Robbie Waugh

Publications

The following Publications have not yet been migrated to the James Hutton Institute's Pure service and relate to the research outputs from the two legacy organisations: The Macaulay Land Use Research Institute and The Scottish Crop Research Institute.

Journals

• Silvar, C.; Casas, A.M.; Igartua, E.; Ponce-Molina, L.J.; Gracia, M.P.; Schweizer, G.; Herz, M.; Flath, K.; Waugh, R.; Kopahnke, D.; Ordon, F. (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., Genes Genomes Genetics, 1, 187-196.
• Russell, J.R.; 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, 564-574.
• Halpin, C.; Daly, P.; Maluk, M.; Kim, S.Y.; McQueen-Mason, S.J.; Gomez, L.D.; Waugh, R.; Stephens, J. (2011) Manipulating lignin for bioenergy applications., Association of Applied Biologists – GM Crops: From Basic Research to Application, Rothamsted Research, Harpenden, 28-29 June 2011. Aspects of Applied Biology, 110, 3-5.
• Newton, A.C.; Flavell, A.J.; George, T.S.; Leat, P.; Mullholland, B.J.; Ramsay, L.; Revoredo-Giha, C.; Russell, J.R.; Steffenson, B.J.; Swanston, J.S.; Thomas, W.T.B.; Waugh, R.; White, P.J.; Bingham, I.J. (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.
• Liu, H.; McNicol, J.W.; Bayer, M.M.; Morris, J.A.; Cardle, L.; Marshall, D.F.; Schulte, D.; Stein, N.; Shi, B.; Tandien, S.; Waugh, R.; Hedley, P.E. (2011) Highly parallel gene-to-BAC addressing using microarrays., Biotechniques, 50, 165-174.
• Druka, A.; Franckowiak, J.D.; Lundqvist, U.; Bonar, N.; Alexander, J.; Houston, K.; Radovic, S.; Shahinnia, F.; Vendramin, V.; Morgante, M.; Stein, N.; Waugh, R. (2011) Genetic dissection of barley morphology and development., Plant Physiology, 155, 617-627.
• Chen, X.W.; 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.
• 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.
• Ramsay, L.; Comadran, J.; Druka, A.; Marshall, D.F.; Thomas, W.T.B.; Macaulay, M.; MacKenzie, K.; Simpson, C.G.; Fuller, J.; Bonar, N.; Hayes, P.M.; Lundqvist, U.; Franckowiak, J.D.; Close, T.J.; Muehlbauer, G.; Waugh, R. (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.
• Rustenholz, C.; Hedley, P.E.; Morris, J.; Choulet, F.; Feuillet, C.; Waugh, R.; Paux, E. (2010) Specific patterns of gene space organisation revealed in wheat by using the combination of barley and wheat genomic resources., BMC Genomics, 11(714).
• Cockram, J.; White, J.; Zuluaga, D.L.; Smith, D.; Comadran, J.; Macaulay, M.; Luo, Z.W.; Kearsey, M.J.; Werner, P.; Harrap, D.; Tapsell, C.; Liu, H.; Hedley, P.E.; Stein, N.; Schulte, D.; Steuernagel, B.; Marshall, D.F.; Thomas, W.T.B.; Ramsay, L.; Mackay, I.; Balding, D.J.; Waugh, R.; O’Sullivan, D.M.; Booer, C.; Pike, S.; Hamilton, G.; Jellis, G.; Davies, N.; Ross, A.; Bury, P.; Habgood, R.; Klose, S.; Vequaud, D.; Christerson, T.; Brosnan, J.; Newton, A.; Russel, J.; Shaw, P.; Bayles, R.; Wang, M. (2010) Genome-wide association mapping to candidate polymorphism resolution in the unsequenced barley genome, Proceedings of the National Academy of Sciences of the United States of America (PNAS), 107, pp. 21611-21616.
• Pattemore, J.A.; Rice, N.; Marshall, D.F.; Waugh, R.; Henry, R.J. (2010) Cereal variety identification using MALDI-TOF mass spectrometry SNP genotyping., Journal of Cereal Science, 52, 356-361.
• Chen, X.W.; Niks, R.E.; Hedley, P.E.; Morris, J.; Druka, A.; Marcel, T.C.; Vels, A.; Waugh, R. (2010) Differential gene expression in nearly isogenic lines with QTL for partial resistance to Puccinia hordei in barley., BMC Genomics, 11(629).
• Phillips, D.; Nibau, C.; Ramsay, L.; Waugh, R.; Jenkins, G. (2010) Development of a molecular cytogenetic recombination assay for barley., Cytogenetic and Genome Research, 129, 154-161.
• Waugh, R.; Marshall, D.F.; Thomas, W.T.B.; Comadran, J.; Russell, J.R.; Close, T.; Stein, N.; Hayes, P.; Muehlbauer, G.; Cockram, J.; O’Sullivan, D.; Mackay, I.; Flavell, A.J.; AGOUEB.; BarleyCAP.; Ramsay, L. (2010) Whole-genome association mapping in elite inbred crop varieties., Genome, 53, 967-972.
• Druka, A.; Franckowiak, J.D.; Lundqvist, U.; Bonar, N.; Alexander, J.; Guzy-Wrobelska, J.; Ramsay, L.; Druka, I.; Grant, I.; Macaulay, M.; Vendramin, V.; Shahinnia, F.; Radovic, S.; Houston, K.; Harrap, D.; Cardle, L.; Marshall, D.F.; Morgante, M.; Stein, N.; Waugh, R. (2010) Exploiting induced variation to dissect quantitative traits in barley., Biochemical Society Transactions, 38, 683-688.
• Moragues, M.; Comadran, J.; Waugh, R.; Milne, I.; Flavell, A.J.; Russell, J.R. (2010) Effects of ascertainment bias and marker number on estimations of barley diversity from high-throughput SNP genotype data., Theoretical and Applied Genetics, 120, 1525-1534.
