St John's College

E-mail:
  nicholas.harberd@plants.ox.ac.uk

Tel  +44 (0)1865 275071
Fax +44 (0)1865 275074

Last Modified: January 2013

Mutation, Evolution and Environmental Response

The relationship with the environment is fundamental to the biology of all organisms, and especially to plants. Our research group investigates key aspects of this relationship, focusing on the ways in which environment changes plant biology over a wide range of timescales: from the short-term physiological adaptation of individual plants to fluctuating environments, to the long-term effects of environment on plant evolution. Our approaches are unified by the use of genetics, with a strong emphasis on whole-genome sequencing, and we work with a variety of model and crop plant systems (Arabidopsis thaliana, Physcomitrella patens, wheat) appropriate to particular research questions. Our coordinated interests cover both fundamental questions (e.g., How does mutation contribute to plant evolution?) and practical outcomes (e.g., Can we improve the salt-tolerance of crop plants?). Specific interests are outlined below (see Current Projects).

Previously (until August 2007) our research group was located at the John Innes Centre, Norwich, and focused on the genetics of plant growth regulation by the phytohormone gibberellin. We revealed the nature and biological properties of the gibberellin-DELLA mechanism (the mechanism via which gibberellin promotes plant growth), and showed that a variant form of this mechanism causes the dwarfism characteristic of the high-yielding wheat varieties of the 'green revolution'. We also showed that the gibberellin-DELLA mechanism integrates the effects of multiple environmental signals, and that it provides plants with the capacity to regulate their growth in response to environmental change. We also determined how the gibberellin-DELLA mechanism evolved during land-plant evolution, showing how the modern angiosperm mechanism was derived by a series of steps from precursor components present in the earliest diverging land-plants.

OPPORTUNITIES

We welcome contacts from prospective graduate students and postdoctoral researchers.

CURRENT PROJECTS

There are currently four interrelated areas of research in the lab:

Mutation and Evolution

We are interested in the role that de novo DNA sequence mutation plays in evolution, and in determining the extent to which the environment influences this process. This project involves whole-genome studies of A. thaliana. We initially developed (in collaboration with Prof. Richard Mott at the University of Oxford Wellcome Trust Centre for Human Genetics) robust methods for the identification of de novo DNA sequence mutations in ‘short-read’ whole genome DNA sequencing datasets. We are now amongst the world leaders in de novo mutation detection, and are applying our methods to understand how de novo mutations arise. For example, although it has long been known that exposure to environmental fast-neutron (FN) irradiation is mutagenic, the genome-wide effects of fast-neutron irradiation were poorly understood. We have recently shown that, in contrast to what was previously thought, FN exposure causes more base substitution mutations than deletion mutations, and that these substitutions exhibit a characteristic molecular mutational spectrum (a reflection of the different frequencies of specific transition and transversion mutations) that is very different from that exhibited by mutations arising spontaneously in control plants (Belfield et al., 2012).

 

In further recent studies, we have investigated the fascinating phenomenon of plant somaclonal variation. When whole plants are regenerated from cells grown in in vitro cell culture conditions, these plants often exhibit high frequencies of heritable phenotypic variation, a phenomenon known as somaclonal variation. Until recently, the underlying causes of somaclonal variation were poorly understood. We have advanced understanding of this phenomenon by showing that base substitution mutation is a major cause of somaclonal variation, and that the molecular mutational spectrum of mutations arising during plant regeneration is again very different from that of mutations arising spontaneously in control plants (Jiang et al., 2011).

 

Currently, we are extending our studies by experimental analysis of the effects of environment on genome-wide inherited de novo mutations in plants, and via comparison of resultant findings with the spectrum of SNP mutations found in natural variant A. thaliana strains and base substitutions distinguishing Arabidopsis species (Belfield et al., unpublished; Jiang et al., unpublished; Gan et al., 2011).

