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Robbie Waugh

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Recent publications

Staff picture: Robbie Waugh
Cell and Molecular Sciences
Robbie.Waugh@hutton.ac.uk
+44 (0)844 928 5428 (*)

The James Hutton Institute
Invergowrie
Dundee DD2 5DA
Scotland UK

Current positions

  • 2011 - Research Leader (PC2), James Hutton Institute (80%)

  • 2012 - Professor, Div. Plant Sciences, University of Dundee (20%)
  • 2008 - Honorary Professor, University of Glasgow
  • 2013 - Trustee Director of ‘The Genome Analysis Centre’, Norwich
  • 2014 - Adjunct Professor, University of Adelaide
  • 2016 – Adjunct Professor, University of Minneapolis (pending)
  • 2014 – Co-Director, Scottish Food Security Alliance (Crops)
  • 2010 – Board Member, ARC Centre of Excellence in Plant Cell Walls, Adelaide

Awards

Fellow of the Royal Society of Biology (2015 onwards)

Fellow of the Royal Society of Edinburgh (2013 onwards)

Honorary Professor, University of Glasgow (2008 onwards)

Education

  • BSc (hons), Strathclyde University (1981)
  • PhD, University of Dundee (1987)

Current research interests 

In late 2015 I was awarded a 5-year ERC advanced grant to extend our work on meiosis and recombination in large genome crop plants. This complements ongoing interests in inflorescence development and architecture and the development and application of genetic (e.g. GWAS) and genomic technologies (e.g. exome sequencing) to explore, largely through collaboration, a range of issues in plant biology (e.g. cell wall biology). Common themes include the impact of natural (e.g. crop wild relatives and landraces) and induced (e.g. mutants, genome editing) diversity, how these can be assessed, generated, captured efficiently and exploited for both discovery science and crop improvement. In future, while maintaining a focus on gene identification we will also conduct more mechanistic studies in order to understand the individual genes and networks of interaction that condition certain biological responses (e.g. inflorescence architecture). Translating research into tangible outcomes remains an important driver and we have had considerable success over an extended period in identifying genes that control a broad range of phenotypic traits. We therefore actively collaborate with the commercial sector, who generally deploy technologies that we have developed, or discoveries we have made, in practical crop improvement programmes.

Bibliography 

Publication metrics (total ca. 250)

