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Dr James Cockram

Dr James CockramGroup Leader

T: +44 1223 342419
E: James Cockram

Research Interests

Application of plant molecular genetics, genomics, comparative genomics and statistical techniques (association mapping, genomic selection, MAGIC populations) to investigate the genetic control of morphological, disease resistance, flowering time and domestication traits in cereal crops, with particular focus on wheat and barley. Development of diagnostic genetic markers for disease, agronomic and statutory requirements in crops.

Funded Grants

1.     BBSRC-DBT Crop Genomics and Technologies call: A genomics-assisted synthetic hexaploid wheat gene isolation and pre-breeding platform for improved heat tolerance and sustainable production. Short name: SWHheat. Duration: 2014-2017. Partners: NIAB, Punjab Agricultural University, National Agri-Food Biotechnology Institute (NABI). See: www.shwheat.org.
2.     BBSRC-LINK: MAGIC Yield: deploying MAGIC populations for rapid development of genetic markers for yield improvement in elite UK winter wheat. Short name: MAGIC Yield. Duration: 2015-2018. Partners: NIAB, Bayer AG, Elsoms Wheat Ltd, KWS UK Ltd, Limagrain UK Ltd, RAGT Seeds Ltd.
3.     FSOV: Wheat effector assisted breeding for resistance to fungal pathogens. Short name: WEAB. Duration: 2014-2018. Partners: NIAB, INRA-BIOGER/GDEC/BGPI, ACNFP, ARVALIS, PRI, Biogemma, Florimund Deprez, RAGT 2n, CETAC.
4.     BBSRC-BBR: The wheat Diverse MAGIC platform: Community Access to Resources, Protocols and Tools. Short name: MAGIC CARPET. Duration: October 2015 – September 2018. Partners: NIAB, Oxford University.
5.     ERA-CAPS: An Effector- and Genomics-Assisted Pipeline for Necrotrophic Pathogen Resistance Breeding in Wheat Short name: EfectaWheat. Duration: October 2015 – September 2018. Partners: NIAB, Aarhus University, Norwegian university of Life Sciences, LfL, Curtin University.

Group members

Benedetta Saccomanno, Research Technician
Nick Fradgley, Research Technician
Dr Huw Jones, Senior Researcher
Laura Bouvet, BBSRC DTP PhD student
Rowena Downie, BBSRC DTP PhD student
Aurelie Jouanin, MAX-CROP PhD student

Positions available

Post-Doc position on genetics of wheat disease resistance, as part of a multi-partner project funded via the ERA-CAPs scheme. Closing data 12th Feb 2016.

DTP rotation projects 2015

Web-resources

NIAB Marker Assisted Selection (MAS)

Additional

Fellow of the McDonald Institute, Cambridge University, Cambridge, UK

Recent publications

Cockram J, Scuderi A, Barber T, Furuki E, Gardner KA, Gosman N, Kowalczyk R, Phan HP, Rose GA, Tan K-C, Oliver RP, Mackay IJ (2015) Fine-mapping the wheat Snn1 locus conferring sensitivity to the Parastagonospora nodorum necrotrophic effector SnTox1 using an eight founder multi-parent advanced generation intercross population. G3: Genes Genomes Genet, 5: 2257-66.

Bentley AR, Horsnell R, Howell P, Gosman N, Howells R, Rose G, Barber T, Cockram J, Greenland A, Mackay I (2015) Optimising wheat flowering time for a changing climate. Aspects of Applied Biology, 124: 23-30.

Stratula O, Cockram J, Kalendar R 2014. Molecular genetic analysis of cereal b-amylase genes using exon-primed inter-crossing (EPIC) PCR. Field and Vegetable Crops Research, 51: 175-189.

Cockram J, Soh E-H, Norris C, O’Sullivan D (2015) Molecular and phenotypic characterization of the alternative seasonal growth habit and flowering time in barley (Hordeum vulgare L.). Molec Breed, 35: 1-11.