 

Plant Responses to Environmental Stress: Salt-Stress

We are working on plant salt-stress responses as a fundamental model of how plants respond physiologically to the challenge of stressful environments, and because salt-stress is a major global threat to the yields of crop plants. Our work involves investigations with A. thaliana and with wheat. Our A. thaliana studies involve both induced mutational and natural variation approaches to the study of the responses of plants to high-salinity soils. In the mutational studies we have selected for mutants exhibiting either increased resistance or increased sensitivity to growth on saline soils. These studies have enabled substantial advance in understanding, because previous studies of A. thaliana salt-stress responses have mostly been conducted in low-transpiration petri-dish environments. In contrast, our studies more closely reflect the reality of plants growing in the wild or in the field, in which the transpiration stream is a major conduit of water and salts through the xylem vasculature from the root to the shoot of plants. In collaboration with Prof. Andrew Smith (University of Oxford Department of Plant Sciences) we have shown that levels of reactive oxygen species (ROS) in the region of the root vasculature regulate the sodium (Na) content of xylem sap, and that these ROS levels are themselves controlled by Na sensitive regulation of the activity of a specific respiratory burst oxidase enzyme (encoded by the gene AtrbohF) catalyzing ROS production. Thus we have discovered a ROS-regulated mechanism for regulation of root-to-shoot delivery of soil Na, a discovery that has major implications both for our understanding of how plants maintain internal ionic homeostasis, and for the hugely important goal of improving the salinity-tolerance of diverse agricultural crops (Jiang et al., submitted).

 

We are also investigating the cause of natural variation in response to soil salinity using a set of ‘MAGIC’ lines derived by intercrossing of 18 different founder A. thaliana lines sourced from throughout the global distribution range of this species. The aim of this project is to correlate phenotypic variation with inheritance of specific founder alleles, thus identifying the genes that are causal in determining the range of soil salinity tolerance in A. thaliana growing in the wild. The identification of these genes will then enable targeting of orthologous genes in crop species, with the eventual aim once again of developing salinity-tolerant crop strains.

 

Finally, we are also investigating the effects of salt-stress on the biology of wheat and of related grass species (see below).

 

Our novel discoveries of previously unknown mechanisms via which plants achieve physiological adaptation to a saline-soil environment have important practical implications. Soil salinity is a major factor limiting agricultural production, and affects an estimated ~20 million hectares of cultivated land world-wide. Furthermore, the global area of salinized cultivated land is rapidly increasing due to the widespread use of irrigation systems, thus threatening global food security. There is therefore an urgent need to understand plant soil-salinity tolerance mechanisms, and to identify genes conferring tolerance. Our elucidation of the mechanisms of transpiration-dependent salt tolerance has particular relevance to crops growing in field environments, and to the need to improve both salinity tolerance and water-use efficiency in agriculture.

 

Wheat: homeoallelic transcript balance, environmental effects and salt-tolerance

Wheat is a crop-plant of major global food-security importance, and presents an exciting scientific challenge due to the size and complexity of its genome. Our research on wheat focuses on understanding the regulation of gene expression at a genome-wide level, with special reference to the effects of the environment on gene expression.

 

The genome complexity of wheat is due in part to its being a polyploid genome comprising three distinct A, B and D homoeologous subgenomes. In essence, many of the individual genes in the wheat genome are represented by three different A, B and D homeoalleles. Very little is known in a genome-wide sense of the relative extents to which individual A, B and D homeoalleles contribute to the overall expression of an individual gene. We are comparing genome-wide RNA-seq datasets obtained from Chinese Spring (euploid) wheat and from nullisomic-tetrasomic lines lacking individual wheat chromosomes to determine, on a gene-by-gene basis, the relative transcript-level contributions of individual homeoalleles.  Our findings (Leach et al., unpublished) are of fundamental biological interest, because they provide the beginnings of a systematic understanding of how homoeologous gene expression is coordinately regulated in polyploids. In addition, our findings have important implications for wheat breeders, because they enable understanding of the relative extents to which individual homeoalleles contribute to the traits that need to be improved to for sustainable increases in yield.