Google Scholar:  H-index = 76, Citations = 19,650

Publication list

  • M Mascher, VJ Schuenemann, U Davidovich, N Marom, A Himmelbach, S Hübner, T Fahima, A Korol, M David, S Riehl, M Schreiber, SH Vohr, RE Green, IK Dawson, J Russell, B Kilian, GJ Muehlbauer, R Waugh, J Krause, E Weiss, N Stein(2016) Genomic evidence from 6000-year old grains sheds new light on barley domestication historyNature Genetics (accepted, in press)
  • J Russell, M Mascher, IK Dawson, S Kyriakidis, C Calixto, F Freund, M Bayer, I Milne, T Marshall-Griffiths, S Heinen, A Hofstad, R Sharma, A Himmelbach, M Knauft, M van Zonneveld, JWS Brown, K Schmid, B Kilian, GJ Muehlbauer, N Stein and R Waugh (2016) Adaptation of barley to different environments revealed in the exomes of a range-wide collection of landraces and wild relatives.Nature Genetics (accepted in press)
  • I Colas, M Macaulay, JD Higgins, D Phillips, A Barakate, M Posch, SJ Armstrong, FCH Franklin, C Halpin, R Waugh, and L Ramsay (2015).  A natural mutation in MutL-Homolog 3 (HvMLH3) affects synapsis progression and crossover resolution in the barley desynaptic mutant des10. New Phytologist (accepted in press) 
  • I Marcotuli, K Houston, JG Schwerdt, R Waugh, GB Fincher, RA Burton, A Blanco, A Gadaleta (2016) Genetic diversity and genome wide association study of β-glucan content in tetraploid wheat grains PLoS One 11 (4), e0152590
  • M Jost, S Taketa, M Mascher, A Himmelbach, T Yuo, F Shahinnia, A Druka, T Schmutzer, B Steuernagel, M Platzer, S Taudien, U Scholz, M Morgante, R Waugh, N Stein(2016) An  homolog of Blade-On-Petiole 1 and 2 (BOP1/2) controls internode length and homeotic changes of the barley inflorescence  Plant Physiology pp. 00124.2016
  • M Jöst, G Hensel, C Kappel, A Druka, A Sicard, U Hohmann, S Beier, A Himmelbach, R Waugh, J Kumlehn, N Stein, M Lenhard (2016)  The INDETERMINATE DOMAIN protein BROAD LEAF1 regulates leaf width by balancing the ratio of longitudinal to transverse cell divisions Current Biology 26: 903-909
  • VME Andriotis, G Saalbach, R Waugh, RA Field, AM Smith (2016)  The Maltase Involved in Starch Metabolism in Barley Endosperm Is Encoded by a Single Gene  PLoS One 11 (3), e0151642
  • H Oakey, B Cullis, R Thompson, J Comadran, C Halpin, R Waugh (2016) Genomic Selection in Multi-environment Crop Trials G3: Genes| Genomes| Genetics, g3. 116.027524
  • R Zhang, MR Tucker, RA Burton, NJ Shirley, A Little, J Morris, K Houston, PE Hedley, R Waugh and G Fincher (2016) The dynamics of transcript abundance during cellularisation of developing barley endosperm  Plant physiology, pp. 01690.2015
  • D Phillips, G Jenkins, M Macaulay, C Nibau, J Wnetrzak, D Fallding, et al 2015 The effect of temperature on the male and female recombination landscape of barley  New Phytologist  DOI: 10.1111/nph.13548
  • M Pourkheirandish, G Hensel, B Kilian, N Senthil, G Chen, M Sameri, et al 2015  Evolution of the Grain Dispersal System in Barley  Cell 162 (3), 527-539
  • I Marcotuli, K Houston, R Waugh, GB Fincher, RA Burton, A Blanco, et al 2015  Genome Wide Association Mapping for Arabinoxylan Content in a Collection of Tetraploid Wheats PloS one 10 (7), e0132787
  • K Houston, RA Burton, B Sznajder, AJ Rafalski, KS Dhugga, DE Mather, et al 2015  A Genome-Wide Association Study for Culm Cellulose Content in Barley Reveals Candidate Genes Co-Expressed with Members of the CELLULOSE SYNTHASE A Gene Family.  PloS one 10 (7), e013089
  • GS Schwerdt, K MacKenzie, F Wright, D Oehme, MJ Wagner, AJ Harvey, et al 2015  Evolutionary Dynamics of the Cellulose Synthase Gene Superfamily in Grasses  Plant physiology, doi: http:/ / dx. doi. org/ 10. 1104/ pp. 15. 00140
  • Tavakol, E., Okagaki, R., Verderio, G., Shariati, V., Hussien, A., Bilgic, H., Scanlon, M.J., Todt, N.R., Close, T.J., Druka, A., et al 2015. The barley Uniculme4 gene encodes a BLADE-ON-PETIOLE-like protein that controls tillering and leaf patterning, Plant physiology, pp. 114.252882.
  • Dawson, I.K., Russell, J., Powell, W., Steffenson, B., Thomas, W.T., Waugh, R. 2015. Barley: a translational model for adaptation to climate change, New Phytologist. 206(3):913-31
