Dr Nanette Christie



Postdoctoral Fellow

Department

Biochemistry, Genetics and Microbiology
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I am a senior postdoctoral researcher involved with different projects related to molecular breeding, statistical genomics and systems genetics. My prime interest lies in Pine genomics, which was fueled by the opportunity I had to play a critical part in the development of a SNP array for tropical pines. Ultimately, I would like to establish an informatics framework towards genome-assisted breeding in Pines – for growth, wood quality and resilience to pests and diseases as well as climate change – using data science and machine learning approaches.

In 2020 the FMG Population Genomics Team together with the international tropical pine SNP consortium, developed a genotyping array for tropical pine species, their hybrids and other closely related species. The SNP array is currently being used to establish pine species references that will aid in species and hybrid identification. The first pine genetic linkage map has been constructed and we can now perform marker-trait association analyses. As a result of advanced phenotyping platforms, next-generation sequencing technologies and cost-effective genomic resources, plant breeding has become a data science. We are therefore setting up an informatics resource in the form of a database with a front-end for hosting SNP genotype, phenotype and environment data as a basis for machine learning and genomic selection pipelines. Other data science projects that I am involved with include combining systems genetics and artificial intelligence to dissect the regulatory pathways of wood formation in Eucalyptus; using machine learning approaches to predict lumber yield and lumber quality from Pine growing conditions; and simulating breeding populations to apply machine learning in genomic selection.

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Publication
Jackson C, Christie N, Reynolds SM, Marais GC, Tii-kuzu Y, Caballero M, Kampman T, Visser EA, Naidoo S, Kain D, Whetten RW, Isik F, Wegrzyn J, Hodge GR, Acosta JJ, Myburg AA. (2021) A genome- wide SNP genotyping resource for tropical pine tree species. Molecular Ecology Resources 10.1111/1755-0998.13484 PDF
Berger DK, Mokgobu T, De Ridder K, Christie N, Aveling TAS. (2020) Benefits of maize resistance breeding and chemical control against northern leaf blight in smallholder farms in South Africa. South African Journal of Science 12(11) 10.17159/sajs.2020/8286
du Toit Y, Coles DW, Mewalal R, Christie N, Naidoo S. (2020) eCALIBRATOR: A Comparative Tool to Identify Key Genes and Pathways for Eucalyptus Defense Against Biotic Stressors. Frontiers in Microbiology 11:216. 10.3389/fmicb.2020.00216
Wierzbicki MP, Christie N, Pinard D, Mansfield SD, Mizrachi E, Myburg AA. (2019) A systems genetics analysis in Eucalyptus reveals coordination of metabolic pathways associated with xylan modification in wood‐forming tissues. New Phytologist 223(4):1952-1972. 10.1111/nph.15972
Naidoo S, Christie N, Acosta JJ, Mphahlele MM, Payn KG, Myburg AA, Külheim C. (2018) Terpenes associated with resistance against the gall wasp, Leptocybe invasa, in Eucalyptus grandis. Plant, Cell & Environment 41(8):1840-1851. 10.1111/pce.13323
Nardini L, Hunt RH, Dahan-Moss YL, Christie N, Christian RN, Coetzee M, Koekemoer LL. (2017) Malaria vectors in the Democratic Republic of the Congo: the mechanisms that confer insecticide resistance in Anopheles gambiae and Anopheles funestus. Malaria Journal 16(1):448. 10.1186/s12936-017-2099-y
Tobias PA, Christie N, Naidoo S, Guest DI, Külheim C. (2017) Identification of the Eucalyptus grandis chitinase gene family and expression characterization under different biotic stress challenges. Tree Physiology 37(5):565-582. 10.1093/treephys/tpx010
Mizrachi E, Verbeke L, Christie N, Fierro AC, Mansfield SD, Davis MF, Gjersing E, Tuskan GA, Van Montagu M, Van de Peer Y, Marchal K, Myburg AA. (2017) Network-based integration of systems genetics data reveals pathways associated with lignocellulosic biomass accumulation and processing. PNAS 114(5):1195-1200. 10.1073/pnas.1620119114 PDF
Christie N, Myburg AA, Joubert F, Murray SL, Carstens M, Lin Y-C, Meyer J, Crampton BG, Christensen SA, Ntuli JF, Wighard SS, Van de Peer Y, Berger DK. (2017) Systems genetics reveals a transcriptional network associated with susceptibility in the maize-gray leaf spot pathosystem. The Plant Journal 89(4):746-763. 10.1111/tpj.13419
Christie N, Tobias P, Naidoo S, Guest D, Külheim C. (2016) The Eucalyptus grandis NBS-LRR Gene Family: Physical Clustering and Expression Hotspots. Frontiers in Plant Science 6(1238)
Reeksting BJ, Coetzer N, Mahomed W, Engelbrecht J, van den Berg N. (2014) De novo sequencing, assembly, and analysis of the root transcriptome of Persea americana (Mill.) in response to Phytophthora cinnamomi and flooding. PLoS ONE 9(2):e86399. 10.1371/journal.pone.0086399 PDF
Nardini L, Christian RN, Coetzer N, Koekemoer LL. (2013) DDT and pyrethroid resistance in Anopheles arabiensis from South Africa. Parasites & Vectors 6:229. 10.1186/1756-3305-6-229
Nardini L, Christian RN, Coetzer N, Ranson H, Coetzee M, Koekemoer LL. (2012) Detoxification enzymes associated with insecticide resistance in laboratory strains of Anopheles arabiensis of different geographic origin. Parasites & Vectors 5(113)
Christian RN, Strode C, Ranson H, Coetzer N, Coetzee M, Koekemoer LL. (2011) Microarray analysis of a pyrethroid resistant African malaria vector, Anopheles funestus, from southern Africa. Pesticide Biochemistry and Physiology 99(2):140–147.
Coetzer N, Myburg AA, Berger DK. (2011) Maize microarray annotation database. Plant Methods 7(31) 10.1186/1746-4811-7-31
Coetzer N, Gazendam I, Oelofse D, Berger DK. (2010) SSHscreen and SSHdb, generic software for microarray based gene discovery: application to the stress response in cowpea. Plant Methods 6(10)