 

In further experiments, we are determining the extent to which environment (salt-stress) affects the relative expression levels of wheat homeoalleles, as a route to understanding wheat salinity responses. Finally, in collaboration with Prof. Ian King (University of Nottingham), we are taking an RNA-seq approach to understanding the salt-tolerance conferred on wheat by the introduction of chromosomes from the wild salt-tolerant wheat relative Thinopyrum bessarabicum.   

 

Evolution of Environmental Responses

Our group has a long-term interest in understanding how plant growth-regulatory (Yasumura et al., 2007) and environmental response mechanisms evolved. We are currently investigating the evolution of ethylene-mediated regulation of plant submergence responses (Yasumura et al., submitted). 

Belfield, Eric, Gan, Xiangchao, Mithani, Aziz, Brown, Carly, Jiang, Caifu, Franklin, Keara, Alvey, Elizabeth, Wibowo, Anjar, Jung, Marko, Bailey, Kit, Kalwani, Sharan, Raggoussis, Jiannis, Mott, Richard, Harberd, Nicholas. (2012) Genome-wide analysis of mutations in mutant lineages selected following fast-neutron irradiation mutagenesis of Arabidopsis thaliana Genome Research..
doi:10.1101/gr.131474.111.

Jiang, C, Belfield, E.J, Mithani, A, Visscher, A, Ragoussis, J, Mott, R, Smith, J.A.C, Harberd, N.P. (2012) ROS-mediated vascular homeostatic control of root-to-shoot soil Na delivery in Arabidopsis EMBO Journal..
doi:10.1038/emboj.2012.273.

Kumar, S.V, Lucyshyn, D, Jaeger, K.E, Alos, E, Alvey, E, Harberd, N.P, Wigge, P.A. (2012) Transcription factor PIF4 controls the thermosensory activation of flowering Nature. 484 (7393): pp 242-245.
doi:10.1038/nature10928.

Yasumura, Y, Pierik, R, Fricker, M.D, Voesenek, L.A.C.J, Harberd, N.P. (2012) Studies of Physcomitrella patens reveal that ethylenemediated submergence responses arose relatively early in land-plant evolution Plant Journal. 72 (6): pp 947-959.
doi:10.1111/tpj.12005.

Yasumura, Y, Pierik, R, Fricker, M.D, Voesenek, L.A.C.J, Harberd, N.P. (2012) Studies of Physcomitrella patens reveal that ethylene-mediated submergence responses arose relatively early in land-plant evolution Plant Journal..
doi:10.1111/tpj.12005.

Gan, X, Stegle, O, Behr, J, Steffen, J.G, Drewe, P, Hildebrand, K.L, Lyngsoe, R, Schultheiss, S.J, Osborne, E.J, Sreedharan, V.T, Kahles, A, Bohnert, R, Jean, G, Derwent, P, Kersey, P, Belfield, E.J, Harberd, N.P, Kemen, E, Toomajian, C, Kover, P.X, Clark, R.M, Ratsch, G, Mott, R. (2011) Multiple reference genomes and transcriptomes for Arabidopsis thaliana Nature. 477 (7365): pp 419-423.
doi:10.1038/nature10414.

Jiang, C, Mithani, A, Gan, X, Belfield, E.J, Klingler, JohnP, Zhu, J.-K, Ragoussis, J, Mott, R, Harberd, Nicholas. (2011) Regenerant Arabidopsis Lineages Display a Distinct Genome-Wide Spectrum of Mutations Conferring Variant Phenotypes Current Biology. 21 (16): pp 1385-1390.
doi:10.1016/j.cub.2011.07.002.

Sauret-Gueto, S, Calder, G, Harberd, N.P. (2011) Transient gibberellin application promotes Arabidopsis thaliana hypocotyl cell elongation without maintaining transverse orientation of microtubules on the outer tangential wall of epidermal cells Plant Journal. 69 (4): pp 628-639.
doi:10.1111/j.1365-313X.2011.04817.x.

Harberd, N.P, Belfield, E, Yasumura, Y. (2009) The angiosperm gibberellin-GID1-DELLA growth regulatory mechanism: How an "inhibitor of an inhibitor" enables flexible response to fluctuating environments Plant Cell. 21 (5): pp 1328-1339.
doi:10.1105/tpc.109.066969.