  • Chapman, J.A., Mascher, M., Buluç, A., Barry, K., Georganas, E., Session, A., Strnadova, V., Jenkins, J., Sehgal, S., Oliker, L., et al 2015. A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome, Genome biology 16, 26.
  • Calixto, C.P., Waugh, R., Brown, J.W. 2015. Evolutionary Relationships Among Barley and Arabidopsis Core Circadian Clock and Clock-Associated Genes, Journal of Molecular Evolution, 1-12.
  • Wu, X., Hornyik, C., Bayer, M., Marshall, D., Waugh, R., Zhang, R. 2014. In silico identification and characterization of conserved plant microRNAs in barley, Central European Journal of Biology 9, 841-852.
  • Schreiber, M., Wright, F., MacKenzie, K., Hedley, P.E., Schwerdt, J.G., Little, A., Burton, R.A., Fincher, G.B., Marshall, D., Waugh, R., Halpin C. 2014. The barley genome sequence assembly reveals three additional members of the CslF (1, 3; 1, 4)-β-glucan synthase gene family, PloS one 9, e90888.
  • Russell, J., van Zonneveld, M., Dawson, I.K., Booth, A., Waugh, R., Steffenson, B., 2014. Genetic diversity and ecological niche modelling of wild barley: refugia, large-scale post-LGM range expansion and limited mid-future climate threats?, PloS one 9, e86021.
  • Muñoz-Amatriaín, M., Cuesta-Marcos, A., Endelman, J.B., Comadran, J., Bonman, J.M., Bockelman, H.E., Chao, S., Russell, J., Waugh, R., Hayes, P.M., et al 2014. The USDA barley core collection: genetic diversity, population structure, and potential for genome-wide association studies, PloS one 9, e94688.
  • Mendiondo, G.M., Medhurst, A., van Roermund, C.W., Zhang, X., Devonshire, J., Scholefield, D., Fernández, J., Axcell, B., Ramsay, L., Waterham, H.R., et al 2014. Barley has two peroxisomal ABC transporters with multiple functions in β-oxidation, Journal of experimental botany 65, 4833-4847.
  • Mayer, K.F., Rogers, J., Doležel, J., Pozniak, C., Eversole, K., Feuillet, C., Gill, B., Friebe, B., Lukaszewski, A.J., Sourdille, P., 2014. A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome, Science 345, 1251788.
  • Marcussen, T., Sandve, S.R., Heier, L., Spannagl, M., Pfeifer, M., Jakobsen, K.S., Wulff, B.B., Steuernagel, B., Mayer, K.F., Olsen, O.-A., et al 2014. Ancient hybridizations among the ancestral genomes of bread wheat, Science 345, 1250092.
  • Liu, H., Bayer, M., Druka, A., Russell, J.R., Hackett, C.A., Poland, J., Ramsay, L., Hedley, P.E., Waugh, R., 2014. An evaluation of genotyping by sequencing (GBS) to map the Breviaristatum-e (ari-e) locus in cultivated barley, BMC genomics 15, 104.
  • Houston, K., Russell, J., Schreiber, M., Halpin, C., Oakey, H., Washington, J.M., Booth, A., Shirley, N., Burton, R.A., Fincher, G.B., 2014. A genome wide association scan for (1, 3; 1, 4)-beta-glucan content in the grain of contemporary 2-row Spring and Winter barleys, BMC genomics 15, 907.
  • Barakate, A., Higgins, J.D., Vivera, S., Stephens, J., Perry, R.M., Ramsay, L., Colas, I., Oakey, H., Waugh, R., Franklin, F.C.H., et al 2014. The synaptonemal complex protein ZYP1 is required for imposition of meiotic crossovers in barley, The Plant Cell 26, 729-740.
  • Baker, K., Bayer, M., Cook, N., Dreißig, S., Dhillon, T., Russell, J., Hedley, P.E., Morris, J., Ramsay, L., Colas, I., et al 2014. The low‐recombining pericentromeric region of barley restricts gene diversity and evolution but not gene expression, The Plant Journal 79, 981-992.
  • Ariyadasa, R., Mascher, M., Nussbaumer, T., Schulte, D., Frenkel, Z., Poursarebani, N., Zhou, R., Steuernagel, B., Gundlach, H., Taudien, S., et al 2014. A sequence-ready physical map of barley anchored genetically by two million single-nucleotide polymorphisms, Plant physiology 164, 412-423.
  • Visioni, A., Tondelli, A., Francia, E., Pswarayi, A., Malosetti, M., Russell, J., Thomas, W., Waugh, R., Pecchioni, N., Romagosa, I., 2013. Genome-wide association mapping of frost tolerance in barley (Hordeum vulgare L.), BMC genomics 14, 424.
