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Otago Medical School staff profiles

Dr John McCallum

PositionSenior Lecturer
DepartmentDepartment of Biochemistry
Research summaryPlant physiology and genetics

Research

My research focuses on the physiology and genetics of crops, especially adaptation and quality traits.

My primary role is leader of the Applied Genetics Programme in kiwifruit breeding at Plant and Food Research, managing genetics and genomics projects aimed at discovery and raising genetic gains in this large, complex breeding programme.

I have a special interest inpromoting modern data science practices to enable integrative genetic studies with large modern data sets.

Publications

Khosa, J., Lee, R., Joshi, S., Shaw, M., McCallum, J., & Macknight, R. (2018). A guide for the cultivation of onion under controlled environment conditions. HortScience, 53(12), 1746-1749. doi: 10.21273/HORTSCI13515-18

Khosa, J. S., Lee, R., Bräuning, S., Lord, J., Pither-Joyce, M., McCallum, J., & Macknight, R. C. (2016). Doubled haploid 'CUDH2107' as a reference for bulb onion (Allium cepa L.) research: Development of a transcriptome catalogue and identification of transcripts associated with male fertility. PLoS ONE, 11(11), e0166568. doi: 10.1371/journal.pone.0166568

Galla, S. J., Buckley, T. R., Elshire, R., Hale, M. L., Knapp, M., McCallum, J., … Wilcox, P., & Steeves, T. E. (2016). Building strong relationships between conservation genetics and primary industry leads to mutually beneficial genomic advances. Molecular Ecology, 25(21), 5267-5281. doi: 10.1111/mec.13837

Schwinn, K. E., Ngo, H., Kenel, F., Brummell, D. A., Albert, N. W., McCallum, J. A., … Davies, K. M. (2016). The onion (Allium cepa L.) R2R3-MYB gene MYB1 regulates anthocyanin biosynthesis. Frontiers in Plant Science, 7, 1865. doi: 10.3389/fpls.2016.01865

Marshall, C. W., Chagné, D., Deusch, O., Gruenheit, N., McCallum, J., Bergin, D., … Wilcox, P. L. (2015). A DNA-based diagnostic for differentiating among New Zealand endemic Podocarpus. Tree Genetics & Genomes, 11, 69. doi: 10.1007/s11295-015-0888-4

Journal - Research Article

Khosa, J., Lee, R., Joshi, S., Shaw, M., McCallum, J., & Macknight, R. (2018). A guide for the cultivation of onion under controlled environment conditions. HortScience, 53(12), 1746-1749. doi: 10.21273/HORTSCI13515-18

Khosa, J. S., Lee, R., Bräuning, S., Lord, J., Pither-Joyce, M., McCallum, J., & Macknight, R. C. (2016). Doubled haploid 'CUDH2107' as a reference for bulb onion (Allium cepa L.) research: Development of a transcriptome catalogue and identification of transcripts associated with male fertility. PLoS ONE, 11(11), e0166568. doi: 10.1371/journal.pone.0166568

Schwinn, K. E., Ngo, H., Kenel, F., Brummell, D. A., Albert, N. W., McCallum, J. A., … Davies, K. M. (2016). The onion (Allium cepa L.) R2R3-MYB gene MYB1 regulates anthocyanin biosynthesis. Frontiers in Plant Science, 7, 1865. doi: 10.3389/fpls.2016.01865

Galla, S. J., Buckley, T. R., Elshire, R., Hale, M. L., Knapp, M., McCallum, J., … Wilcox, P., & Steeves, T. E. (2016). Building strong relationships between conservation genetics and primary industry leads to mutually beneficial genomic advances. Molecular Ecology, 25(21), 5267-5281. doi: 10.1111/mec.13837

Marshall, C. W., Chagné, D., Deusch, O., Gruenheit, N., McCallum, J., Bergin, D., … Wilcox, P. L. (2015). A DNA-based diagnostic for differentiating among New Zealand endemic Podocarpus. Tree Genetics & Genomes, 11, 69. doi: 10.1007/s11295-015-0888-4