Koini, M.A, Alvey, L, Allen, T, Tilley, C.A, Harberd, N.P, Whitelam, G.C, Franklin, K.A. (2009) High Temperature-Mediated Adaptations in Plant Architecture Require the bHLH Transcription Factor PIF4 Current Biology. 19 (5): pp 408-413.
doi:10.1016/j.cub.2009.01.046.

Achard, P, Renou, J.-P, Berthome, R, Harberd, N.P, Genschik, P. (2008) Plant DELLAs Restrain Growth and Promote Survival of Adversity by Reducing the Levels of Reactive Oxygen Species Current Biology. 18 (9): pp 656-660.
doi:10.1016/j.cub.2008.04.034.

De, Grauwe L, Chaerle, L, Dugardeyn, J, Decat, J, Rieu, I, Vriezen, W.H, Moritz, T, Beemster, G.T.S, Phillips, A.L, Harberd, N.P, Hedden, P, Van, Der Straeten D. (2008) Reduced gibberellin response affects ethylene biosynthesis and responsiveness in the Arabidopsis gai eto2-1 double mutant New Phytologist. 177 (1): pp 128-141.
doi:10.1111/j.1469-8137.2007.02263.x.

Navarro, L, Bari, R, Achard, P, Lison, P, Nemri, A, Harberd, N.P, Jones, J.D.G. (2008) DELLAs Control Plant Immune Responses by Modulating the Balance of Jasmonic Acid and Salicylic Acid Signaling Current Biology. 18 (9): pp 650-655.
doi:10.1016/j.cub.2008.03.060.

Jiang, C, Gao, X, Liao, L, Harberd, N.P, Fu, X. (2007) Phosphate starvation root architecture and anthocyanin accumulation responses are modulated by the gibberellin-DELLA signaling pathway in Arabidopsis Plant Physiology. 145 (4): pp 1460-1470.
doi:10.1104/pp.107.103788.

Our work (1997-2012) has been funded by the BBSRC, The Gatsby Charitable Foundation, the European Union and the King Abdullah University of Science and Technology.

Publications (1997-2007)