• Chen, X.W.; Hackett, C.A.; Niks, R.E.; Hedley, P.E.; Booth, C.; Druka, A.; Marcel, T.C.; Vels, A.; Bayer, M.M.; Milne, I.; Morris, J.; Ramsay, L.; Marshall, D.F.; Cardle, L.; Waugh, R. (2010) An eQTL analysis of partial resistance to Puccinia hordei in barley., PLoS ONE, 5, 1-15.
• Druka, A.; Potokina, E.; Luo, Z.W.; Jiang, N.; Chen, X.W.; Kearsey, M.J.; Waugh, R. (2010) Expression quantitative trait loci analysis in plants., Plant Biotechnology Journal, 8, 10-27.
• 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.; Chao, S.; Varshney, R.K.; Szucs, P.; Sato, K.; Hayes, P.M.; Matthews, D.E.; Kleinhofs, A.; Muehlbauer, G.J.; deYoung, J.; Marshall, D. F.; Madishetty, K.; Fenton, R. D.; Condamine, P.; Graner, A.; Waugh, R. (2009) Development and implementation of high-throughput SNP genotyping in barley., BMC Genomics, 10(582).
• Potokina, E.; Druka, A.; Luo, Z.W.; Waugh, R.; Kearsey, M.J. (2009) The transcriptome analysis of barley (Hordeum vulgare L.) using the Affymetrix Barley1 GeneChip., Russian Journal of Genetics, 45, 1317-1328.
• Thiel, T.; Graner, A.; Waugh, R.; Grosse, I.; 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)
• Schreiber, A.W.J.; Sutton, T.; Caldo, R.A.; Kalashyan, E.; Lovell, B.; Mayo, G.; Muehlbauer, G.; Druka, A.; Waugh, R.; Wise, R.P.; Langridge, P.; Baumann, U. (2009) Comparative transcriptomics in the Triticeae., BMC Genomics, 10(285).
• Waugh, R.; Jannink, J.L.; Muehlbauer, G.J.; Ramsay, L. (2009) The emergence of whole genome association scans in barley., Current Opinion in Plant Biology, 12, 218-222.
• Wang, M.H.; Hu, XH.; Li, G.; Leach, L.J.; Potokina, E.; Druka, A.; Waugh, R.; Kearsey, M.J.; Luo, Z.W. (2009) Robust detection and genotyping of single feature polymorphisms from gene expression data., PLoS Computational Biology, 5, 1-10.
• Song, B.K.; Hein, I.; Druka, A.; Waugh, R.; Marshall, D.F.; Nadarajah, K.; Yap, S.J.; Ratnam, W. (2009) The 172-kb genomic DNA region of the O. rufipogon ylg1.1 locus: comparative sequence analysis with O. sativa ssp. Japonica and O. sativa ssp. Indica., Functional and Integrative Genomics, 9, 97-108.
• Schulte, D.; Close, T.J.; Graner, A.; Langridge, P.; Matsumoto, T.; Muehlbauer, G.J.; Sato, K.; Schulman, A.H.; Waugh, R.; Wise, R.P.; Stein, N. (2009) International Barley Sequencing Consortium – at the threshold of efficient access to the barley genome., Plant Physiology, 149, 142-147.
• Potokina, E.; Druka, A.; Luo, Z.W.; Moscou, M.; Wise, R.; Waugh, R.; Kearsey, M.J. (2008) Tissue-dependent limited pleiotropy affects gene expression in barley., Plant Journal, 56, 287-296.
• Druka, A.; Potokina, E.; Luo, Z.W.; Bonar, N.; Druka, I.; Zhang, L.; Marshall, D.F.; Steffenson, B.J.; Close, T.J.; Wise, R.P.; Kleinhofs, A.; Williams, R.W.; Kearsey, M.J.; Waugh, R. (2008) Exploiting regulatory variation to identify genes underlying quantitative resistance to the wheat stem rust pathogen Puccinia graminis f. sp. tritici in barley., Theoretical and Applied Genetics, 117, 261-272.

Books / chapters

• Halpin, C.; Shafiei, R.; Kam, J.; Wilson, Y.; Daly, P.; Maluk, M.; Zwirek, M.; McQueen-Mason, S.; Gomez, L.D.; Whitehead, C.; Comadran, J.; Uzrek, N.; Waugh, R. (2011) Towards biomass ideotypes for bioenergy – optimising lignin for biofuel and combustion., In: Bridgwater, A.V. (ed.). Proceedings of the Bioten Conference on Biomass Bioenergy and Biofuels 2010. CPL Press., pp72-77.
• Druka, A.; Waugh, R. (2010) Barley genomics and malting quality improvement., In: Zhang, G. & Li, C. (eds.). Genetics and Improvement of Barley Malt Quality. Springer, 238-259.
• Snape, J.W.; Powell, W.; Waugh, R. (2010) Hordeum species., In: Brenner, S. & Miller, J.H. (eds.). Encyclopedia of Genetics. Elsevier Science Inc., 971-973.
• Hein, I.; Kumlehn, J.; Waugh, R. (2008) Functional validation in the Triticeae., In: Jorgensen, R. (ed.). Genetics and Genomics of the Triticeae. Chapter 13, 359-286.
• Druka, A.; Waugh, R.; Hedley, P.E. (2008) Gene expression profiling., In: Rapley, R. & Walker, J.R. (eds.). Molecular Biomethods Handbook. 2nd edition. Humana Press, Chapter 14, 194-212.
• Powell, W.; Waugh, R.; Bradshaw, J.E.; Russell, J.R.; Ramsay, L. (2006) Introduction to classical genetics and plant breeding., In: Christou, P. & Klee, H. (eds.). Handbook of Plant Biotechnology. 2nd ed. John Wiley and Sons Ltd, Chichester, pp3-29.
