University of Dundee

Professor Claire Halpin FRSE FRSB

Manipulation of plant metabolism using reverse genetics
Associate Dean of Research and Professor of Plant Biology and Biotechnology
University of Dundee at JHI, Errol Road, Invergowrie, Dundee
Full Telephone: 
+44 (0) 1382 568775, int ext


XylemSEMMy research focuses on two main areas, lignin biosynthesis and meiotic recombination, although I also maintain an active interest in enabling techniques for plant biotechnology.

Lignin is an essential component of many plant cell walls, where it waterproofs and rigidifies the structure, protecting it from degradation. This complicates the release of cell wall sugars or cellulose during ruminant digestion and in biofuel and paper production, although lignin itself is a useful staring material for the production of valuable chemicals. The lignin biosynthesis pathway has been well-studied but is still yielding surprises and important basic features are poorly understood. The spatial organisation of the pathway, how it is regulated, and how it coordinates with other aspects of cell wall development and wider plant metabolism, are areas of intensive current research. A major applied focus is to understand how lignin can be manipulated in plant biomass to enable the production of second generation biofuels.

The Halpin group are using association genetics in barley (in collaboration with Robbie Waugh, JHI) along with barley and Arabidopsis mutants and transgenics where lignin has been manipulated, to discover new genes related to lignin biosynthesis and to determine how lignin properties affect different bioenergy applications. We are one of 6 research hubs in the BBSRC Sustainable Bioenergy Centre (BSBEC Within BSBEC, we lead the ‘Cell Wall Lignin Programme’ which aims to identify barley genotypes that facilitate efficient biofuel production from straw, and provide molecular markers for breeding improved energy crops. Our Arabidopsis work is funded by programme grants from the Global Climate and Energy Project (, in collaboration with lignin experts in Belgium and the USA.

Our research on meiotic recombination also focusses on barley where, in common with many other important crop species, large areas of chromosomes rarely, if ever, recombine. This limits the creation and exploitation of genetic diversity that is a fundamental process underlying crop breeding programmes. Greater understanding of how recombination is controlled in barley might allow us to manipulate the process to improve the available genetic diversity and the speed and accuracy of plant breeding.  We are building on knowledge of recombination generated in Arabidopsis to evaluate the role of orthologous barley genes in recombination using both transgenic and mutant plants.


Barakate A, Keir E, Oakey H, Halpin C. 2020. Stimulation of homologous recombination in plants expressing heterologous recombinases. BMC Plant Biology. 20(1):1-10.

Houston K, Qiu J, Wege S, Hrmova M, Oakey H, Qu Y, Smith P, Situmorang A, Macaulay M, Flis P, Bayer M, Roy S, Halpin C, Russell J, Schreiber M, Byrt C, Gilliham M, Salt DE, Waugh R. 2020. Barley sodium content is regulated by natural variants of the Na+ transporter HvHKT1;5. Communications Biology. 3(1):1-9.

Nguyen DT, Gomez LD, Harper A, Halpin C, Waugh R, Simister R, Whitehead C, Oakey H, Nguyen HT, Nguyen TV, Duong TX, McQueen-Mason SJ. 2020. Association mapping identifies quantitative trait loci (QTL) for digestibility in rice straw. Biotechnology for Biofuels. 13:Article 165.

Colas I, Barakate A, Macaulay M, Schreiber M, Stephens J, Vivera S, Halpin C, Waugh R, Ramsay L. 2019. desynaptic5 carries a spontaneous semi-dominant mutation affecting Disrupted Meiotic cDNA 1 in barley. Journal of Experimental Botany. 70(10):2683-2698.

Colas I, Barakate A, Macaulay M, Schreiber M, Stephens J, Vivera S, Halpin C, Waugh R, Ramsay L. 2019. desynaptic5 carries a spontaneous semi-dominant mutation affecting Disrupted Meiotic cDNA 1 in barley. Journal of Experimental Botany. 70(10):2683-2698.

Daly P, McClellan C, Maluk M, Oakey H, Lapierre C, Waugh R, Stephens J, Marshall D, Barakate A, Tsuji Y, Goeminne G, Vanholme R, Boerjan W, Ralph J, Halpin C. 2019. RNAi-suppression of barley caffeic acid O-methyltransferase modifies lignin despite redundancy in the gene family. Plant Biotechnology Journal. 17(3):594-607.

Darrier B, Russell J, Milner SG, Hedley PE, Shaw PD, Macaulay M, Ramsay L, Halpin C, Mascher M, Fleury DL, Langridge P, Stein N, Waugh R. 2019. A comparison of mainstream genotyping platforms for the evaluation and use of barley genetic resources. Frontiers in Plant Science. 10:1-14.

Halpin C. 2019. Lignin engineering to improve saccharification and digestibility in grasses. Current Opinion in Biotechnology. 56:223-229.

Rapazote-Flores P, Bayer M, Milne L, Mayer C-D, Fuller J, Guo W, Hedley PE, Morris J, Halpin C, Kam J, McKim SM, Zwirek M, Casao MC, Barakate A, Schreiber M, Stephen G, Zhang R, Brown JWS, Waugh R, Simpson CG. 2019. BaRTv1.0: an improved barley reference transcript dataset to determine accurate changes in the barley transcriptome using RNA-seq. BMC Genomics. 20:1-17.

Oakey H, Cullis B, Thompson R, Comradan J, Halpin C, Waugh R. 2016. Genomic Selection in multi-environment crop trials. G3 : Genes, Genomes, Genetics. 6(5):1313-1326.