Muterko A, Balashova I, Cockram J, Kalendar R, Sivolap Y (2015) The New Wheat Vernalization Response Allele Vrn-D1s is Caused by DNA Transposon Insertion in the First Intron. Plant Molecular Biology Reporter 33: 294-303

Murketo A, Kalendar R, Cockram J, Balashova I (2015) Discovery, evaluation and distribution of haplotypes and new alleles of the Photoperiod-A1 gene in wheat. Plant Mol Biol, 88: 149-164.

Joanin A, Cockram J, et al. Development of wheat varieties with reduced contents of coeliac-immunogenic epitopes through conventional and GM strategies. Proc 28th Meeting Working Group on Prolamin Analysis and Toxicity (PWG). Ed Peter Koehler. 25-27th September, 2015, Nantes, France.

Kole C, Muthamilarasan M, Henry R, Edwards D, Sharma R, Abberton M, Batley J, Bentley A, Blakeney M, Bryant J, Cai H, Cakir M, Cseke LJ, Cockram J, et al. (2015) Application of genomics for generation of climate resilient crops: Progress and prospects. Frontiers in Plant Science 6: 563.

Bentley AR, Hori K, Yano M, Greenland A, Cockram J (2014) Flowering time. pp 59-62. In ‘Application of Genomics to the Production of Climate Resilient Crops: Challenges and opportunities’. International Climate Resilient Crops Genomics Consortium (ICRCGC) White Paper. D. Edwards, R. Henry, C. Kole (eds.). Available for download at http://www.climatechangegenomics.org/.

Bentley AR, Horsnell R, Howell P, Gosman N, Howells R, Rose G, Barber T, Cockram J, Greenland A, Mackay IJ (2014) Optimising wheat flowering time for a changing climate. Aspects of Applied Biology in press.

Bentley AR, Scutari M, Gosman N, Faure S, Bedford F, Howell P, Cockram J, Rose GA, Barber T, Irigoyen J, Horsnell R, Pumfrey C, Winnie E, Schacht J, Beauchêne K, Praud S, Greenland A, Balding D, Mackay IJ (2014) Applying association mapping and genomic selection to the dissection of key traits in elite European wheat. Theoretical and Applied Genetics 127: 2619-2633.

Mackay I, Bansept-Basler P, Barber T, Bentley AR, Cockram J, Elderfield J, Gosman N, GreenlandAJ, Horsnell R, Howells R, O’Sullivan DM, Rose GA, Howell P (2014). An eight-parent multiparent advanced generation intercross population for winter-sown wheat: creation, properties and validation. G3: Genes Genomes Genetics, 4: 1603-1610.

Yahia Y, Hannachi H, Monoforte AJ, Cockram J, Loumerem M, Zarouri B, Ferchini A (2014). Genetic diversity in Vicia faba L. Populations cultivated in tunisia revealed by simple sequence repeat analysis. Plant Genet Res, e-pub ahead of print.

Lister DL, Jones H, Jones MK, O'Sullivan DM, Cockram J (2013). Analysis of DNA polymorphism in ancient barley herbarium material: validation of the KASP SNP genotyping platform. Taxon 62(4): 779-789.

Bentley AR, Jensen EF, Mackay IJ, HönickaH. FladungM, Hori K, Yano M, Mullet JE, Armstead IP, Hayes C, ThorogoodD, Lovatt A, Morris R, Pullen N,Mutasa-Göttgens E, Cockram J (2013). Flowering time. In: Genomics and Breeding for Climate-Resilient Crops, Vol2 (Ed: C Cole), pp1-67. Springer-Verlag Berline Heidelberg.

Jones H, Norris C, Cockram J, Lee D (2013). Variety Protection and Plant Breeders’ Rights in the ‘DNA era’. In: Diagnostics in plant breeding (Eds T Lübberstedt & RK Varshney), Springer, Netherlands, pp396-402.

Jones H, Norris C, Smith D, Cockram J, Lee D, O’Sullivan DM, Mackay I (2013). Evaluation of the use of high density SNP genotyping to implement UPOV Model 2 for DUS testing in barley. Theor Appl Genet, Epub ahead of print.

