A major focus of our work is in the control of growth. We are interested in how the characteristic final size of plant cells, organs and seeds is set and influenced by the supply of nutrients. We use genetics, biochemistry and physiology in the experimental plant Arabidopsis thaliana in this research. Our work has identified several new genes and processes that contribute to the regulation of cell expansion, the final size of organs and seeds, and the integration of growth with available nutrient supplies. A long- term aim is to use this knowledge to enhance yield in crop plants.
Another focus of our work is on structural genomics of plants. This work involves the sequencing, assembly and analysis of plant genes, defining their relationships and their physical locations on chromosomes, and revealing how evolution and domestication shape plant genomes. This work provides key foundations for genetic analysis, genome– led breeding and systems- level analysis such as gene expression and protein interactions. We have worked on the Arabidopsis and rice genomes in the past, and most recently completed analysis of the compact genome of Brachypodium distachyon, a member of the Pooideae subfamily of grasses. This permitted three-way comparison with the genomes of sorghum (Pancoideae) and rice (Erhardtoideae) that revealed at the whole genome level conserved syntenic blocks of genes across diverse grass species. This provides a foundation for analysis of the larger more complex genomes of other pooid grasses, particularly the Triticeae. Our current work aims to create useful gene sequences from hexaploid wheat using whole genome shotgun sequencing, to lay the foundations for completing the genome sequence, and contributing to long-range physical mapping of chromosomes and the complete genome.
Linking growth with carbon and nitrogen utilization
Dr Femke de Jong
(supported by the BBSRC)
Plant growth is dependent on a supply of photosynthate and essential mineral nutrients such as nitrate and phosphate. Elite crop plants make relatively efficient use of these nutrients, but the molecular basis of this is not known, and progress to improving crop yields sustainably is consequently limited. Using Arabidopsis we are identifying transcriptional networks linking nitrate uptake with photosynthate availability and growth. This will help identify candidate genes and genetic variation in wheat underlying enhanced growth responses in limiting fertilizer conditions.
Cell expansion control by the cell wall
Dr Mathilde Seguela and Mr Neil McKenzie
(funded by a Marie Curie post-doctoral Fellowship)
The outcome of cell proliferation and cell expansion sets the final size of organs. Cell expansion involves the coordination of cell wall dynamics with internal cellular activities such as gene expression. We have identified genes involved in relaying changes in cell wall properties (in our case caused by MUR4 that affects arabinose synthesis) to altered activity of genes involved in cell wall modification. This regulatory system reveals how the state of cell walls is signaled to the nucleus and will help explain how the final size of cells is measured and maintained.
Organ size control in Arabidopsis
Mr Jack Dumenil (PhD student), Dr Fiona Corke and Ms Caroline Smith
(supported by a BBSRC CASE studentship with BASF and the EU Agronomics Project)
The final size of plant organs and seeds are determined by the number of cells that enter organogenesis, and their final size. The number of cells entering organogenesis is set by an initial period of cell proliferation, which is followed by cell cycle arrest and subsequent cell expansion. We have identified a set of genes that influences the duration of cell proliferation in organ primordia, leading to larger organs and seeds. Among these is a family of membrane – bound mono-ubiquitin receptors, and we are exploring the mechanisms by which these modulate cell proliferation.
Collaborators: Dr Cyril Zipfel, The Sainsbury Laboratory.
Wheat chromosome physical mapping
Mr Neil McKenzie, Dr Jon Wright, Mr Darren Waite
(supported by the EC Triticeae Genome project and the BBSRC)
The very large polyploid genome of bread poses interesting challenges for genome analysis. Low gene density and extensive tracts of retroelements require a long- range sequence scaffold linking genes. We are working with the International Wheat Genome Sequencing consortium (www.wheatgenome.org ) and The BBSRC Genome Analysis Centre to construct BAC- based physical maps of chromosomes 3DL, 2B and 4B. New approaches to sequence- based fingerprinting will be used to integrate the map with sequence assemblies. We also use a whole- genome BAC library for gene isolation and physical mapping.
Whole chromosome and genome shotgun sequencing of wheat
Mr Andreas Magusin, Mr Darren Waite, Mr Neil McKenzie
(Supported by the BBSRC)
Increasing the productivity of wheat crops requires new approaches to breeding and gene isolation in wheat, its ancestors and relatives. Genome sequence provides a framework for this research, therefore we are working in a collaboration to generate gene sequence assemblies and access sequence diversity in key breeding lines from whole genome shotgun sequence. This sequence provides the foundation for rapidly obtaining more accurate and complete genome sequences in the coming years. This work is carried out in collaboration with Neil Hall and Anthony Hall (Liverpool University), Keith Edwards and Gary Barker (University of Bristol), Paul Kersey and Ewan Birney (European Bioinformatics Institute) Klaus Mayer (IBIS, Helmholz-Zentrum, Munich) Dick McCombie (Cold Spring Harbor Laboratory), Jane Rogers and Mario Caccamo (The Genome Analysis Centre), Jan Dvorak (UC Davis) and Bikram Gill (Kansas State University).