Colas I, Macaulay M, Higgins JD, Phillips D, Barakate A, Posch M, Armstrong S, Franklin FCH, Halpin C, Waugh R, Ramsay L. 2016. A spontaneous mutation in MutL-Homolog 3 (HvMLH3) affects synapsis progression and crossover resolution in the barley desynaptic mutant des10. New Phytologist. 212(3):693-707.

Bennett AE, Grussu D, Kam J, Caul S, Halpin C. 2015. Plant lignin content altered by soil microbial community. New Phytologist. 206(1):166-174.

Schwerdt JG, MacKenzie K, Wright F, Oehme D, Wagner JM, Harvey AJ, Shirley NJ, Burton RA, Schreiber M, Halpin C, Zimmer J, Marshall DF, Waugh R, Fincher GB. 2015. Evolutionary dynamics of the cellulose synthase gene superfamily in grasses. Plant Physiology. 168(3):968-983.

Houston K, Russell J, Schreiber M, Halpin C, Oakey H, Washington JM, Booth A, Shirley N, Burton RA, Fincher GB, Waugh R. 2014. A genome wide association scan for (1,3;1,4)-β-glucan content in the grain of contemporary 2-row Spring and Winter barleys. BMC Genomics. 15:Article 907.

Bao Z, Benson SM, Cui Y, Dionne JA, Maher K, Boerjan W, Halpin C, Nelson R, Nichols D, Ralph J, Ramakrishnan TS. 2014. In search of clean, affordable energy. Oilfield Review. 26(1):4-15.

Vanholme,R., Cesarino,I., Rataj,K., Xiao,Y., Sundin,L., Goeminne,G., Kim,H., Cross,J., Morreel,K., Araujo,P., Welsh,L., Haustraete,J., McClellan,C., Vanholme,B., Ralph,J., Simpson,G.G., Halpin,C.* and Boerjan,W.* (2013) Caffeoyl Shikimate Esterase (CSE) Is an Enzyme in the Lignin Biosynthetic Pathway in Arabidopsis. Science 341, 1103-1106 *joint corresponding/senior authors (Abstract / reprint)

Houston, K., McKim, S.M., Comadran, J., Bonar, N., Druka, I., Uzrek, N., Cirillo, E., Guzy-Wrobelska, J., Collins, N.C., Halpin. C., Hansson, M., Dockter, C., Druka, A., and Waugh, R. (2013) Variation in the interaction between alleles of HvAPETALA2 and microRNA172 determines the density of grains on the barley inflorescence. PNAS. Published online before print, September 24, 2013, doi: 10.1073/pnas.1311681110

Tilston,E.L., Halpin,C. and Hopkins,D.W. (2013) Decomposition of tobacco roots with modified phenylpropanoid content by fungi with contrasting lignocellulose degradation strategies.  Biol. Fertil. Soils 49, 305-311.

Steiner,H-Y., Halpin,C., Jez, J.M., Kough,J., Parrott,W., Underhill,L., Weber,N. and Hannah,L.C. (2013) Evaluating the Potential for Adverse Interactions within Genetically Engineered Breeding Stacks. Plant Physiol 161, 1587-1594.

Higgins,J.D., Perry,R.M., Barakate,A., Ramsey,L., Waugh,R., Halpin,C., Armstrong,S.J. and Franklin,F.C.H. (2012) Spatiotemporal asymmetry of the meiotic program underlies the predominantly distal distribution of meiotic crossovers in Barley. Plant Cell 24, 4096-4109. 

Weber,N., Halpin,C., Hannah,L.C., Jez,J.M., Kough,J. and Parrott,W. (2012) Crop Genome Plasticity and Its Relevance to Food and Feed Safety of Genetically Engineered Breeding Stacks. Plant Physiol. 160, 1842-1853. 

Vanholme,R., Storme,V., Vanholme,B., Sundin,L., Christensen,J.H., Goeminne,G., Halpin,C., Rohde,A., Morreel,K. and Boerjan,W. A systems biology view of the plant’s response to lignin perturbations. Plant Cell 24, 3506-3529.

Barakate,A., Stephens,J., Goldie,A., Hunter,W.N., Marshall,D., Hancock,R.D., Lapierre,C., Morreel,K., Boerjan,W. and Halpin,C. (2011). Syringyl lignin is unaltered by severe sinapyl alcohol dehydrogenase suppression. Plant Cell 23, 4492-4506.

Gomez, L.D., Whitehead,C., Barakate,A., Halpin,C., and McQueen-Mason,S.J., (2010) Automated Saccharification Assay for Determination of Digestibility in Plant Materials. Biotechnol. Biofuels 3, 23.

Johnson,S.N., Hallett,P.D., Gillespie,T.L. and Halpin,C. (2010) Below-ground herbivory and root toughness: a potential model system using lignin-modified tobacco. Physiol. Entomol. 35, 186–19

Tilston,E.L., Halpin,C. and Hopkins,D.W. (2008) Tissue culture propagation alters plantmicrobe interactions in tobacco rhizosphere. Biol. Fertil. Soils 44, 897-901

Dauwe,R., Morreel,K., Goeminne,G., Gielen,B., Rohde,A., Van Beeumen,J., Ralph,J., Boudet,A., Kopka,J., Rochange,S., Halpin,C., Messens,E., and Boerjan,W. (2007) Molecular phenotyping of lignin-deficient tobacco reveals associated changes in cell wall metabolism, primary metabolism and photorespiration. Plant J. 52, 263-85.

Halpin,C., Webster,E.A., Boerjan,W., Pilate,G. and Hopkins,D.W. (2007) Genetically modified lignin below ground. Nature Biotechnol. 25, 168-169