• Ritter, E.; Lucca, F.; Sanchez, I.; Ruiz de Galarreta, J.I.; Aragones, A.; Castanon, S.; Bryan, G.J.; Waugh, R.; Lefebvre, V.; Rousselle-Bourgeois, F.; Gebhardt, C.; van Eck, H.; van Os, H.; Taco, J.; Bakker, E.; Bakker, J. (2005) Genomic resources in potato and possibilities for exploitation., In: Haverkort, A.J. & Struik, P.C (eds.). Potato in progress; science meets practice. Wageningen Academic Publishers, Netherlands, pp55-65.
• Trognitz, B.R.; Bonierbale, M.; Landeo, J.A.; Forbes, G.; Bradshaw, J.E.; Mackay, G.R.; Waugh, R.; Huarte, M.A.; Colon, L. (2001) Improving potato resistance to disease under the Global Initiative on Late Blight., In: Cooper, H.D., Spillane, C. & Hodgkin, T. (eds.). Broadening the Genetic Base of Crop Production. CABI/FAO/IPGRI, pp385-398.
• Cooper-Bland, S.; Baird, E.; Kumar, A.; De Maine, M.J.; Forster, B.P.; Waugh, R.; Powell, W. (1998) Inter- and intra-specific somatic hybridisation in potato and molecular characterisation of hybrids using randomly amplified polymorphic DNA (RAPD) markers., In: Naqvi, S.S.M. (ed.). New Genetical Approaches to Crop Improvement. Atomic Energy Research Centre, Tando Jam 70060, Pakistan, pp605-618.
• Lanham, P.; Fennell, S.; Mcnicol, P.A.; Forster, B.P.; Waugh, R.; Powell, W. (1998) The development of RAPD markers in Arachis., In: Naqvi, S.S.M. (ed.). New Genetical Approaches to Crop Improvement. Atomic Energy Research Centre, Tando Jam 70060, Pakistan, pp595-604
• Russell, J.R.; Hosein, F.; Johnson, E.; Forster, B.P.; Powell, W.; Waugh, R. (1998) The use of randomly amplified polymorphic DNA to discriminate between closely related Theobroma cacao genotypes., In: Naqvi, S.S.M. (ed.). New Genetical Approaches to Crop Improvement. Atomic Energy Research Centre. Tambo Jam 70060, Pakistan, 579-584.
• Chalmers, K.J.; Waugh, R.; Forster, B.P.; Powell, W. (1998) Genetic resources and macrogeographical differentiation in Hordeum spontaneum., In: Naqvi, S.S.M. (ed.). New Genetical Approaches to Crop Improvement. Atomic Energy Research Centre, Tando Jam 70060, Pakistan, pp573-578.
• Waugh, R.; Russell, J.R. (1998) Screening for useful variation: RAPD markers., In: Karp, A. & Issaci, P.G. (eds.). Molecular tools for screening Biodiversity: Plants and Animals. Springer, The Netherlands, Chapter 23, pp459-463.
• Thomas, W.T.B.; Russell, J.R.; Bonar, N.; Booth, A.; Fuller, J.D.; Lawrence, P.; Macaulay, M.; Ramsay, L.; Waugh, R.; Powell, W. (1997) Simple sequence repeats SSRs and QTL mapping in barley crosses.., In: H. Buerstmayer & P. Ruckenbauer (eds.). Application of Marker Aided Selection in Cereal Breeding Programs. Eucarpia Section Cereals Meeting. Tulln, Austria, 28-29.
• Russell, J.R.; Milbourne, D.; Waugh, R. (1997) Comparison of PCR marker systems to examine genetic diversity., In: Karp, A., Isaac, P.G. & Ingram, D.S. (eds.). Molecular Tools for Screening Biodiversity: Plants and Animals. Chapman and Hall.
• Hayes, P.; Chen, F.Q.; Corey, A.; Pan, A.H.; Chen, T.H.H.; Baird, E.; Powell, W.; Thomas, W.T.B.; Waugh, R.; Bedo, Z.; Karsai, I.; Blake, T.; Oberthur, L. (1997) The Dicktoo x Morex Population – A model for dissecting components of winterhardiness in barley., In: Li, P.H. & Chen, T.H.H. (eds.). Plant Cold Hardiness. Plenum Press. New York, pp77-87.
• Van De Ven, W.T.G.; Duncan, N.; Ramsay, G.; Phillips, M.S.; Powell, W.; Waugh, R. (1996) Genetic variation and systematics in relationships in Vicia., In: Pickersgill, B. & Lock, J.M. (eds.). Advances in Legume Systematics 8: Legumes of Economic Importance. Royal Botanic Gardens. Kew, pp31-40
• van den Berg, J.; Chasalow, S.; Waugh, R. (1996) RFLP analysis of plant nuclear genomes: Isolation of markers, construction linkage maps and detection of linkage in plant molecular biology., In: Clark, M. (ed.). Plant Molecular Biology. Springer Verlag, Heidelberg, pp343-397.
• Russell, J.R.; Hosein, F.; Johnson, E.; Van der Ven, W.T.G.; Waugh, R.; Powell, W. (1995) The use of RAPD markers to genetically differentiate between cocoa (Theobroma cacao L.) populations., In: Baradat, A.M.S., Adams, W.T., Muller-Stack, G. (eds.). Population Genetics and Conservation of Forest Trees. Kugler Publications, pp135-138.
• Newton, A. C.; Leakey, R. R. B.; Powell, W.; Chalmers, K.; Waugh, R.; Tchoundjeu, Z.; Mathias, P. J.; Alderson, P. G.; Mesen, J. F.; Baker, P.; Ramnarine, S. (1994) Domestication of mahoganies., In: Leakey, R. R. B. & Newton, A. C. (eds.) Tropical trees: the potential for domestication and the rebuilding of forest resources. HMSO, London, 256-266. (ITE Symposium, 29).
