UCD Research: Agriculture & Food Science

People

Dr David Magee B.A., Ph.D.

Contact Details

Title	Post-Doctoral Researcher
Address	School of Agriculture, Food Science & Veterinary Medicine 223 Veterinary Sciences Centre Univeristy College Dublin Belfield Dublin 4
Telephone:	+353-1-7166228
Email:	ei.dcu@eegam.divad

Title	Post Doctoral Researcher Level Ii
Address	School of Agriculture & Food Science Agriculture and Food Science Belfield Dublin 4
Email:	ei.dcu@eegaM.divaD

Biography:

Qualifications and Work experience:
1994 - 1998: B.A. (Hons) moderatorship in Science (specialising in genetics), Trinity College Dublin.
1998 - 2002: PhD in Population Genetics, Smurfit Institute of Genetics, Trinity College Dublin.
Feb 2002 - June 2002: Researcher, Victorian Institute of Animal Science, Melbourne, Australia.
July 2003 - Oct 2003: Contractual lecturer in Human Genetics, Deakin University, Melbourne, Australia.
May 2004 - Oct 2004: Post-doctoral researcher (6 month contract), Dept. of Biochemistry, Trinity College Dublin.
Nov 2004 - March 2007: Senior R&D Scientist, Biotrin International, Dublin.
Apr 2007 - Present: Post-doctoral researcher, Animal Genomics Group, UCD.
Jun 2011 - Post-graduate diploma in statistics (Department of statistics, Trinity College Dublin)
Jul 2012 - Bioinformatics for transcriptomics module (University of Manchester)

Research Interests

1) Development of high-throughput genetic markers for beef traits using variation in genes subject to genomic imprinting. Genomic imprinting, a form of epigenetic regulation, affects over 100 mammalian genes and results in the expression of those genes from only one of the two parentally-inherited chromosomes. Studies have shown that imprinted genes play a crucial role in the growth and development of the mammalian foetus and they have also been implicated in regulating maternal behaviour during pregnancy. This project will use the knowledgebase of imprinted genes available for humans and mice to identify candidate genes that are also imprinted in cattle. Genomic imprinting patterns for these genes will be investigated across different breeds and individuals, and their physiological roles with regard to growth and development in domestic cattle will be defined. A selected subset of these bovine imprinted genes will then be examined using DNA samples from a control non-beef population and DNA samples collected from animals representing two breeds of beef cattle (Charolais and Limousin), that have been performance-tested at the National Bull Performance Test Centre. Computational analyses will define unique alleles (haplotypes) for these genes and economically-relevant polymorphisms (ERPs) will be identified using quantitative genetic analyses in conjunction with performance data for growth, carcass and meat quality traits.

2) Studies of molecular genetic diversity in Old and New World Cattle. This work involves the use of genetic markers [e.g. mitochondrial DNA sequence data, variable autosomal genetic markers such as single nucleotide polymorphisms (SNPs) and microsatellites, and Y chromosome haplotypes] to study the demographic history and origins of domestic cattle from the Near East, Africa, Asia and the Americas. Most of this work was carried out when I was a postgraduate researcher in the Molecular Population Genetics Laboratory at Trinity College; however, I am continuing some of this work at UCD.

3) Functional genomic investigations of the bovine host response to mycobacterial infection. This project involves the use of pan-genomic microarrays and RNA-sequencing (RNA-seq) technologies to investigate gene expression profiles in response to mycobacterial infection . Additional studies include the use of quantitative real-time reverse transcriptase polymerase chain reaction (qRT-PCR) to validate differentially expressed genes identified from microarray and RNA-seq studies. Results from these studies will shed light on mechanisms governing the immune response to bovine tuberculosis and Johne's disease. In addition, these studies are revealing genes and gene products that may form the basis of new tools for BTB diagnosis

Book Chapters

Magee DA, Mannen H, Bradley DG.; (2007) 'Duality in Bos indicus mtDNA diversity: Support for geographical complexity in zebu domestication' In: The Evolution and History of Human Populations in South Asia. Netherlands: Springer.

[DOI] [Details]

Bradley DG and Magee DA.; (2006) 'Genetics and Cattle Domestication' In: Documenting Domestication: New Genetic and Archaeological Paradigms. Berkeley, California, USA: University of California Press. [Details]

Peer Reviewed Journals

Mullen, M. P., Creevey, C. J., Berry, D. P., McCabe, M. S., Magee, D. A., Howard, D. J., Killeen, A. P., Park, S. D., McGettigan, P. A., Lucy, M. C., Machugh, D. E., Waters, S. M. (2012) 'Polymorphism discovery and allele frequency estimation using high-throughput DNA sequencing of target-enriched pooled DNA samples'. BMC Genomics, 13 .

