Applications should be sent by email along with three reference contacts (with email contacts); CV; and academic transcripts.
FUNDING: While there are funds for running expenses for the project, the student needs to have applied and secured a NRF postgraduate (or alternate bursary), and this covers the fees
CONTACT: PROFESSOR CHRISSIE REY EMAIL: This email address is being protected from spambots. You need JavaScript enabled to view it.; telephone: 011-7176324
IMPROVEMENT OF CASSAVA AS A CROP
BACKGROUND
Cassava is an important food security crop and source of starch for industrial applications and biofuels. Cassava mosaic disease (CMD), caused by cassava mosaic geminiviruses (CMGs) and transmitted by whitefly Bemisia tabaci Gennadius, is one of the two most important viral diseases of cassava in Africa. Our laboratory is interested in exploring new aspects to host-pathogen interactions which will help to devise strategies for managing or reducing crop losses. These projects include genetic engineering for virus resistance; genomics for identifying natural resistance genes in cassava; or characterizing the recovery phenotype in cassava cultivars that show symptom and disease recovery after infection. In addition we are interested in geminivirus and whitefly phylogeny and genetic diversity. In our laboratory we work with South African cassava mosaic virus, (SACMV)and we also work with African cassava mosaic virus and East African cassava mosaic virus to screen our transgenic plants.
Masters Student
Screening and development of transgenic cassava for geminivirus resistance
The overall objectives of this research are to screen already established transgenic cassava lines for resistance, and to transform cassava with other anti-viral hairpin RNAi constructs.
PhD Student
Genetics of resistance and susceptibility in geminivirus infection of crops
There are arguably only two approaches to controlling or reducing virus disease and preventing crop yield losses: Genetic engineering using a pathogen-derived approach which induces basal innate immunity (RNA silencing); or to mine genes that are involved in susceptibility or resistance in crops, such as cassava, and use those to manipulate the host plant. In order to identify candidate genes, one approach is to compare the entire transciptome of a resistant and susceptible cassava plant. Today, sequencing and assembly methodologies are automated and can be applied to entire genomes. The recent new innovations in Genome Sequence Analyzers (such as the Roche GS 20/FLX (454 parallel sequencing platform), Illumina Solexa Technology or Applied Biosystem SOLiD) can generate millions of bases of DNA, allowing for an increase in the scale of research centred on the discovery of new genes. Furthermore, these high throughput systems allow the sequencing and quantification of entire transcriptomes, which is a powerful tool to compare expressed genes in pathogen-resistant and susceptible plant hosts. Deep-sequencing of two cassava transcriptomes (susceptible and resistant at 3 dpi for each) was carried out using multiplex sequencing and the sequencing platform of the recently upgraded SOLiD 4 SYSTEM Genome Analyzer at the University of Zurich Functional Genomics Center and data in now available to compare susceptible and resistant varieties. We are interested in identifying genes involved in disease or resistance traits. We also have sequenced the small RNA genome of SACMV-infected susceptible and tolerant landraces in comparison to wild-type.
Aims
- To use bioinformatics tools to compare and analyse subsets of the data to look for conserved and unique data from several plant species, and our data in cassava Arabidopsis and Nicotiana benthamiana.
- Identification of up-or down-regulated genes possibly involved in virus disease replication or movement or in resistance
- Validation of gene functionality using virus-induced gene silencing or other reverse genetics approaches
- Developing yeast 2H assays to identify SACMV coat protein and Rep-interacting proteins
- Building models for virus-host interactions