Yasumura, Y., Crumpton-Taylor, M., Fuentes, S. & Harberd, N. P. (2007). Step-by-step acquisition of the gibberellin-DELLA growth-regulatory mechanism during land-plant evolution. Current Biology 17, 1225-1230.
Achard, P., Baghour, M., Chapple, A., Hedden, P., Van Der Straeten, D., Genschik, P., Moritz, T. & Harberd, N. P. (2007). The plant stress hormone ethylene controls floral transition via DELLA-dependent regulation of floral meristem-identity genes. Proceedings of the National Academy of Sciences of the United States of America 104, 6484-6489.
Jiang, C., Gao, X., Liao, L., Harberd, N.P. & Fu, X. (2007). Phosphate starvation root architecture and anthocyanin accumulation responses are modulated by the gibberellin-DELLA signaling pathway in Arabidopsis. Plant Physiology 145, 1460-1470. 
Achard, P., Liao, L., Jiang, C., Desnos, T., Bartlett, J., Fu, X. & Harberd, N. P. (2007). DELLAs contribute to plant photomorphogenesis. Plant Physiology 143, 1163-1172.
Harberd, N. (2006). Seed to Seed: the secret life of plants. Bloomsbury (UK/USA).
Achard, P., Cheng, H., De Grauwe, L., Decat, J., Schoutteten, H., Moritz, T., Van Der Straeten, D., Peng, J. & Harberd, N. P. (2006). Integration of plant responses to environmentally activated phytohormonal signals. Science 311, 91-94.
Sablowski, R. & Harberd, N. P. (2005). Plant genes on steroids. Science 307, 1569-1570.
Alvey, L. & Harberd, N. P. (2005). DELLA proteins: integrators of multiple plant growth regulatory inputs? Physiologia Plantarum 123, 153-160.
Vriezen, W. H., Achard, P., Harberd, N. P. & Van Der Straeten, D. (2004).Ethylene-mediated enhancement of apical hook formation in etiolated Arabidopsis thaliana seedlings is gibberellin dependent. Plant Journal 37, 505-516.
Fu, X., Richards, D. E., Fleck, B., Xie, D., Burton, N. & Harberd, N. P. (2004).The Arabidopsis mutant sleepy1gar2-1 protein promotes plant growth by increasing the affinity of the SCFSLY1 E3 ubiquitin ligase for DELLA protein substrates. Plant Cell 16, 1406-1418.
Cheng, H., Qin, L., Lee, S., Fu, X., Richards, D. E., Cao, D., Luo, D., Harberd, N. P. & Peng, J. (2004). Gibberellin regulates Arabidopsis floral development via suppression of DELLA protein function. Development 131, 1055-1064.
Achard, P., Herr, A., Baulcombe, D. C. & Harberd, N. P. (2004). Modulation of floral development by a gibberellin-regulated microRNA. Development 131, 3357-3365.
Petty, L. M., Harberd, N. P., Carre, I. A., Thomas, B. & Jackson, S. D. (2003).Expression of the Arabidopsis gai gene under its own promoter causes a reduction in plant height in chrysanthemum by attenuation of the gibberellin response. Plant Science 164, 175-182.
Hynes, L. W., Peng, J., Richards, D. E. & Harberd, N. P. (2003). Transgenic expression of the Arabidopsis DELLA proteins GAI and gai confers altered gibberellin response in tobacco. Transgenic Research 12, 707-714.
Harberd, N. P. (2003). Relieving DELLA restraint. Science 299, 1853-1854.
Fu, X. & Harberd, N. P. (2003). Auxin promotes Arabidopsis root growth by modulating gibberellin response. Nature 421, 740-743.
Ait-ali, T., Rands, C. & Harberd, N. P. (2003). Flexible control of plant architecture and yield via switchable expression of Arabidopsis gai. Plant Biotechnology journal 1, 337-343.
Achard, P., Vriezen, W. H., Van Der Straeten, D. & Harberd, N. P. (2003).Ethylene regulates arabidopsis development via the modulation of DELLA protein growth repressor function. Plant Cell 15, 2816-2825.
Peng, J., Richards, D. E., Moritz, T., Ezura, H., Carol, P. & Harberd, N. P. (2002). Molecular and physiological characterization of Arabidopsis GAI alleles obtained in targeted Ds-tagging experiments. Planta 214, 591-596.
Peng, J. & Harberd, N. P. (2002). The role of GA-mediated signalling in the control of seed germination. Current opinion in plant biology 5, 376-381.
Lee, S., Cheng, H., King, K. E., Wang, W., He, Y., Hussain, A., Lo, J., Harberd, N. P. & Peng, J. (2002). Gibberellin regulates Arabidopsis seed germination via RGL2, a GAI/RGA-like gene whose expression is up-regulated following imbibition. Genes & Development 16, 646-658.
