Functional Genomics Group publications (2005 - present)

2013

Steinberg, F., Gallon, M., Winfield, M., Thomas, E., Bell, A.J., Heesom, K.J., Travare, J.M. and Cullen, P.J. 2013. A global analysis of SNX27-retromer assembly and cargo specificity reveals a function in glucose and metal ion transport. Nature Cell Biology 15: 446-448.

2012

Allen, A.M, Barker, G.L.A., Wilkinson, P., Burridge, A., Winfield, M., Coghill, J., Uauy, C., Griffiths, S., Jack, P., Berry, S., Werner, P., Melichar, J.P.E., McDougall, J., Gwilliam, R., Robinson, P. and Edwards, K.J. 2012. Discovery and development of exome-based, co-dominant single nucleotide polymorphism markers in hexaploid wheat (Triticum aestivum L.). Plant Biotechnology Journal 11(3): 279-295.
Brenchley, R., Spannagl, M., Pfeiffer, M., Barker, G.L.A., D'Amore, R., Allen, A.M., McKenzie, N., Kramer, M., Kerhornou, A., Bolser, D. Kay, S., Waite, D., Trick, M, Bancroft, I., Gu, Y., Huo, N., Luo, M-C., Sehgal, S., Gill., B., Kianian, S., Anderson, O., Kersey, P., Dvorak, J., McCombie, W.R., Hall, A., Mayer, M.F.X., Hall, N., Edwards, K.J., Bevan, M.W. and Hall, N. 2012. Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature 491: 705-710.
Wilkinson, P.A., Winfield, M.O., Barker, G.L.A., Allen, A.M., Burridge, A., Coghill, J.A., and Edwards, K.J. 2012. CerealsDB 2.0: an integrated resource for plant breeders and scientists. BMC Bioinformatics 13: 219.
Winfield, M.O., Wilkinson, P.A., Allen, A.M., Barker, G.L.A., Coghill, J.A., Burridge, A., Hall, A., Brenchley, R.C., D'Amore, R., Hall, N., Bevan, M.W., Todd, R., Gerhardt, D.J., Jeddeloh, J.A. and Edwards, K.J. 2012. Targeted re-sequencing of the allohexaploid wheat exome. Plant Biotechnology Journal 10(6): 733-742.

2011

Allen, A.M, Barker, G.L.A., Berry, S.T., Coghill, J.A., Gwilliam, R., Kirby, S., Robinson, P., Brenchley, R.C., D'Amore, R., McKenzie, N., Hall, A., Bevan, M., Hall, N. and Edwards, K.J. 2011. Transcript-specific, single-nucleotide polymorphism discovery and linkage analysis in hexaploid bread wheat (Triticum aestivum L.). Plant Biotechnology Journal 9(9): 1086-1099.
Grierson, C.S., Barnes, S. R., Chase, M.W., Clarke, M., Grierson, D., Edwards, K.J., Jellis, G.J., Jones, J.D., Knapp, S., Oldroyd, G., Poppy, G., Temple, P., Williams, R. and Bastow, R. 2011. One hundred important questions facing plant science research. New Phytologist 192(1): 6-12.
Hegarty, M.J., Batstone, T.E., Barker, G.L.A., Edwards, K.J., Abbott, R.J. and Hiscock, S.J. 2011. Nonadditive changes to cytosine methylation as a consequence of hybridization and genome duplication in Senecio. Molecular Ecology 20(1): 105-113.

