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Robbie Waugh

Programme Leader: Genetics

Contact

SCRI,
Invergowrie,
Dundee,
DD2 5DA,
Scotland, United Kingdom.

Tel: +44(0) 1382 562731 (switchboard)

Email: Robbie.Waugh@scri.ac.uk

 

Photograph of Robbie WaughRecent Publications | Posters

Current Research

  • We aim to develop and exploit genomics and informatics technologies and resources, in conjunction with traditional skills in genetics and plant breeding, to identify genes underlying both simple and complex traits.
  • We are particularly interested in exploiting natural genetic variation via the development and application of appropriate technologies and applying them to appropriate genetic materials. In particular, we are exploring the potential of Association Genetics in barley using highly parallel SNP genotyping in an attempt to identify genes / loci in elite barley germplasm that control traits manuipulated by UK breeders.
  • We are conducting a program of research to genetically characterise the majority of the morphological and developmental variation that has been described in barley by mapping c. 1000 well characterised mutants.  This forward genetics approach is complemented by a well established reverse genetics resource (Barley Dis-TILLING population).
  • We are investigating the genetic complexity of the barley transcriptome by expression QTL mapping in in a reference barley population and exploring whether patterns of gene expression can be used as a surrogate to dissect complex traits. Our current focus is on networks of genes that are differentially expressed in this population in response to pathogen infection.
  • We are centrally involved in barley structural genomics through extensive BAC end sequencing and linking BAC contigs to the barley genetic map.

