Dr Nanette Christie



Postdoctoral Fellow

Department

Biochemistry, Genetics and Microbiology
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Large-scale genetic and genomic data are increasingly available for many plant species due to new high-throughput ’omics and molecular technologies. In parallel, population-wide phenotypic data are also becoming available to an increasing extent. We need to find meaningful ways to integrate and analyse these complex layers of data. Throughout this process, proper data science techniques including appropriate statistical reasoning and sophisticated computational methods are essential. 

 

We have developed systems genetics data analysis pipelines to analyse data from large breeding populations. This is integral to studying the genetic architecture of gene expression and metabolite variation underlying the phenotypic traits of interest. We have also developed a browser for genome-wide expression association data in forest trees, called qtlXplorer, to query and visualise systems genetics data, as part of the PlantGenIE.org web resource. Understanding the regulatory gene networks underlying important traits in Eucalyptus trees will enable directed genetic engineering and molecular breeding for genetic improvement of wood quality and disease resistance in the long term. 

 

Together with an international consortium of pine genomics researchers, we are in the process of generating a multi-species SNP genotyping chip for tropical pines, to help the pine forestry industry in South Africa to discriminate different species and better identify hybrids. We are also working towards a Genome Diversity Atlas for pine species grown in South Africa. These molecular resources will be crucial for genome-wide assessment of genetic diversity, molecular breeding and gene conservation. Ultimately, we aim to establish an informatics resource towards genomic selection in pine breeding.

 

I have a passion for empowering people to properly analyse, visualise and interpret their data. I present occasional workshops on R programming and various topics in Statistics to postgraduate students and people working in the forestry industry. I am excited to develop new skills and to start applying genomic selection and machine learning methods to ultimately improve genetic gains in the South African forestry industry. 

 

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Publication
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)