Miss Nanette Coetzer
PhD Student
Molecular Plant-Pathogen Interactions
Research Interests
I am a PhD student under supervision of Prof. Dave Berger in the Bioinformatics lab. My project is part of a collaborative project (http://www.fabinet.up.ac.za/mppi/maize) on the quantitative disease resistance to the fungal pathogen Grey Leaf Spot (GLS) in African maize varieties. Quantitative Trait Locus (QTL) and expression QTL (eQTL) analyses were performed to identify genomic regions where variation resides that potentially control GLS disease resistance. The aim of my project is to use a range of bioinformatics and statistical approaches to gain an understanding of the molecular basis of quantitative disease resistance, and address the hypothesis that certain phenotypes are controlled to some extent by gene expression differences.
- Maize Microarray Annotation Database: http://maizearrayannot.bi.up.ac.za/
My MSc project was the development of software for microarray based screening and sequence management of cDNA libraries. SSHscreen is an R package using limma functions from the BioConductor project for screening SSH cDNA libraries on glass slide microarrays. It quantitatively describes each clone in terms of up/down regulation and rarity/abundance in the treated sample. SSHdb is an interactive web-based tool for management of sequence and annotation data for clones after SSHscreen analysis. Inputs to this database include ranked gene-lists or top tables from SSHscreen, as well as available FASTA sequences for individual clones. For each input FASTA sequence, vector and adaptor fragments are removed, redundant partners in the library are marked and BLAST searches against the NCBI nr database are performed in order to further annotate each clone with putative functions.
- SSHscreen: http://microarray.up.ac.za/SSHscreen/
- SSHdb: http://sshdb.bi.up.ac.za/
Publications
- Coetzer N, Gazendam I, Oelofse D and Berger DK (2010) SSHscreen and SSHdb, generic software for microarray based gene discovery: application to the stress response in cowpea. Plant Methods 6:10.
- 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 99:140–147.
- Coetzer N, Myburg AA and Berger DK (2011) Maize microarray annotation database. Plant Methods 7 (1), 31 (http://www.plantmethods.com/content/7/1/31)