Recent Publications

  • Close, T.J., Bhat, P.R., Lonardi, S., Wu, Y., Rostoks, N., Ramsay, L., Druka, A., Stein, N., Svensson, J.T., Wanamaker, S., Bozdag, S., Roose, M.L., Moscou, M.J., Varshney, R., Chao, S., Szücs, P., Sato, K., Hayes, P.M., Matthews, D.E., Marshall, D.F., Muehlbauer, G.J., Graner, A., DeYoung, J., Madishetty, K., Fenton, R.D., Condamine, P., Waugh, R. 2009. Development and Implementation of High-Throughput SNP Genotyping in Barley (submitted).
  • Moragues, M., Comadran, J., Waugh, R., Milne, I., Flavell, A., Russell, J. 2009. Effects of ascertainment bias and marker number on estimations of barley diversity from high throughput SNP genotype data. Theoretical and Applied Genetics (in press).
  • Druka, A., Potokina, E., Luo, Z., Jiang, N., Chen, X., Kearsey, M., Waugh, R. 2009. eQTL analysis in Plants. Plant Biotechnology Journal (in press).
  • Chen, X., Hackett, C.A., Niks, R.E., Hedley, P., Booth, C., Druka, A., Marcel, T.C., Vels, A., Bayer, M., Milne, I., Morris, J., Ramsay, L., Marshall, D., Milne, L., Waugh, R. 2009. An eQTL analysis of Partial Resistance to Puccinia hordei in Barley. PLoS One (in press).
  • Feuillet, C., Langridge, P.and Waugh, R. 2009. The Aaronsohn-ITMI International Conference. Israel Journal of Plant Sciences 55, 315-321.
  • Waugh, R., Jannink, J-L., Muehlbauer, G. and Ramsay, L. 2009. The Emergence of Whole Genome Association Scans in Barley. Current Opinions in Plant Biology 12, 218-222.
  • Schulte, D., Close, T.J., Graner, A., Langridge, P., Matsumoto, T., Muehlbauer, G., Sato, K., Schulman, A.H., Waugh, R., Wise, R.P., Stein, N. 2009. The International Barley Sequencing Consortium-At the Threshold of Efficient Access to the Barley Genome. Plant Physiology 149(1), 142-147.
  • Szücs, P., Blake, V.C., Bhat, P.R., Chao,S., Close, T.J., Cuesta-Marcos, A., Muehlbauer, G.J., Ramsay, L., Waugh, R., and Hayes, P.M. 2009. An integrated resource for barley linkage map and malting quality QTL alignment . The Plant Genome 2, 134-140.
  • Potokina, E., Druka, A., Luo, Z., Waugh, R., Kearsey, M.J. 2009. Transcriptome analysis of barley (Hordeum Vulgare L.) using the Affymetrix Barley1 Genechip. Russian Journal of Genetics 45, 1493-1505.
  • Thiel, T., Graner, A., Waugh, R., Close, T.J., Stein, N. 2009. Evidence and evolutionary analysis of ancient whole-genome duplication in barley predating the divergence from rice. BMC Evolutionary Biology 9:209, 14908-14913.
  • Salse, J., Abrouk, M., Bolot, S., Guilhot, N., Courcelle, E., Faraut, T., Waugh, R., Close. T.J., Stein, N., Messing, J., Feuillet, C. 2009. Paleogenomics in grasses reveals the structure and evolution of the monocot ancestral genome. Proceedings of the National Academy of Sciences USA 106 (early edition).
  • Schreiber, A.W., Sutton, T., Caldo, R.A., Kalashyan, E., Lovell, B., Mayo, G., Muehlbauer, G.J., Druka, A., Waugh, R., Wise, R.P., Langridge, P., and Baumann, U. 2009. Comparative transcriptomics in the Triticeae. BMC Genomics 10, 285.
  • Druka, A., Druka, I., Centeno, A., Li, H., Sun, Z., Thomas, W., Bonar, N., Steffenson, B., Ullrich, S., Kleinhofs, A., Wise, R., Close, T., Potokina, E., Luo, Z., Wagner, C., Schweizer, G., Marshall, D., Kearsey, M., Williams, R., and Waugh, R. 2008. Towards systems genetic analyses in barley: Integration of phenotypic, expression and genotype data into GeneNetwork. BMC Genetics 9, 73.
  • Potokina, E., Druka, A., Luo, Z.W., Wise, R., Waugh, R. and Kearsey, M.J. 2008. eQTL analysis of 16,000 barley genes reveals a complex pattern of genome wide transcriptional regulation. The Plant Journal 53, 90-101.
  • Potokina, E., Druka, A., Luo, Z.W., Moscou, M., Wise, R., Waugh, R. and Kearsey, M.J. 2008. Cis-regulatory mutations and limited pleiotropy. The Plant Journal 56, 287–296.
  • Lyons, M; Cardle, L; Rostoks, N; Waugh, R; Flavell, AJ. 2008. Isolation, analysis and marker utility of novel miniature inverted repeat transposable elements from the barley genome. Molecular Genetics and Genomics 280(4), 275-285.
  • Jiang, N., Lindsey J. Leach, E. P., Tianye, J., Druka, A., Waugh, R., Kearsey, M.J. and Luo, Z.W. 2008 Methods for Evaluating Gene Expression from Affymetrix Microarray Datasets. BMC Bioinformatics 9, 284.
  • Druka, A., Potokina, E., Luo, Z.W., Bonar, N., Druka, I., Zhang, L., Marshall, D.F. Kearsey, M. and Waugh, R. 2008. Exploiting regulatory variation to identify genes and loci underlying quantitative traits in barley. Theoretical and Applied Genetics 117(2), 261-272.
  • Song, B-K., Hein, I., Druka, A., Waugh, R., Marshall, D., Nadarajah, K., Yap, S-J. & Ratnam, W. 2008. The 172-kb genomic DNA region of the O. rufipogon yld1.1 locus: comparative sequence analysis with O. sativa ssp. japonica, and O. sativa ssp. indica. Functional and Integrative Genomics 9(1), 97-108.