2010
Pethica, R., Barker, G., Kovacs, T. and Gough, J. 2010. TreeVector: Scalable, Interactive, Phylogenetic Trees for the Web. PLoS ONE 5(1): e8934.
Postel, U., Thompson, F., Barker, G., Viney, M and Morris, S. 2010. Migration-related changes in gene expression in leg muscle of the Christmas Island red crab Gecarcoidea natalis: seasonal preparation for long-distance walking. Journal of Experimental Biology 213: 1740-1750
Winfield, M.O., Lu, C., Wilson, I.D., Coghill, J.A. and Edwards, K.J. 2010. Plant responses to cold: transcriptome analysis of wheat. Plant Biotechnology Journal 8: 749-771.
Zeale, M.R.K., Butlin, R.K., Barker, G., Lees, D.C. and Jones, G. 2010. Taxon-specific PCR for DNA barcoding arthropod prey in bat faeces. Molecular Ecology Resources no. doi: 10.1111/j.1755-0998.2010.02920.x
2009
Barker, G.L.A, and Edwards, K.J. 2009. A genome-wide analysis of single nucleotide polymorphism diversity in the world's major cereal crops. Plant Biotechnology Journal 7: 312-317.
Edwards, K.J., Reid, A.L. Coghill, J.A., Berry, S.T. and Barker, G.L.A 2009. Multiplex SNP-based genotyping in allohexaploid wheat using padlock probes. Plant Biotechnology Journal 7: 375-390.
S.C. Harvey, G.L.A. Barker, A. Shorto and M.E. Viney 2009 Natural variation in gene expression in the early development of dauer larvae of Caenorhabditis elegans. BMC Genomics 10: 325.
Hegarty, M.J., Barker, G.L., Brennan, A.C., Edwards, K.J., Abbott, R.J. and Hiscock, S.J. 2009. Extreme changes to gene expression associated with homoploid hybrid speciation. Molecular Ecology 18: 877-889.
Iossa, G., Soulsbury, C.D., Baker, P.J., Edwards, K.J. and Harris, S. 2009. Behavioural changes associated with a population density decline in the facultatively social red fox. Behavioural Ecology 20: 385 - 395.
Soulsbury, C.D., Iossa, G. and Edwards, K.J. 2009. The influence of evolutionary distance between cross-species microsatellites and primer base-pair composition on allelic dropout rates. Conservation Genetics 10: 797-802.
Thompson, F.J., Barker, G.L.A., Nolan, T., Gems, D and Viney, M.E. 2009. Transcript profiles of long- and short-lived adults implicate protein synthesis in evolved differences in ageing in the nematode Strongyloides ratti. Mechanisms of Ageing and Development 130: 167–172.
Wan, Y., Underwood, C., Toole, G., Skeggs, P., Zhu, T., Leverington, M., Griffiths, S., Wheeler, T., Gooding, M., Poole, R., Edwards, K.J., Gezan, S., Welham, S., Snape, J., Mills, C., Mitchell, R.A.C. and Shewry, P.R. 2009. A novel transcriptomics approach to identify candidate genes for grain quality traits in wheat. Plant Biotechnology Journal 7: 401-410.
Winfield, M.O., Lu, C., Wilson, I.D., Coghill, J.A. and Edwards, K.J. 2009. Cold- and light-induced changes in the transcriptome of wheat leading to phase transition from vegetative to reproductive growth. BMC Plant Biology 9: 55.

2008

Berghoff, S.M., Kronauer, D.J.C., Edwards, K.J. and Franks, N.R. 2008. Conservation genetics of the army ant Eciton burchellii in Panama. Journal of Evolutionary Biology 21: 1125-1132.
Edwards, A.G., Weale, A.R., Denny, J., Edwards, K.J., Helps, C., Lear, P.A. and Bailey, M. 2008. Antigen-receptor V segment usage in mucosal T-cells. Immunology 123: 181-186.
Hegarty, M.J., Barker, G.L., Brennan, A.C., Edwards, K.J., Abbott, R.J. and Hiscock, S.J. 2008. Changes in gene expression associated with hybrid speciation in plants: further insights from transcriptome studies in Senecio. Proceedings of the Royal Society B: Biological Sciences 363: 3055-3069.
King, J., Thorogood, D., Edwards, K.J., Armstead, I.P., Roberst, L., Skot, K., Hanley, Z. and King, I.P. 2008. Development of a genomic microsatellite library in perennial ryegrass (Lolium perenne L.) and its use in trait mapping. Annals of Botany 101: 845-854.
Poole, R.L., Barker, G.L.A, Werner, K., Biggi, G. Coghill, J., Gibbings, G., Berry, S., Dunwell, J.M. and Edwards, K.J. 2008. Analysis of wheat SAGE tags reveals evidence for widespread antisense transcription. BMC Genomics 9: 475.
Prioul, J.L., Mechin, V., Lessard, P., Thévenot, C., Grimmer, M., Chateau-Joubert, S., Coates, S., Hartings, H., Kloiber-Maitz, M., Murigneux, A., Sarda, X., Damerval, C. and Edwards, K.J. 2008. A joint transcriptomic, proteomic and metabolic analysis of maize endosperm development and starch filling. Plant Biotechnology Journal 6: 855-869.
Stramer, B., Winfield, M., Shaw, T., Woolner, S. and Martin, P. 2008. Gene induction following wounding of wild-type versus macrophage-deficient Drosophila embryos. EMBO reports 9: 465-471.
Fiona J. Thompson, Gary L.A. Barker, Louise Hughes, Mark E. Viney. 2008. Genes important in the parasitic life of the nematode Strongyloides ratti. Molecular and Biochemical parasitology. 158:112-119.
Wan, Y., Poole, R.L., Huttly, A.K., Toscano-Underwood, C., Feeney, K., Welham, S., Gooding, M.J., Mills, E.N.C., Edwards, K.J., Shewry, P.R. and Mitchell, R.A.C. 2008. Transcriptome analysis of grain development in hexaploid wheat. BMC Genomics 9: 121.

2007

Donnison, I.S., Gay, A.P., Thomas, H., Edwards, K.J., Edwards, D., James, C.L., Thomas, A.M. and Ougham, H.J. 2007. Modification of nitrogen remobilization, grain fill and leaf senescence in maize (Zea mays) by transposon insertional mutagenesis in a protease gene. New Phytologist 173: 481-494.
Poole, R., Barker, B., Wilson, I. D, Coghill J.A., and Edwards, K.J. 2007. Measuring global gene expression in polyploidy; a cautionary note from allohexaploid wheat. Functional and Integrative Genomics 7: 207-219.
Soulsbury, S.D., Iossa, G., Edwards, K.J., Baker, P.J. and Harris, S. 2007. Allelic dropout from a high-quality DNA source. Conservation Genetic 8: 733-738.