  • Tondelli, A., Xu, X., Moragues, M., Sharma, R., Schnaithmann, F., Ingvardsen, C., Manninen, O., Comadran, J., Russell, J., Waugh, R., 2013. Structural and temporal variation in genetic diversity of European spring two-row barley cultivars and association mapping of quantitative traits, The Plant Genome 6.
  • Sharma, S.K., Bolser, D., de Boer, J., Sønderkær, M., Amoros, W., Carboni, M.F., D’Ambrosio, J.M., de la Cruz, G., Di Genova, A., Douches, D.S., 2013. Construction of reference chromosome-scale pseudomolecules for potato: integrating the potato genome with genetic and physical maps, G3: Genes| Genomes| Genetics 3, 2031-2047.
  • Oakey, H., Shafiei, R., Comadran, J., Uzrek, N., Cullis, B., Gomez, L.D., Whitehead, C., McQueen-Mason, S.J., Waugh, R., Halpin, C., 2013. Identification of crop cultivars with consistently high lignocellulosic sugar release requires the use of appropriate statistical design and modelling, Biotechnology for biofuels 6, 185.
  • McCouch, S., Baute, G.J., Bradeen, J., Bramel, P., Bretting, P.K., Buckler, E., Burke, J.M., Charest, D., Cloutier, S., Cole, G., 2013. Agriculture: feeding the future, Nature 499, 23-24.
  • Mascher, M., Richmond, T.A., Gerhardt, D.J., Himmelbach, A., Clissold, L., Sampath, D., Ayling, S., Steuernagel, B., Pfeifer, M., D'Ascenzo, M., 2013a. Barley whole exome capture: a tool for genomic research in the genus Hordeum and beyond, The Plant Journal 76, 494-505.
  • Mascher, M., Muehlbauer, G.J., Rokhsar, D.S., Chapman, J., Schmutz, J., Barry, K., Muñoz‐Amatriaín, M., Close, T.J., Wise, R.P., Schulman, A.H., 2013b. Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ), The Plant Journal 76, 718-727.
  • King, J., Armstead, I., Harper, J., Ramsey, L., Snape, J., Waugh, R., James, C., Thomas, A., Gasior, D., Kelly, R., 2013. Exploitation of interspecific diversity for monocot crop improvement, Heredity 110, 475-483.
  • Houston, K., McKim, S.M., Comadran, J., Bonar, N., Druka, I., Uzrek, N., Cirillo, E., Guzy-Wrobelska, J., Collins, N.C., Halpin, C., 2013. Variation in the interaction between alleles of HvAPETALA2 and microRNA172 determines the density of grains on the barley inflorescence, Proceedings of the National Academy of Sciences 110, 16675-16680.
  • Fisk, S.P., Cuesta-Marcos, A., Cistué, L., Russell, J., Smith, K.P., Baenziger, S., Bedo, Z., Corey, A., Filichkin, T., Karsai, I., 2013. FR-H3: a new QTL to assist in the development of fall-sown barley with superior low temperature tolerance, Theoretical and Applied Genetics 126, 335-347.
  • Borrell, A.K., Edwards, D., Jain, M., Kumanduri, V., Ma, J., Nevo, E., Raghuvanshi, S., South Campus, D., Schneider, I.H.U., Tuberosa, R., 2013. Appendix II Reviewers, Cereal Genomics II, 420.
  • Zakhrabekova, S., Gough, S.P., Braumann, I., Müller, A.H., Lundqvist, J., Ahmann, K., Dockter, C., Matyszczak, I., Kurowska, M., Druka, A., 2012. Induced mutations in circadian clock regulator Mat-a facilitated short-season adaptation and range extension in cultivated barley, Proceedings of the National Academy of Sciences 109, 4326-4331.
  • Wang, M., Jiang, N., Jia, T., Leach, L., Cockram, J., Waugh, R., Ramsay, L., Thomas, B., Luo, Z., 2012. Genome-wide association mapping of agronomic and morphologic traits in highly structured populations of barley cultivars, Theoretical and Applied Genetics 124, 233-246.
  • Shahinnia, F., Druka, A., Franckowiak, J., Morgante, M., Waugh, R., Stein, N., 2012. High resolution mapping of Dense spike-ar (dsp. ar) to the genetic centromere of barley chromosome 7H, Theoretical and Applied Genetics 124, 373-384.
  • Houston, K., Druka, A., Bonar, N., Macaulay, M., Lundqvist, U., Franckowiak, J., Morgante, M., Stein, N., Waugh, R., 2012. Analysis of the barley bract suppression gene Trd1, Theoretical and Applied Genetics 125, 33-45.
  • Higgins, J.D., Perry, R.M., Barakate, A., Ramsay, L., Waugh, R., Halpin, C., Armstrong, S.J., Franklin, F.C.H., 2012. Spatiotemporal asymmetry of the meiotic program underlies the predominantly distal distribution of meiotic crossovers in barley, The Plant Cell 24, 4096-4109.