  • Feuillet, C., Langridge, P. and Waugh, R. 2008 Cereal breeding takes a walk on the wild side. Trends in Genetics 24, 24-32.
  • Bradshaw, J.E., Hackett, C.A., Pande, B., Waugh, R. and Bryan, G. 2007. QTL mapping of yield, agronomic and quality traits in tetraploid potato. Theoretical and Applied Genetics 116, 193-211.
  • Bevan, M. and Waugh, R. 2007. Applying plant genomics to crop improvement. Genome Biology 8, 302-302.
  • Waugh, R., Leader, D.J., McCallum, N. and Caldwell, D. 2006. Harvesting the potential of induced biological diversity. Trends in Plant Science 11, 71-79.
  • Varshney, R.K., Marcel, T.C., Ramsay, L., Russell, J.R., Roder, M., Stein, N., Waugh, R., Langridge, P., Niks, R. and Graner, A. 2006. A high density barley microsatellite consensus map with 777 SSR loci. Theoretical and Applied Genetics 114, 1091-1098.
  • van Os H., Andrzejewski, S., Bakker, E., Barrena, I., Bryan, G., Caromel, B., Ghareeb, B., Isidore, E., de Jong, W., van Koert, P., Lefebvre, V., Milbourne, D., Ritter, E., Rouppe van der Voort, J.N.A.M., Rousselle-Bourgeois, F., van Vliet, J., Waugh, R., Visser, R.G.F., Bakker, J., van Eck, H.J. 2006. Construction of a 10,000 marker ultra-dense genetic recombination map of potato: providing a framework for accelerated gene isolation and a genome-wide physical map. Genetics 173, 1075-1087.
  • Rostoks, N., Ramsay, L., MacKenzie, K., Cardle, L., Bhat, P.R., Roose, M.L., Svensson, J.T., Stein, N., Varshney, R.K., Marshall, D.F., Graner, A., Close, T.J. and Waugh, R. 2006 . "Recent history of artificial outcrossing facilitates whole-genome association mapping in elite inbred crop varieties." Proceedings of the National Academy of Sciences USA 103, 18656-61.
  • Waugh, R., Leader, D.J., McCallum, N. and Caldwell, D. 2006. Harvesting the potential of induced biological diversity. Trends in Plant Science 11, 71-79.
  • Druka, A., Muehlbauer, G., Druka, I., Caldo, R., Baumann, U., Rostoks, N., Schreiber, A., Wise, R., Close, T., Kleinhofs, A., Graner, A., Schulman, A., Langridge, P., Sato, K., Hayes, P., McNicol, J., Marshall, D. and Waugh, R. 2006. An Atlas of gene expression from seed to seed through barley development. Functional and Integrative Genomics 6, 202-211.
  • Spooner, D.M., McLean, K., Ramsay, G., Waugh, R. and Bryan, G.J. 2005. A single domestication for potato based on multilocus AFLP genotyping. Proceedings of the National Academy of Sciences USA 102, 14694-14699.
  • Rostoks, N., Mudie, S., Cardle, L., Russell, J., Ramsay, L., Booth, A., Svensson, J.T., Wanamaker, S.I., Walia, H., Rodriguez, E.M., Hedley, P.E., Liu, H., Morris, J., Close, T.J., Marshall, D.F. and Waugh, R. 2005. Genome-wide SNP discovery and linkage analysis in barley based on genes responsive to abiotic stress. Molecular Genetics and Genomics 274, 515-524.
  • Kanyuka, K., Druka, A., Caldwell, D.G., Tymon, A., McCallum, N., Waugh, R. and Adams, M.J. 2005. Evidence that the recessive bymovirus resistance locus rym4 in barley corresponds to the eukaryotic translation initiation factor 4E gene. Molecular Plant Pathology 6, 449-458.
  • Rostoks, N., Borevitz, J.O., Hedley, P.E., Russell, J., Mudie, S., Morris, J., Cardle, L., Marshall, D.F. and Waugh, R. 2005. Single-feature polymorphism discovery in the barley transcriptome. Genome Biology 6 (6), art. no. R54 2005.
  • Piffanelli, P., Ramsay, L., Waugh, R., Benabdelmouna, A., D'Hont, A., Hollricher, K., Jorgensen, J.H., Schulze-Lefert, P. and Panstruga, R. 2004. A barley cultivation-associated polymorphism conveys resistance to powdery mildew. Nature 430, 887-891.
  • Caldwell, D.G., McCallum, N., Shaw, P., Muehlbauer, G.J., Marshall, D.F. and Waugh, R. 2004. A structured mutant population for forward and reverse genetics in barley (Hordeum vulgare L.). The Plant Journal 40, 143-150.
  • Bradshaw, J.E., Pande, B., Bryan, G.J., Hackett, C.A., McLean, K., Stewart, H.E. and Waugh, R. 2004. Interval mapping of quantitative trait loci for resistance to late blight [Phytophthora infestans (Mont.) de Bary], height and maturity in a tetraploid population of potato (Solanum tuberosum subsp. tuberosum). Genetics 168, 983-995.
  • Isidore, E., van Os, H., Andrzejewski, S., Bakker, J., Barrena, I., Bryan, G.J., Caromel, B., van Eck, H., Ghareeb, B., De Jong, W., van Koert, P., Lefebvre, V., Milbourne, D., Ritter, E., Rouppe van der Voort, J., Rousselle-Bourgeois, F., van Vliet, J. and Waugh, R. 2003. Toward a marker-dense meiotic map of the potato genome: Lessons from Linkage Group I. Genetics 165, 2107-2116.
  • Thangavelu, M., James, A.B., Bankier, A., Bryan, G.J., Dear, P.H. and Waugh, R. 2003. HAPPY mapping in a plant genome: reconstruction and analysis of a high-resolution physical map of a 1.9 Mbp region of Arabidopsis thaliana Chromosome 4. Plant Biotechnology Journal 1, 23-31.