• Russell, J.R.; Hosein, F.; Johnson, E.; Forster, B.P.; Powell, W.; Waugh, R. (1992) The use of randomly amplified polymorphic DNA markers to discriminate between closely related Theobroma cacao genotypes., In: Siddiqui, K.A. (ed.). New Vistas in Plant Genetics. Atomic Energy Agricultural Research Centre.
• Lanham, P.; Fennell, S.; Mcnicol, P.A.; Forster, B.P.; Waugh, R.; Powell, W. (1992) The development of RAPD markers in Arachis., In: Siddiqui, K.A. (ed.). New Vistas in Plant Genetics. Atomic Energy Agricultural Research Centre.
• Cooper-Bland, S.C.; Baird, E.; Kumar, A.; De M.; Forster, B.P.; Waugh, R.; Powell, W. (1992) Inter- and intraspecific somatic hybridisation in potato and molecular characterisation of somatic hybrids using randomly amplified polymorphic DNA RAPD markers., In: Siddiqui, K.A. (ed.). New Vistas in Plant Genetics. Atomic Energy Agricultural Research Centre.
• Chalmers, K.J.; Waugh, R.; Forster, B.P.; Powell, W. (1992) Genetic resources and macrogeographical differentiation in H. spontaneum from Israel., In: Siddiqui, K.A. (ed.). New Vistas in Plant Genetics. Pakistan Press.
• Waugh, R.; Brown, J.W.S. (1991) Plant gene structure and expression., In: Grierson, D. (ed.). Plant Genetic Engineering. Plant Biotechnology Series. Blackie Scientific, pp1-36.
• Waugh, R.; Mandrand-Berthelot, M.A.; Boxer, D.H. (1984) Genetic analysis of hydrogenase in E. coli K12., In: Poole, R.K. & Dow, C.S. (eds.). Microbial Gas Metabolism – Mechanistic, Metabolic and Biotechnological Aspects. Academic Press, pp109-115.

Technical / contract reports

• Ramsay, L.; Thomas, W.T.B.; Comadran, J.; Marshall, D.F.; Shaw, P.; Waugh, R. (2011) Genetic diversity in modern barley varieties., Annual Report of the Scottish Crop Research Institute for 2010, pp23-24.
• Russell, J.R.; Dawson, I.K.; Booth, A.; Flavell, A.J.; Steffenson, B.J.; Weltzien, E.; Ceccarelli, S.; Waugh, R. (2010) Relationship between genetic distances and geographic distances among populations of barley landraces., Annual Report of the Scottish Crop Research Institute for 2009, pp20-21.
• Waugh, R. (2009) Genetics., Annual Report of the Scottish Crop Research Institute for 2008, pp19-25.
• Druka, A.; Potokina, E.; Kearsey, M.J.; Luo, Z.W.; Waugh, R. (2008) The genetics of gene expression., Annual Report of the Scottish Crop Research Institute for 2007, pp16-17.
• Waugh, R. (2008) Genetics., Annual Report of the Scottish Crop Research Institute for 2007, p11-13.
• Ramsay, L.; Rostoks, N.; Marshall, D.F.; Mudie, S.; Close, T.J.; Waugh, R. (2006) Breeding facilitates whole genome LD-mapping., Annual Report of the Scottish Crop Research Institute for 2006, pp16-17.
• Waugh, R. (2006) Genetics., Annual Report of the Scottish Crop Research Institute for 2006, pp9-11.
• Bryan, G.J.; McLean, K.; Waugh, R.; Spooner, D.M.; Ramsay, G. (2005) A single domestication for cultivated potato., Annual Report of the Scottish Crop Research Institute for 2004/2005, pp16-17.
• Waugh, R. (2005) Genetics., Annual Report of the Scottish Crop Research Institute for 2004/2005, pp13-15.
• Davies, H.V.; Waugh, R. (2004) Genes to products., Annual Report of the Scottish Crop Research Institute for 2003/2004, pp135-137.
• Macaulay, M.; Russell, J.R.; Ramsay, L.; Marshall, D.F.; Powell, W.; Waugh, R.; Thomas, W.T.B. (2004) Lessons from barley recommended lists., Annual Report of the Scottish Crop Research Institute for 2003/2004, pp144-145.
• Ramsay, L.; Caldwell, K.; Russell, J.R.; Macaulay, M.; Thomas, W.T.B.; Powell, W.; Waugh, R. (2003) Linkage disequilibrium in barley., Annual Report of the Scottish Crop Research Institute for 2002/2003, p114.
• Davies, H.V.; Viola, R.; Waugh, R. (2003) Genes to Products Overview., Annual Report of the Scottish Crop Research Institute for 2002/2003, pp106-108.
• Blok, V.C.; Armstrong, M.R.; Banks, B.; Birch, P.R.J.; Bryan, G.J.; Castelli, L.; Jones, J.T.; Kumar, A.; Phillips, M.S.; Purvis, A.; Ramsay, G.; Waugh, R.; Wishart, J. (2002) Investigating gene expression in nematode-infected roots., Annual Report of the Scottish Crop Research Institute for 2001/2002, pp122-124.
• Hackett, C.A.; Bradshaw, J.E.; Luo, Z.W.; Stewart, H.E.; Pande, B.; Bryan, G.J.; Waugh, R.; McNicol, J.W. (2002) QTL mapping in autotetraploid species: theory and application to Map QTL affecting blight resistance in potato., Annual Report of the Scottish Crop Research Institute for 2001/2002, pp159-161.
• Thomas, W.T.B.; Waugh, R.; Ramsay, L.; Russell, J.R.; Powell, W.; Meyer, R.C.; Young, G.R.; Lawrence, P.E.; Booth, A.; Swanston, J.S.; Newton, A.C. (2002) Molecular markers for agriculturally important traits in barley., Annual Report of the Scottish Crop Research Institute for 2001/2002, 162-164.