  • Forster, B., Franckowiak, J., Lundqvist, U., Thomas, W., Leader, D., Shaw, P., Lyon, J., Waugh, R., Shu, Q., Nakagawa, H., 2012. Mutant phenotyping and pre-breeding in barley, Plant mutation breeding and biotechnology, 327-346.
  • Consortium, I.B.G.S., 2012. A physical, genetic and functional sequence assembly of the barley genome, Nature 491, 711-716.
  • Comadran, J., Kilian, B., Russell, J., Ramsay, L., Stein, N., Ganal, M., Shaw, P., Bayer, M., Thomas, W., Marshall, D., 2012. Natural variation in a homolog of Antirrhinum CENTRORADIALIS contributed to spring growth habit and environmental adaptation in cultivated barley, Nature genetics 44, 1388-1392.
  • Song, B.-K., Waugh, R., Marshall, D., Nadarajah, K., Ratnam, W., 2011. Comparative physical mapping using overgo-tagged site reveals strong conservation of synteny between cultivated and common wild rice in the 1.2 mb yld1. 1 region, Asia-Pacific Journal of Molecular Biology and Biotechnology [P] 19, 157-168.
  • Silvar, C., Casas, A., Igartua, E., Ponce-Molina, L.J., Gracia, M., Schweizer, G., Herz, M., Flath, K., Waugh, R., Kopahnke, D., 2011. Resistance to powdery mildew in Spanish barley landraces is controlled by different sets of quantitative trait loci, Theoretical and Applied Genetics 123, 1019-1028.
  • Schmalenbach, I., March, T.J., Bringezu, T., Waugh, R., Pillen, K., 2011. High-resolution genotyping of wild barley introgression lines and fine-mapping of the threshability locus thresh-1 using the Illumina GoldenGate assay, G3: Genes, Genomes, Genetics 1, 187-196.
  • Russell, J., Dawson, I.K., Flavell, A.J., Steffenson, B., Weltzien, E., Booth, A., Ceccarelli, S., Grando, S., Waugh, R., 2011. Analysis of> 1000 single nucleotide polymorphisms in geographically matched samples of landrace and wild barley indicates secondary contact and chromosome‐level differences in diversity around domestication genes, New Phytologist 191, 564-578.
  • Ramsay, L., Comadran, J., Druka, A., Marshall, D.F., Thomas, W.T., Macaulay, M., MacKenzie, K., Simpson, C., Fuller, J., Bonar, N., 2011. INTERMEDIUM-C, a modifier of lateral spikelet fertility in barley, is an ortholog of the maize domestication gene TEOSINTE BRANCHED 1, Nature genetics 43, 169-172.
  • Newton, A.C., Flavell, A.J., George, T.S., Leat, P., Mullholland, B., Ramsay, L., Revoredo-Giha, C., Russell, J., Steffenson, B.J., Swanston, J.S., 2011. Crops that feed the world 4. Barley: a resilient crop? Strengths and weaknesses in the context of food security, Food Security 3, 141-178.
  • Mayer, K.F., Martis, M., Hedley, P.E., Šimková, H., Liu, H., Morris, J.A., Steuernagel, B., Taudien, S., Roessner, S., Gundlach, H., 2011. Unlocking the barley genome by chromosomal and comparative genomics, The Plant Cell Online 23, 1249-1263.
  • Liu, H., McNicol, J., Bayer, M., Morris, J., Cardle, L., Marshall, D.F., Schulte, D., Stein, N., Shi, B.-J., Taudien, S., 2011b. Highly parallel gene-to-BAC addressing using microarrays, Biotechniques 50, 165-174.
  • Hofinger, B.J., Russell, J.R., Bass, C.G., Baldwin, T., Dos Reis, M., Hedley, P.E., Li, Y., Macaulay, M., Waugh, R., Hammond-Kosack, K.E., 2011. An exceptionally high nucleotide and haplotype diversity and a signature of positive selection for the eIF4E resistance gene in barley are revealed by allele mining and phylogenetic analyses of natural populations, Molecular ecology 20, 3653-3668.
  • Halpin, C., Daly, P., Maluk, M., Kim, S., McQueen-Mason, S., Gomez, L., Waugh, R., Stephens, J., 2011. Manipulating lignin for bioenergy applications, Aspects of Applied Biology, 3-5.
  • Consortium, P.G.S., 2011. Genome sequence and analysis of the tuber crop potato, Nature 475, 189-195.
  • Comadran, J., Ramsay, L., MacKenzie, K., Hayes, P., Close, T.J., Muehlbauer, G., Stein, N., Waugh, R., 2011. Patterns of polymorphism and linkage disequilibrium in cultivated barley, Theoretical and Applied Genetics 122, 523-531.
  • Chen, X., Hedley, P.E., Morris, J., Liu, H., Niks, R.E., Waugh, R., 2011. Combining genetical genomics and bulked segregant analysis-based differential expression: an approach to gene localization, Theoretical and Applied Genetics 122, 1375-1383.