[Details]

Sikora KM, Magee DA, Berkowicz EW, Lonergan P, Evans AC, Carter F, Comte A, Waters SM, Machugh DE, Spillane C (2012) 'PHLDA2 is an imprinted gene in cattle'. Animal Genetics, 43 (5):587-590. [DOI] [Details]

Machugh DE, Taraktsoglou M, Killick KE, Nalpas NC, Browne JA, Park SD, Hokamp K, Gormley E, Magee DA (2012) 'Pan-genomic analysis of bovine monocyte-derived macrophage gene expression in response to in vitro infection with Mycobacterium avium subspecies paratuberculosis'. Veterinary Research, 43 (1). [DOI] [Details]

Magee DA, Taraktsoglou M, Killick KE, Nalpas NC, Browne JA, Park SD, Conlon KM, Lynn DJ, Hokamp K, Gordon SV, Gormley E, MacHugh DE (2012) 'Global gene expression and systems biology analysis of bovine monocyte-derived macrophages in response to in vitro challenge with Mycobacterium bovis'. PLoS ONE, 7 (2). [DOI] [Details]

Berkowicz EW, Magee DA, Berry DP, Sikora KM, Howard DJ, Mullen MP, Evans RD, Spillane C, MacHugh DE (2012) 'Single nucleotide polymorphisms in the imprinted bovine insulin-like growth factor 2 receptor gene (IGF2R) are associated with body size traits in Irish Holstein-Friesian cattle'. Animal Genetics, 43 (1):81-87. [DOI] [Details]

Sikora K.M., Magee D.A., Berkowicz E.W., Berry D.P., Howard D.J., Mullen M.P., Evans R.D., Machugh D.E., Spillane C.; (2011) 'DNA sequence polymorphisms within the bovine guanine nucleotide-binding protein Gs subunit alpha (Gsα)-encoding (GNAS) genomic imprinting domain are associated with performance traits'. BMC Genetics, 12 . [DOI] [Details]
Killick KE, Browne JA, Park SD, Magee DA, Martin I, Meade KG, Gordon SV, Gormley E, O'Farrelly C, Hokamp K, MacHugh DE (2011) 'Genome-wide transcriptional profiling of peripheral blood leukocytes from cattle infected with Mycobacterium bovis reveals suppression of host immune genes'. BMC Genomics, 12 . [DOI] [Details]
Berkowicz EW, Magee DA, Sikora KM, Berry DP, Howard DJ, Mullen MP, Evans RD, Spillane C, MacHugh DE (2011) 'Single nucleotide polymorphisms at the imprinted bovine insulin-like growth factor 2 (IGF2) locus are associated with dairy performance in Irish Holstein-Friesian cattle'. Journal of Dairy Research, 78 (1):1-8. [DOI] [Details]
Taraktsoglou M, Szalabska U, Magee DA, Browne JA, Sweeney T, Gormley E, MacHugh DE. (2011) 'Transcriptional profiling of immune genes in bovine monocyte-derived macrophages exposed to bacterial antigens'. Veterinary Immunology and Immunopathology, 140 (1-2):130-139. [Details]
Mullen MP, Berry DP, Howard DJ, Diskin MG, Lynch CO, Giblin L, Kenny DA, Magee DA, Meade KG, Waters SM (2011) 'Single Nucleotide Polymorphisms in the Insulin-Like Growth Factor 1 (IGF-1) Gene are Associated with Performance in Holstein-Friesian Dairy Cattle'. Frontiers, 2 . [DOI] [Details]
Beecher C, Daly M, Childs S, Berry DP, Magee DA, McCarthy TV, Giblin L (2010) 'Polymorphisms in bovine immune genes and their associations with somatic cell count and milk production in dairy cattle'. BMC Genetics, 11 . [DOI] [Details]
Chen S, Lin BZ, Baig M, Mitra B, Lopes RJ, Santos AM, Magee DA, Azevedo M, Tarroso P, Sasazaki S, Ostrowski S, Mahgoub O, Chaudhuri TK, Zhang YP, Costa V, Royo LJ, Goyache F, Luikart G, Boivin N, Fuller DQ, Mannen H, Bradley DG, Beja-Pereira A. (2010) 'Zebu cattle are an exclusive legacy of the South Asia neolithic'. Molecular Biology and Evolution, 27 (1):1-6. [Details]
Magee DA, Park SD, Scraggs E, Murphy AM, Doherty ML, Kijas JW, MacHugh DE (2010) 'Technical note: High fidelity of whole-genome amplified sheep (Ovis aries) deoxyribonucleic acid using a high-density single nucleotide polymorphism array-based genotyping platform'. Journal of animal science, 88 (10):3183-3186. [DOI] [Details]
Magee DA, Sikora KM, Berkowicz EW, Berry DP, Howard DJ, Mullen MP, Evans RD, Spillane C, MacHugh DE (2010) 'DNA sequence polymorphisms in a panel of eight candidate bovine imprinted genes and their association with performance traits in Irish Holstein-Friesian cattle'. BMC Genetics, 11 . [DOI] [Details]
Mullen MP, Berry DP, Howard DJ, Diskin MG, Lynch CO, Berkowicz EW, Magee DA, MacHugh DE, Waters SM (2010) 'Associations between novel single nucleotide polymorphisms in the Bos taurus growth hormone gene and performance traits in Holstein-Friesian dairy cattle'. Journal of dairy science, 93 (12):5959-5969. [DOI] [Details]
Magee, D. A.,Berkowicz, E. W.,Sikora, K. M.,Sweeney, T.,Kenny, D. A.,Kelly, A. K.,Evans, R. D.,Wickham, B. W.,Bradley, D. G.,Spillane, C.,MacHugh, D. E.; (2010) 'High concordance of bovine single nucleotide polymorphism genotypes generated using two independent genotyping strategies'. Animal biotechnology, 21 (44):257-62257. [Details]
Edwards, C. J.Edwards, C. J.,Magee, D. A.Magee, D. A.,Park, S. D.Park, S. D.,McGettigan, P. A.McGettigan, P. A.,Lohan, A. J.Lohan, A. J.,Murphy, A.Murphy, A.,Finlay, E. K.Finlay, E. K.,Shapiro, B.Shapiro, B.,Chamberlain, A. T.Chamberlain, A. T.,Richards, M. B.Richards, M. B.,Bradley, D. G.Bradley, D. G.,Loftus, B. J.Loftus, B. J.,Machugh, D. E.Machugh, D. E.; (2010) 'A complete mitochondrial genome sequence from a mesolithic wild aurochs (Bos primigenius)'. PLoS ONE, 5 (22). [Details]
Magee, D.A., Berry, D.P., Berkowicz, E.W., Sikora, K.M., Howard, D.J., Mullen, M.P., Evans, R.D., Spillane, C., Machugh, D.E.; (2010) 'Single nucleotide polymorphisms within the bovine DLK1-DIO3 imprinted domain are associated with economically important production traits in cattle'. J Hered, . [Details]
Magee DA, Berkowicz EW, Sikora KM, Berry DP, Park SD, Kelly AK, Sweeney T, Kenny DA, Evans RD, Wickham BW, Spillane C, Machugh DE (2010) 'A catalogue of validated single nucleotide polymorphisms in bovine orthologs of mammalian imprinted genes and associations with beef production traits'. Animal, 4 (12):1958-1970. [DOI] [Details]
Waters, S.M., McCabe, M.S., Howard, D.J., Giblin, L., Magee, D.A., Machugh, D.E., Berry, D.P.; (2010) 'Associations between newly discovered polymorphisms in the Bos taurus growth hormone receptor gene and performance traits in Holstein-Friesian dairy cattle'. Animal Genetics, . [Details]
Magee DA, Meghen C, Harrison S, Troy CS, Cymbron T, Gaillard C, Morrow A, Maillard JC, Bradley DG (2002) 'A partial african ancestry for the creole cattle populations of the Caribbean'. JOURNAL OF HEREDITY, 93 (6):429-432. [Details]
Troy, CS, MacHugh, DE, Bailey, JF, Magee, DA, Loftus, RT, Cunningham, P, Chamberlain, AT, Sykes, BC, Bradley, DG, ; (2001) 'Genetic evidence for Near-Eastern origins of European cattle'. Nature, 410 (6832):1088-1091. [Details]
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Conference Publications