• Caldwell, D.; McCallum, N.; Mudie, S.; Hedley, P.E.; Ramsay, L.; Liu, H.; Marshall, D.F.; Waugh, R. (2002) A physical/chemical mutation grid for barley functional genomics., Annual Report of the Scottish Crop Research Institute for 2001/2002, pp157-158.
• Ramsay, L.; Hedley, P.E.; Liu, H.; McCallum, N.; Mudie, S.; Cardle, L.; Harrower, B.E.; Machray, G.C.; Marshall, D.F.; Waugh, R. (2002) Barley transcriptome resources., Annual Report of the Scottish Crop Research Institute for 2001/2002, pp151-152.
• Bryan, G.J.; Milbourne, D.; Isidore, E.; McNicoll, J.; Tierney, I.; Purvis, A.; Williamson, S.; Ramsay, L.; McLean, K.; Waugh, R. (2002) Application of a potato UHD genetic linkage map for BAC landing and contig initiation in a region of linkage group V., Annual Report of the Scottish Crop Research Institute for 2001/2002, pp143-146.
• Forster, B.P.; Bengough, A.G.; Ellis, R.P.; Thomas, W.T.B.; Clark, S.; Gordon, D.C.; El-Meniae, R.; Keith, R.; Waugh, R.; Hedley, P.E.; Daniell, T.J. (2002) Genomics of the root-soil interface., Annual Report of the Scottish Crop Research Institute for 2001/2002, pp153-154.
• Davies, H.V.; Waugh, R. (2002) Genes to Products., Annual Report of the Scottish Crop Research Institute for 2001/2002, pp133-134.
• Whisson, S.C.; van der Lee, T.; Bryan, G.J.; Waugh, R.; Govers, F.; Birch, P.R.J. (2001) Phytophthora infestans genomics: positional cloning of avirulence genes., Annual Report of the Scottish Crop Research Institute for 2000/2001, pp132-135.
• James, A.B.; Bryan, G.J.; Dear, PH.; Thangavelu, M.; Ramsay, L.; Waugh, R. (2001) High density, high throughput physical mapping in plants., Annual Report of the Scottish Crop Research Institute for 2000/2001, pp79-81.
• Milbourne, D.; Isidore, E.; van Os, H.; Bryan, G.J.; van Eck, H.; Rousselle-Bourgeois, F.; Ritter, E.; Bakker, J.; Waugh, R. (2001) A 1260 point genetic linkage map of potato Chromosome 1: paving the way for Ultra Density genetic linkage maps in crop species., Annual Report of the Scottish Crop Research Institute for 2000/2001, pp75-78.
• Cardle, L.; Macaulay, M.; Marshall, D.F.; Milbourne, D.; Ramsay, L.; Waugh, R. (2000) SSR frequency and occurrence in plant genomes., Annual Report of the Scottish Crop Research Institute for 1999/2000, pp108-110.
• De Jong, W.; Davidson, J.; Bryan, G.J.; Birch, P.R.J.; Waugh, R.; Marshall, D.F. (2000) Gene discovery in potato., Annual Report of the Scottish Crop Research Institute for 1999/2000, pp105-107.
• Bryan, G.J.; De Jong, W.; Provan, J.; Milbourne, D.; McNicoll, J.; Davidson, J.; Ramsay, G.; Waugh, R. (1999) Potato genomics: a general strategy for the molecular genetic characteristics of Solanum germplasm., Annual Report of the Scottish Crop Research Institute for 1998/99, pp101-104.
• Ellis, R.P.; Russell, J.R.; Ramsay, L.; Waugh, R.; Powell, W. (1999) Barley domestication – Hordeum spontaneum, a source of new genes for crop improvement., Annual Report of the Scottish Crop Research Institute for 1998/99, 97-100.
• Waugh, R.; Collins, A.; Milbourne, D.; Ramsay, L.; Meyer, R.C.; Hackett, C.A.; Bradshaw, J.E.; Gebhardt, C.; Bonnel, E.; Bonar, N. (1998) Development of markers for potato genetics and breeding., Annual Report of the Scottish Crop Research Institute for 1997/98, 86-88.
• Milbourne, D.; Meyer, R.C.; Hackett, C.A.; Bradshaw, J.E.; Stewart, H.E.; Phillips, M.S.; Waugh, R. (1997) Identification of genetic markers linked to quantitative resistance to late blight and white potato cyst nematode in tetraploid potato., Annual Report of the Scottish Crop Research Institute for 1996/97, 40.

Conference papers

• Hedley, P.E.; Liu, H.; Morris, J.A.; Waugh, R. (2010) Development of high-throughput map anchoring methods in cereals., Triticeae Genome 2nd Annual Workshop, Sabanci University, Istanbul, 12-14 April 2010.
• Barral Baron, G.; Booth, A.; Ramsay, L.; Russell, J.R.; Waugh, R.; Thomas, W.T.B.; Werner, P. (2010) Dissecting nitrogen use efficiency of cereals using an association genetics approach., Association of Applied Biologists – Water and Nitrogen Use Efficiency in Plants and Crops, Olde Barn Hotel, Marston, Lincs, UK 15-16 December 2010.
• Muehlbauer, G.J.; Waugh, R.; Ramsay, L.; Thomas, W.T.B.; Marshall, D.F.; Newton, A.C. (2010) Potential impacts of a new oat genomics toolbox: Lessons from the barley CAP., Plant & Animal Genome XVIII, San Diego, California, USA, 9-13 January 2010.
• Rustenholz, C.; Choulet, F.; Hedley, P.E.; Laugier, C.; Waugh, R.; Feuillet, C.; Paux, E. (2010) The transcriptional map of wheat chromosome 3B., Plant & Animal Genome XVIII, San Diego, California, USA, 9-13 January 2010.
