Research Positions Available:

29 November 2011

ADVERTISEMENT :  ONE MSc. AND ONE  POSTDOCTORAL STUDENT

PLANT BIOTECHNOLOGY LABORATORY, SCHOOL OF MOLECULAR AND CELL BIOLOGY,

UNIVERSITY OF THE WITWATERSRAND

START DATE: January 2012 (AS SOON AS POSSIBLE)

REQUIREMENTS:

Both positions require the appropriate qualifications and should preferably be South African permanent residents or citizens.  The background required to do this project would be microbiology (preferably some plant virology); molecular biology; plant biotechnology and some knowledge and practice of general plant transformation and tissue culture.  Some basic bioinformatics is also required.Applications should be sent by email along with three reference contacts (with email contacts); CV; and academic transcripts.  

CONTACT:  PROFESSOR CHRISSIE REY

EMAIL: Chrissie.rey@wits.ac.za; 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 characterising the recovery phenotype in cassava cultivars that show symptom and disease recovery after infection

MASTERS PROJECT

RNA silencing is a process that suppresses the expression of certain genes through sequence-specific interactions with RNA at the post-transcriptional stage (PTGS), involving small interfering RNAs (siRNAs), or at transcription (usually induced by DNA methylation), and can also be used to engineer virus resistance.   Recovery is a phenotype observed in virus-infected plant hosts characterised by initially severe symptoms which are observed to gradually attenuate until the host appears almost symptomless. It has been reported that a correlation exists between the cassava recovery phenotype post infection with ACMV and SLCMV and the production of virus-derived siRNAs through post-transcriptional gene silencing (PTGS). However, much research remains to be done to better understand the recovery phenotype observed in cassava post infection by other CMGs such as South African cassava mosaic virus (SACMV).Research Objectives The overall objectives of this research are to understand the mechanisms of disease resistance or recovery in relation to cassava begomoviruses. 

Specific Aims

1. To deep sequence the siRNA species populations occurring in the greatest numbers from the enriched siRNA isolates of TME3 (tolerant cultivar) and T200 (susceptible cultivar) at the 3 time points post infection, including 67dpi, when the recovery phenotype is expected to be observable. Deep sequencing of the isolated siRNAs will be performed at the ARC-Biotechnology Platform at Onderstepoort using the Illumina iScan.  

2. To use bioinformatics tools to analyse the siRNA populations in order to determine if the siRNAs that contribute to the recovery phenotype being induced in the resistant host plant TME3 are different in virus target regions or numbers compared with the susceptible variety.  Deep sequencing the isolated siRNAs will allow for observation of which parts of the genome of SACMV are targeted. The data collected from the deep sequencing may also aid in comparison of the abundance (quantities) of vsRNAs at each time point and between the susceptible and recovery-phenotype cassava landraces.

POSTDOCTORAL FELLOW
There are arguably only two approaches to controlling or reducing viral diseases 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.

Aims

1. To use bioinformatics tools to compare and analyse subsets of the data.

2. Identification of up-or down-regulated genes possibly involved in virus disease replication or movement or in resistance

3. Validation of gene functionality using virus-induced gene silencing