2006

Baudo, M.M., Lyons, R., Powers, S., Pastori, G.M., Edwards, K.J., Holdsworth, M.J. and Shewry, P.R. 2006. Transgenesis has less impact on the transcriptome of wheat grain than conventional breeding. Plant Biotechnology Journal 4: 369-380.
Goto-Yamamoto, N., Mouri,H., Azumi, M and Edwards, K.J. 2006. Development of Grape Microsatellite Markers and Microsatellite Analysis Including Oriental Cultivars. Am. J. Enol. Vitic 57: 105-108.
Hegarty, M.J., Barker, G.L., Wilson, I.D., Abbott, R.J., Edwards, K.J. and Hiscock, S.J. 2006. Transcriptome shock following interspecific hybridisation in Senecio is ameliorated by genome duplication. Current Biology 16: 1652-1659.
Kan, Y., Wan, Y., Mitchel, R.A.C., Beaudoin, F., Leader, D., Edwards, K.J., Poole, R.L., Wang, D. and Shewry, P.R.. 2006. Transcriptome Analysis Reveals Novel Storage Protein Transcripts in Seeds of Aegilops and Wheat. Journal of Cereal Science 44: 75-85.
Daniel J. C. Kronauer, D.J.C., Berghoff, S.M., Powell, S., Denny, A.J., Edwards, K.J., Franks, N.J. and Boomsma, J.J. 2006. A reassessment of the mating system characteristics of the army ant Eciton burchellii. Naturwssenschaften 93: 402-406.
Martin, A., Lee, J., Kichey, T., Gerentes, D., Zivy, M., Tatout, C., Dubois, F., Balliau, T., Valot, B., Davanture, M., Terce-Laforgue, T., Quillere, I., Coque, M., Gallais, A., Gonzalez-Moro, M.B., Bethencourt, Habash, D.Z., Lea, P.J., Charcosset, A., Perez, P., Murigneux, A., Sakakibara, H., Edwards, K.J. and Hirel, B. 2006. Two cytosolic glutamine synthetase isoforms of maize are specifically involved in the control of grain production. Plant Cell 8: 3252-3274.
Philippar, K., Büchsenschütz, K., Edwards, D., Löffler, J., Lüthen, L., Kranz, E., Edwards K.J. and Hedrich, R. 2006. The auxin-induced K+ channel gene ZmK1 in maize functions in coleoptile growth and is required for embryo development. Plant Molecular Biology 61: 757-768.
Lavinia Robba, Stephen J. Russell, Gary L. Barker and Juliet Brodie 2006. Assessing the use of the mitochondrial cox1 marker for use in DNA barcoding of red algae (Rhodophyta). Am. J. Bot. 93: 1101-1108.
Sethy, N.K., Shokeen, B., Edwards, K.J. and Bhatia, S. 2006. Development of microsatellite markers and analysis of intraspecific genetic variability in chickpea (Cicer arietinum L.). Theoretical and Applied Genetics 112: 1416-1428.

2005

Donnison, I.S., O’Sullivan, D.M., Thomas, A., Canter, P., Moore, B., Armstead, I., Thomas, H., Edwards, K.J. and King, I.P. 2005. Construction of a Festuca pratensis BAC library for map based cloning in Festulolium substition lines. Theoretical and Applied Genetics 110: 846-851.
Hansen, O.K., Vendramin, G.G., Sebastiani, F. and Edwards, K.J. 2005. Development of microsatellite markers in Abies nordmanniana (Stev.) Spach and cross-species amplification in the Abies genus. Molecular Ecology Primer Notes 5: 784-787.
Hegarty, M., Jones, J., Wilson, I.D., Barker, G., Coghill, J., Sanchez-Baracaldo, P., Liu, G., Buggs, R.J.A., Abbott, R., Edwards, K.J. and Hiscock, S. 2005. Development of anonymous cDNA microarrays to study changes to the Senecio floral transcriptome during hybrid speciation. Molecular Ecology 14: 2493-2510.
Lu, C., Hawkesford, M., Barraclough, P., Poulton, P., Wilson, I.D., Barker, G. and Edwards, K.J., 2005. Markedly different gene expression in wheat grown with organic or inorganic fertilizer. Proceedings of the Royal Society B: Biological Sciences 272: 1901-1908.
Sprunck, S., Baumann, U., Edwards, K.J., Langridge, P. and Dresselhaus, T. 2005. The Transcript composition of egg cells changes significantly following fertilization in wheat (Triticum. aestivum L.). The Plant Journal. 41: 660-672.
Wilson, I.D., Barker, G.L.A., Lu, C., Coghill, J.A., Beswick, R.W., Lenton, J.R. and Edwards, K.J. 2005. Alteration of the embryo transcriptome of hexaploid winter wheat (Triticum aestivum cv. Mercia) during maturation and germination. Functional and Integrative Genomics 5: 144-154.