• Cockram, J.; White, J.; Zuluaga, D.; Mackay, I.; Luo, Z.W.; Kearsey, M.J.; Comadran, J.; Marshall, D.F.; Ramsay, L.; Thomas, W.T.B.; Harrap, D.; Werner, P.; Tapsell, C.; Balding, D.J.; Waugh, R.; O’Sullivan, D. (2010) Genome-wide association mapping in barley: From simulations to fine-mapping., Plant & Animal Genome XVIII, San Diego, California, USA, 9-13 January 2010.
• Shahinnia, F.; Druka, A.; Waugh, R.; Morgante, M.; Stein, N. (2010) Positional cloning of the gene dense spike (dsp1) on barley chromosome 7H bu utilisation of next generation grass-genomic tools., Plant & Animal Genome XVIII, San Diego, California, USA, 9-13 January 2010.
• Shaw, P.; Cardle, L.; Milne, I.; Waugh, R.; Flavell, A.; Thomas, W.T.B.; Grzebyta, J.; Bayer, M.; Marshall, D.F. (2009) Germinate 2: A platform for Illumina SNP genotyping experiments and high volume phenotypic data., Plant & Animal Genome XVII, San Diego, California, 10-14 January 2009.
• Russell, J.R.; Moragues, M.; Dawson, I.K.; Waugh, R.; Marshall, D.F.; Milne, I.; Grando, S.; Tondelli, A.; Cattivelli, L.; Hubner, S.; Fridman, E.; Flavell, A.J. (2009) Genetic diversity analysis of wild and landrace barleys using the BODA1 Illumina genotyping platform., 19th International Triticeae Mapping Initiative – 3rd COST Tritigen Workshop, Clermont-Ferrand, France, 31 August – 4 September 2009 (Talk).
• Rustenholz, C.; Choulet, F.; Hedley, P.E.; Waugh, R.; Feuillet, C.; Paux, E. (2009) Impact of the genome structure on the gene space organisation, function and regulation of wheat chromosome 3B., 19th International Triticeae Mapping Initiative – 3rd COST Tritigen Workshop, Clermont-Ferrand, France, 31 August – 4 September 2009 (Talk).
• Russell, J.R.; Waugh, R.; Marshall, D.F.; Hayes, P.; Matus, I.; Del Pozo, A.; Close, T.J.; Baum, M.; Grando, S.; Ceccarelli, S. (2009) Genomic dissection of tolerance to drought stress in wild barley., Annual Research Meeting of Generation Challenge Program (CGIAR), Bamako, Mali, 20-23 September 2009 (Talk).
• Waugh, R.; Marshall, D.F.; Thomas, W.T.B.; Comadran, J.; Russell, J.R.; Close, T.; Stein, N.; Hayes, P.; Muehlbauer, G.; Cockram, J.; O’Sullivan, D.; Mackay, I.; Flavell, A.J.; Ramsay, L. (2009) Whole-genome association mapping in elite inbred crop varieties., OECD Genome Association, Perth, Australia, 9-12 November 2009 (Invited plenary).
• Waugh, R.; Ramsay, L.; Comadran, J.; Marshall, D.F.; Thomas, W.T.B.; Russell, J.R.; Close, T.; Stein, N.; Hayes, P.; Muehlbauer, G.J.; Cockram, J.; O’Sullivan, D.; Mackay, I.; Flavell, A.J. (2009) Whole-genome scans in elite barley germplasm as a strategy for gene isolation., 19th International Triticeae Mapping Initiative – 3rd COST Tritigen Workshop, Clermont-Ferrand, France, 31 August – 4 September 2009 (Talk).
• Waugh, R.; Marshall, D.F.; Thomas, W.T.B.; Comadran, J.; Russell, J.R.; Close, T.; Stein, N.; Hayes, P.; Muehlbauer, G.; Cockram, J.; O’Sullivan, D.; Mackay, I.; Ramsay, L. (2009) Whole-genome association mapping in elite inbred crop varieties as a platform for gene discovery., ACPFG Genomics Symposium: The Genomics of Salinity, Adelaide, Australia, 16-18 November 2009 (Invited plenary).
• Waugh, R. (2008) Genetics of barley quality., 3rd Conference Worldwide Distilled Spirits, Edinburgh, Scotland, September 2008.
• Ramsay, L.; Comadran, J.; Thomas, W.T.B.; Marshall, D.F.; Druka, A.; MacKenzie, K.; Bhat, P.; Close, T.J.; Waugh, R. (2008) Barley genomics: Development and application of SNP genotyping., 5th UK Cereal Genetics and Genomics Workshop, Rothamsted, 16-18 April 2008.
• Druka, A.; Harrap, D.; Waugh, R. (2008) Genomic dissection of barley morphology and development: The ERA-PG BARCODE project., 5th UK Cereal Genetics and Genomics Workshop, Rothamsted, 16-18 April 2008.
• Waugh, R.; Marshall, D.F.; Druka, A.; Comadran, J.; Russell, J.R.; Chen, X.W.; Thomas, W.T.B.; Close, T.J.; Stein, N.; Ramsay, L. (2008) Genomic dissection of phenotypic variation in barley., BSPP Cereal Pathosystems Conference 2008, Queen Mary, University of London, 16-17 December 2008, p63.
• Russell, J.R.; Baum, M.; Ceccarelli, S.; Close, T.M.; Grando, S.; Hayes, P.M.; Matus, I.; Marshall, D.F.; Del Poza, A.; von Korff Schmising, M.; Waugh, R. (2008) Genomic dissection of tolerance to drought stress in wild barley., 10th International Barley Genetics Symposium, Alexandria, Egypt, 5-10 April 2008.