Scientific posters/conferences

AttachmentSize
File An update on the GERMINATE project the database and tools 791.72 KB
File The Genotype Visualisation Tool (GVT) 1.07 MB
File The Plant Genomics Database Infrastructure at the Scottish Crop Research Institute 424.92 KB
File Barley SNP Databases and GVT 2.05 MB
File The Visualization and Analysis of Barley SNPs 817.23 KB
File Barley Mutant and SNP Databases at SCRI 993.59 KB
File Germinate 2 A Platform for Storage and Analysis of Experimental Plant Data 4.72 MB
File Bioinformatics Resources at the Scottish Crop Research Institute 1.58 MB
File Germinate 2: Storage Visualization and Analysis of High Volume Genotypic Phenotypic and Pedigree Data 992.31 KB
File Levels of intra-specific AFLP diversity in tuber bearing potato species with different breeding systems and ploidy levels 275.19 KB
File Single nucleotide polymorphism discovery and mapping in barley 4.01 MB
File Allele-Specific Differential Gene Expression in Two Barley Cultivars and Reciprocal F1 Hybrids 2.87 MB
File Genome-wide SNP discovery and linkage analysis in barley based on genes responsive to abiotic stress 4.63 MB
File Barley Nec1 gene is a homologue of the Arabidopsis Hlm1 encoding the cyclic nucleotide-gated ion channel 4 4.27 MB
File Association Genetics of UK Elite Barley 877.79 KB
File Steptoe x Morex - the weakest link? 1.11 MB
File Association Genetics of UK Elite Barley (AGOUEB) 348.03 KB
File Two row-Spring barley Association Panel - A resource for fine-mapping saccharification yield and crop biofuel-related traits 1.66 MB
File Genetic dissection of barley morphology and development 6.63 MB
File Transcript-Level Variation in Barley Seedling Leaves Challenged with Puccinia hordei and the Molecular Basis of Partial Resistance to Leaf Rust 1.16 MB
File Manipulating meiosis: crossovers from Arabidopsis to crops 772.81 KB
File Control of Meiotic Recombination in Barley 894.59 KB
File Meiotic Recombination in Barley
881.97 KB

  • Email: info@hutton.ac.uk
  • Phone: +44 (0)844 928 5428
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Registered office: The James Hutton Institute, Invergowrie Dundee DD2 5DA. Charity No SCO41796

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The James Hutton Research Institute is the result of the merger in April 2011 of MLURI and SCRI. This merger formed a new powerhouse for research into food, land use, and climate change.