Killick KE, Magee DA, Taraktsoglou M, Park SDE et al (2011) Systems biology analyses of the bovine macrophage response to Mycobacterium bovis infection identifies the NF-κB complex as a key regulatory network hub 4th International Symposium on Animal Functional Genomics, Dublin, Ireland [Details]

Nalpas NC, Park SDE, Magee DA, Taraktsoglou M et al (2011) Whole-transcriptome high-throughput RNA sequence analysis of the bovine macrophage response to Mycobacterium bovis challenge in vitro 4th International Symposium on Animal Functional Genomics, Dublin, Ireland [Details]

Park SDE, Magee DA, McGettigan PA, Teasdale M, et al. (2011) A complete nuclear genome sequence from the extinct Eurasian wild aurochs (Bos primigenius) 4th International Symposium on Animal Functional Genomics, Dublin, Ireland [Details]

Edwards CJ, Magee DA, Park SDE, McGettigan PA et al (2009) A complete mitochondrial genome sequence from the extinct wild aurochs (Bos primigenius) Bovine Genome Consortium meeting, Cold Spring Harbour, New York, USA [Details]

Magee DA; (2000) Mitochondrial DNA diversity and possible dual origins for BOS INDICUS Proceedings of the 27th International Conference on Animal Genetics, Minneapolis, USA, 2000 [Details]

Dissertations/Theses

Magee DA; (2002) Molecular genetic investigations of the diversity and origins of Old and New World cattle populations . Trinity College Dublin, Ireland: Dissertations/Theses [Details]