Fu, X., Richards, D. E., Ait-Ali, T., Hynes, L. W., Ougham, H., Peng, J. & Harberd, N. P. (2002). Gibberellin-mediated proteasome-dependent degradation of the barley DELLA protein SLN1 repressor. Plant Cell 14, 3191-3200.
Fleck, B. & Harberd, N. P. (2002). Evidence that the Arabidopsis nuclear gibberellin signalling protein GAI is not destabilised by gibberellin. Plant Journal 32, 935-947.
Richards, D. E., King, K. E., Ait-Ali, T. & Harberd, N. P. (2001). How gibberellin regulates plant growth and development: A Molecular Genetic Analysis of Gibberellin Signaling. Annual Review of Plant Physiology and Plant Molecular Biology 52, 67-88.
King, K. E., Moritz, T. & Harberd, N. P. (2001). Gibberellins are not required for normal stem growth in Arabidopsis thaliana in the absence of GAI and RGA. Genetics 159, 767-776.
Fu, X., Sudhakar, D., Peng, J., Richards, D. E., Christou, P. & Harberd, N. P. (2001). Expression of Arabidopsis GAI in transgenic rice represses multiple gibberellin responses. Plant Cell 13, 1791-1802.
Desnos, T., Puente, P., Whitelam, G. C. & Harberd, N. P. (2001). FHY1: a phytochrome A-specific signal transducer. Genes andDevelopment 15, 2980-2990.
Richards, D. E., Peng, J. & Harberd, N. P. (2000). Plant GRAS and metazoan STATs: one family? Bioessays 22, 573-577.
Collett, C. E., Harberd, N. P. & Leyser, O. (2000). Hormonal interactions in the control of Arabidopsis hypocotyl elongation. Plant Physiology 124, 553-562.
Peng, J., Richards, D. E., Moritz, T., Cano-Delgado, A. & Harberd, N. P. (1999a). Extragenic suppressors of the Arabidopsis gai mutation alter the dose-response relationship of diverse gibberellin responses. Plant Physiology 119, 1199-1208.
Peng, J., Richards, D. E., Hartley, N. M., Murphy, G. P., Devos, K. M., Flintham, J. E., Beales, J., Fish, L. J., Worland, A. J., Pelica, F., Sudhakar, D., Christou, P., Snape, J. W., Gale, M. D. & Harberd, N. P. (1999b). 'Green revolution' genes encode mutant gibberellin response modulators. Nature 400, 256-261.
Ezura H., Higashi, K. & Harberd, N. P. (1999). Phytochrome B influences in-vitro shoot morphogenesis in Arabidopsis thaliana (L.) Heyhn. Plant Biotechnology 16, 279-284.
Cowling, R. J. & Harberd, N. P. (1999). Gibberellins control Arabidopsis hypocotyl growth via regulation of cellular elongation. Journal of Experimental Botany 50, 1351-1357.
Harberd, N. P., King, K. E., Carol, P., Cowling, R. J., Peng, J. & Richards, D. E. (1998). Gibberellin: inhibitor of an inhibitor of...? Bioessays 20, 1001-1008.
Cowling, R. J., Kamiya, Y., Seto, H. & Harberd, N. P. (1998). Gibberellin dose-response regulation of GA4 gene transcript levels in Arabidopsis. Plant Physiology 117, 1195-1203.
Peng, J. & Harberd, N. P. (1997). Transposon-associated somatic gai-loss sectors in Arabidopsis. Plant Science 130, 181-188.
Peng, J. & Harberd, N. P. (1997). Gibberellin deficiency and response mutations suppress the stem elongation phenotype of phytochrome-deficient mutants of Arabidopsis. Plant Physiology 113, 1051-1058.
Peng, J., Carol, P., Richards, D. E., King, K. E., Cowling, R. J., Murphy, G. P. & Harberd, N. P. (1997). The Arabidopsis GAI gene defines a signaling pathway that negatively regulates gibberellin responses. Genes and Development 11, 3194-3205.

Prof. David Baulcombe, University of Cambridge.
Prof. Dominique Van Der Straeten, Ghent, Belgium.
Prof. Ian King, University of Nottingham.
Dr. Ioannis Ragoussis, WTCHG, Oxford.
Prof. Jinrong Peng, ICMB, Singapore.
Prof. John Snape, JIC, Norwich.
Prof. Jonathan Jones, Sainsbury Lab, Norwich.
Dr. Margaret Boulton, JIC, Norwich.
Prof. Ottoline Leyser, Sainsbury Laboratory, Cambridge University.
Prof. Pascal Genschik, IBMP, Strasbourg, France.
Dr. Patrick Achard, IBMP, Strasbourg, France.
Prof. Richard Mott, WTCHG, Oxford.
Mr. Steve Reader, JIC, Norwich.
Dr. Thomas Moritz, Umeå, Sweden.
Dr. Toshi Foster, HortResearch, New Zealand.
Dr. Xiangdong Fu, Beijing, China.
Prof. Yuji Kamiya, RIKEN, Japan.