Cockram J, Jones H, Norris C, O’Sullivan DM (2012). Evaluation of diagnostic molecular markers for DUS phenotypic assessment in the cereal crop, barley (Hordeum vulgare ssp. vulgare L.). Theor Appl Genet,125: 1735-1749. doi: 10.1007/s00122-012-1950-3

Cockram J, Thiel T, Steuernagel B, Stein N, Taudien S, Bailey PC, O’Sullivan DM (2012). Genome dynamics explain the evolution of flowering time CCT domain gene families in the Poaceae. PLoS1,7:e45307.

Cockram J, Hill C, Burns C, Arroo RRJ, Wooley JG, Flockart I, Robinson T, Atkinson CJ, Davies, MJ, Dungey N, Greenland AJ, Smith LLMJ, Bentley S (2012). Screening a diverse collection of Artemisia annua germplasm for accessions with elevated levels of the anti-malarial compound, artemisinin. Plant Genet Res,10: 152-154.

Jones, H., Civan, P., Cockram, J., Leigh, F.J., Smith, L.M.J., Jones, M.K., Charles, M.P., Molina-Cano, J.-L., Powell, W., Jones, G., Brown, T.A. (2011) Evolutionary history of barley cultivation in Europe revealed by genetic analysis of extant landraces. BMC Evolutionary Biology, 11: 320.

Mameaux S*, Cockram J*, Thiel T, Steuernagel B, Stein N, Taudien S, Jack P, Werner P, Gray JC, Greenland AJ, Powell W. Molecular, phylogenetic and comparative genomic analysis of the cytokinin oxidase/dehydrogenase gene family in the Poaceae (2011). Plant Biotechnology Journal: DOI: 10.1111/j.1467-7652.2011.00645.x * joint first authors.

Cockram, J., Jones, H., O’Sullivan, D.M. Genetic variation at flowering time loci in wild and cultivated barley (2011). Plant Genetic Resources: characterization and utilization, 9: 264-267.

Cockram, J., White, J., Zuluaga, D.L., Smith, D., Comadran, j. et al (2010). Genome-wide association mapping to candidate polymorphism resolution in the un-sequenced barley genome. Proc. Natl. Acad. Sci. U.S.A., 107, 21611-21616.

Waugh R, Marshall D, Thomas B, Comadran J, Russell J, Close T, Stein N, Hayes P, Muehlbauer G, Cockram J, O'Sullivan D, Mackay I, Flavell A, Agoueb A, Barleycap , Ramsay L. (2010) Whole-genome association mapping in elite inbred crop varieties. Genome, 53: 967-972.

Cockram, J.
, Howells, R.M., O'Sullivan, D.M. Segmental chromosomal duplications harbouring group IV CONSTANS-like genes in cereals. Genome, accepted.

Cockram, J
., Norris, C., O’Sullivan, D.M. (2009) PCR markers diagnostic for seasonal growth habit in barley. Crop Science 49: 403-410.

Cockram, J., White, J., Leigh, F.J., Lea, V.J., Chiapparino, E., Laurie, D.A., Mackay, I.J., Powell, W., O’Sullivan, D.M. (2008) Association mapping of partitioning loci in barley (Hordeum vulgare ssp. vulgare L.). BMC Genetics, 9:16.

Cockram J, Jones H, Leigh F, White J, Mackay IJ, Powell W, O’Sullivan DM (2008) Proceedings of the 10th International Barley Genetics Symposium, 5-10 April 2008, Alexandria, Egypt, pp94-104.

Cockram, J., Mackay, I.J., O’Sullivan, D.M. (2007a) The role of double-stranded break repair in the creation of phenotypic diversity at cereal VRN1 loci. Genetics 177:1-5

Cockram, J., Chiapparino, E., Taylor, S.A., Stamati, K., Donini, P., Laurie, D.A. O'Sullivan, D.M. (2007b) Haplotype analysis of vernalization loci in European barley germplasm reveals novel VRN-H1 alleles and a predominant winter VRN-H1/VRN-H2 multi-locus haplotype. Theoretical and Applied Genetics115: 993-1001

Cockram, J., Jones, H., Leigh, F.J., O’Sullivan, D., Powell, W., Laurie, D.A., Greenland, A.J. (2007c) Control of flowering time in temperate cereals: genes, domestication and sustainable productivity. J Exp Bot 58:1231-1244