholme B, Swennen R, May ST and Keulemans J (2009). Heterologous oligonucleotide microarrays for transcriptomics in a non-model species; a proof-of-concept study of drought stress in Musa. BMC Genomics 10: 436
4. Mueller et al. (2005) The tomato sequencing project, the first corner stone of the International Solanaceae Project (SOL). Comparative and Functional Genomics, 6: 153-158