Tsukazaki, H., Yaguchi, S., Sato, S., Hirakawa, H., Katayose, Y., Kanamori, H., … McCallum, J. A., … Wako, T. (2015). Development of transcriptome shotgun assembly-derived markers in bunching onion (Allium fistulosum). Molecular Breeding, 35, 55. doi: 10.1007/s11032-015-0265-x

Khosa, J. S., McCallum, J., Dhatt, A. S., & MacKnight, R. C. (2015). Enhancing onion breeding using molecular tools. Plant Breeding, 9-20. doi: 10.1111/pbr.12330

Baldwin, S., Revanna, R., Pither-Joyce, M., Shaw, M., Wright, K., Thomson, S., … Lee, R., Macknight, R., & McCallum, J. (2014). Genetic analyses of bolting in bulb onion (Allium cepa L.). Theoretical & Applied Genetics, 127(3), 535-547. doi: 10.1007/s00122-013-2232-4

Lee, R., Baldwin, S., Kenel, F., McCallum, J., & Macknight, R. (2013). FLOWERING LOCUS T genes control onion bulb formation and flowering. Nature Communications, 4, 2884. doi: 10.1038/ncomms3884

Revanna, R., Turnbull, M. H., Shaw, M. L., Wright, K. M., Butler, R. C., Jameson, P. E., & McCallum, J. A. (2013). Measurement of the distribution of non-structural carbohydrate composition in onion populations by a high-throughput microplate enzymatic assay. Journal of the Science of Food & Agriculture, 93(10), 2470-2477. doi: 10.1002/jsfa.6062

Masamura, N., McCallum, J., Khrustaleva, L., Kenel, F., Pither-Joyce, M., Shono, J., … Shigyo, M. (2012). Chromosomal organization and sequence diversity of genes encoding lachrymatory factor synthase in Allium cepa L. Genes Genomes Genetics, 2(6), 643-651. doi: 10.1534/g3.112.002592

Baldwin, S., Pither-Joyce, M., Wright, K., Chen, L., & McCallum, J. (2012). Development of robust genomic simple sequence repeat markers for estimation of genetic diversity within and among bulb onion (Allium cepa L.) populations. Molecular Breeding, 30(3), 1401-1411. doi: 10.1007/s11032-012-9727-6

McManus, M. T., Joshi, S., Searle, B., Pither-Joyce, M., Shaw, M., Leung, S., … McCallum, J. (2012). Genotypic variation in sulfur assimilation and metabolism of onion (Allium cepa L.) III: Characterization of sulfite reductase. Phytochemistry, 83, 34-42. doi: 10.1016/j.phytochem.2012.07.028

Baldwin, S., Revanna, R., Thomson, S., Pither-Joyce, M., Wright, K., Crowhurst, R., … Macknight, R., & McCallum, J. A. (2012). A toolkit for bulk PCR-based marker design from next-generation sequence data: Application for development of a framework linkage map in bulb onion (Allium cepa L.). BMC Genomics, 13, 637. doi: 10.1186/1471-2164-13-637

McCallum, J., Baldwin, S., Shigyo, M., Deng, Y., van Heusden, S., Pither-Joyce, M., & Kenel, F. (2012). AlliumMap: A comparative genomics resource for cultivated Allium vegetables. BMC Genomics, 13, 168. doi: 10.1186/1471-2164-13-168

McCallum, J., Thomson, S., Pither-Joyce, M., Kenel, F., Clarke, A., & Havey, M. J. (2008). Genetic diversity analysis and single-nucleotide polymorphism marker development in cultivated bulb onion based on expressed sequence tag—simple sequence repeat markers. Journal of the American Society for Horticultural Science, 133(6), 810-818.

McCallum, J., Clarke, A., Pither-Joyce, M., Shaw, M., Butler, R., Brash, D., … Havey, M. J. (2006). Genetic mapping of a major gene affecting onion bulb fructan content. Theoretical & Applied Genetics, 112(5), 958-967. doi: 10.1007/s00122-005-0199-5

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