• Moragues, M.; Russell, J.R.; Ceccarelli, S.; Grando, S.; Baum, M.; Macaulay, M.; Booth, A.; Waugh, R.; Ramsay, L.; Comadran, J.; Close, T.J.; de Young, J.; Flavell, A.J. (2008) High throughput SNP-based marker analysis of landrace barley., 10th International Barley Genetics Symposium, Alexandria, Egypt, 5-10 April 2008.
• Waugh, R.; Ramsay, L.; Marshall, D.F.; Kearsey, M.J.; O’Sullivan, D.M.; Tapsell, C.; Klose, S.; Bury, P.; Habgood, R.; Gymer, P.; Christerson, T.; Allvin, B.; Davies, N.; Brosnan, J.; Booer, C.; Thomas, W.T.B. (2008) High density genome scan of progress in UK winter and spring malting barley., 10th International Barley Genetics Symposium, Alexandria, Egypt, 5-10 April 2008.
• Marshall, D.F.; Close, T.; Ramsay, L.; Druka, A.; Thomas, W.T.B.; Flavell, A.J.; Shaw, P.; Milne, I.; Waugh, R. (2008) Barley genomics and genetic analysis – new trends in barley genomics., 10th International Barley Genetics Symposium, Alexandria, Egypt, 5-10 April 2008.
• Marshall, D.F.; Waugh, R.; Dicks, J.; Nwankwo, D.; Ellis, N.; Shaw, P.; Barnard, V.; Ambrose, M.; Flavell, A.J. (2008) New developments in the germinate project., Plant & Animal Genome XVI, San Diego, CA, 12-16 January 2008, 311 (Abstract).
• Russell, J.R.; Baum, M.; Ceccarelli, S.; Close, T.M.; Grando, S.; Hayes, P.; Matus, I.; Marshall, D.F.; Del Poza, A.; von Korff Schmising, M.; Waugh, R. (2007) Genomic dissection of tolerance to drought stress in wild barley., Generation Challenge Programme Annual Research Meeting, South Africa, 12-16 September 2007.
• Druka, A.; Waugh, R. (2007) GENESYS: The exploitation of genetic variation in gene network inference., BBSRC CISB Meeting, Census for Life, Newcastle-upon-Tyne, 19-20 November 2007.
• Rostoks, N.; Mudie, S.; Bonar, N.; Cardle, L.; Marshall, D.F.; Waugh, R. (2007) SNP and haplotype diversity in coding and non-coding regions of European spring and winter barley., II International Vavilov Conference Crop Genetic Resources in the 21st Century, St Petersburg, Russia, 26-30 November 2007.
• Ramsay, G.; McLean, K.; Waugh, R.; Spooner, D.M.; Bradshaw, J.E.; Bryan, G.J. (2006) Clarifying the origin of potato and its implication for breeding., EAPR-EUCARPIA The Science of Selection: Potato Breeding Methodology for the 21 Century, Carlow, Ireland, 20-22 November 2006.
• Ramsay, G.; McLean, K.; Waugh, R.; Spooner, D.M.; Bryan, G.J. (2006) The domestication of potato., Plant GEMs (Plant Genomics European Meetings) 5. Venice, 11-14 October 2006.
• Baumann, U.; Caldo, R.; Langridge, P.; Mayo, G.; Schreiber, A.W.; Sutton, T.; Waugh, R.; Wise, R. (2006) Results from the wheat reference experiment: simularities and differences of the transcriptomes of wheat and barley., 8th International Congress of Plant Molecular Biology, Adelaide, Australia, 20-25 August 2006.
• Ramsay, G.; McLean, K.; Waugh, R.; Spooner, D.M.; Bryan, G.J. (2006) On the domestication of potato: evidence from molecular studies., International Solanaceae Conference and Solanaceae Genomics Network, Madison, Wisconsin, 23-27 July 2006.
• Waugh, R.; Rostoks, N.; Ramsay, L.; Marshall, D.F.; Thomas, W.T.B.; Druka, A.; Wanamaker, S.; Svensson, J.T.; Bhat, P.; Graner, A.; Stein, N.; Varshney, R.K.; Kearsey, M.J.; Luo, Z.W.; Potokina, E.; Close, T.J. (2006) Towards whole genome association genetic scans in barley., Eucarpia Cereals Meeting, Lleida, Spain, 14-17 November 2006.

Conference posters / abstracts

• Thomas, W.T.B.; Comadran, J.; Ramsay, L.; Shaw, P.; Marshall, D.; Newton, A.C.; O’Sullivan, D.; Cockram, J.; Mackay, I.; Bayles, R.; White, J.; Waugh, R.; AGOUEB Consortium. (2011) Detecting and mapping loci for disease resistance in UK elite barley cultivars., Fourth International Workshop on Barley Leaf Blights, West Park Centre, Dundee, 27-29 June 2011.
• Barakate, A.; Stephens, J.; Higgins, J.; Ramsay, L.; Colas, I.; Halpin, C.; Waugh, R.; Jenkins, G.; Phillips, D.; Armstrong, S.; Franklin, C. (2011) Manipulation of meiotic recombination in barley., 3rd British Meiosis Meeting, Sheffield, April 2011.
• Colas, I.; Ramsay, L.; Waugh, R.; Meiosys Consortium. (2011) The use of the barley desynaptic mutants to study recombination in cereals ., EMBO Meiosis Meeting, Paestum, Italy, 17-21 September 2011.
• Colas, I.; Ramsay, L.; Waugh, R.; Meiosys Consortium. (2011) Meiotic recombination in barley: approaches to analyze barley desynaptic mutants., Chromatin and Chromosomes: The New Frontiers of Science, The University of Birmingham, June 2011.
• Colas, I.; Ramsay, L.; Waugh, R.; Meiosys Consortium. (2011) Meiotic recombination in barley: approaches to analyze barley desynaptic mutants., British Meiosis Meeting, University of Sheffield, April 2011.
• Shaw, P.; Milne, I.; Cardle, L.; Waugh, R.; Flavell, A.J.; Stephen, G.; Bayer, M.; Graham, M.; Kennedy, J.; Marshall, D.F. (2011) Germinate 2 – Storage, visualization and analysis of high volume genotypic, phenotypic and pedigree data., Plant and Animal Genome XIX, San Diego, California, USA, 15-19 January 2011. (Poster)
• Colas, I.; Ramsay, L.; Waugh, R. (2011) Control of meiotic recombination in barley., Plant and Animal Genome XIX, San Diego, California, USA, 15-19 January 2011. (Poster)
• Comadran, J.; Ramsay, L.; William, T.; Macaulay, M.; Marshall, D.F.; Shaw, P.; Cockram, J.; White, J.; Mackay, I.; Liu, Z.; Kearsey, M.J.; O’Sullivan, D.; Waugh, R. (2011) Genetic selection footprints in elite barley cultivars., Plant and Animal Genome XIX, San Diego, California, USA, 15-19 January 2011. (Poster)
• Flavell, A.J.; Xu, X.; Comadran, J.; Thomas, W.T.B.; Marshall, D.F.; Waugh, R.; Russell, J.R.; Ho, T. (2011) Focussed association genetics scanning for yield-related traits in barley., Plant and Animal Genome XIX, San Diego, California, USA, 15-19 January 2011. (Poster)
• Close, T.J.; Graner, A.; Langridge, P.; Li, C.; Matsumoto, T.; Muehlbauer, G.J.; Sato, K.; Schulman, A.; Waugh, R.; Wise, R.; Zhang, G.; Stein, N. (2011) International Barley Genome Sequencing Consortium û The barley genome is in sight., Plant and Animal Genome XIX, San Diego, California, USA, 15-19 January 2011. (Poster)
• Tavakol, E.; Verderio, G.; Fusca, T.; Ciannamea, S.; Close, T.J.; Druka, A.; Waugh, R.; Mayer, K.F.X.; Martis, M.; Arivadasa, R.; Schulte, D.; Zhou, R.; Stein, N.; Muehlbauer, J.G.; Rossini, L. (2011) Fine mapping and steps towards map-based cloning of cul4, a mendelian locus required for tillering in barley., Plant and Animal Genome XIX, San Diego, California, USA, 15-19 January 2011. (Poster)
• Feuillet, C.; Stein, N.; Dolezel, J.; Mayer, K.; Rossini, L.; Fahima, T.; Korol, A.; Schulman, A.H.; Waugh, R.; Budak, H.; Greenland, A.; Bevan, M.; Keller, B.; Langendijk, E.; Praud, S.; Korzun, V.; Morgante, M.; Tuberosa, R. (2010) The Triticeae Genome Project: Genomics for Triticeae improvement., 20th International Triticeae Mapping Initiative Conference, Beijing, China, 1-5 September 2010. (Poster)
• Druka, A.; Bonar, N.; Houston, K.; Waugh, R. (2010) Genetic dissection of barley morphology and development., Scottish Plant Biology Meeting, University of Dundee, 22 April 2010 (Poster).
• Flavell, A.J.; Xu, X.; Comadran, J.; Thomas, W.T.B.; Marshall, D.F.; Russell, J.R.; Waugh, R.; Tondelli, A.; Cattivelli, L.; Schnaithmann, F.; Pillen, K.; Schulman, A.H.; Ingvardsen, C.; Rasmussen, S.; Sharma, R.; Kilian, B. (2010) An incremental approach for mapping useful traits in barley – The EXBARDIV project., 2nd International Symposium: Genomics of Plant Genetic Resources, Bologna, Italy, 24-27 April 2010 (Poster).
• Shaw, P.; Cardle, L.; Milne, I.; Waugh, R.; Flavell, A.J.; Stephen, G.; Bayer, M.M.; Graham, M.; Kennedy, J.; Marshall, D.F. (2010) Germinate 2 – storage, visualization and analysis of high volume genotypic, phenotypic and pedigree data., Plant & Animal Genome XVIII, San Diego, California, USA, 9-13 January 2010 (Abstract).
• Druka, A.; Bonar, N.; Houston, K.; Waugh, R. (2010) Genetic dissection of barley morphology and development., Monogram Network Workshop, Norwich, 2-4 March 2010 (Poster).
• Fisk, S.; Hayes, P.; Henson, C.; Schmitt, M.; Baenziger, S.; Cooker, B.; Bedo, Z.; Waugh, R.; Cistu, L.; Cuesta-Marcos, A.; Filichkina, T.; Corey, A. (2010) Simultaneous genetic analysis of winter hardiness traits and development of winter malting barley varieties., Plant & Animal Genome XVIII, San Diego, California, USA, 9-13 January 2010 (Abstract).
• Waugh, R.; Russell, J.R.; Dawson, I.K.; Ramsay, L.; Comadran, J.; Thomas, W.T.B.; Marshall, D.F.; Xu, X.; Flavell, A.J. (2010) Whole genome association scans in stratified germplasm collections., Plant & Animal Genome XVIII, San Diego, California, USA, 9-13 January 2010 (Abstract).
• Chen, X.W.; Hackett, C.A.; Niks, R.E.; Hedley, P.E.; Druka, A.; Marcel, T.C.; Waugh, R. (2010) eQTL analysis of partial resistance to Puccinia hordei Otth in barley., Plant & Animal Genome XVIII. San Diego, California, USA, 9-13 January 2010 (Abstract).
• Houston, K.; Druka, A.; Bonar, N.; Franckowiak, J.D.; Lundqvist, U.; Alexander, J.; Morgante, M.; Stein, N.; Harrap, D.; Waugh, R. (2010) Fine mapping and identification of the candidate genes for barley third outer glume (trd) locus., Plant & Animal Genome XVIII, San Diego, California, USA, 9-13 January 2010 (Poster).