Research Programmes - Plant Biotechnology

  • Plant Virology Group, University of Pretoria

    Plant Virology Group, University of Pretoria
    29th May 2014

    Control of virus diseases generally is achieved by the use of resistant plants or by controlling the spread of the virus between plants. The research program of the Plant Virology Group of the Department of Microbiology and Plant Pathology at the University of Pretoria focuses on research on control of the most important virus diseases of two high value crops, namely grapevine leafroll disease of wine grapes, and the Citrus disease caused by citrus tristeza virus (CTV). The group also studies citrus greening disease, associated with a fastidious bacterium “Candidatus” Liberibacter africanus (Laf), which has an epidemiology not unlike that of plant viruses.

    Grapevine leafroll disease has been controlled for decades within the South African Vine Certification Scheme but reinfection of cleaning planting material still occurs in industry. A number of sources and means of spread have been identified by members of the Plant Virology Group in South Africa. Following these studies a successful control strategy has been developed by us. Assessments of the efficacy of these control strategies have been conducted at a model wine estate, Vergelegen Wine Estate in Somerset West, where the success of the control strategy has been unequivocally demonstrated. Current research by the research group focuses on refinements of the control strategies. Research is also conducted on developing a next generation sequencing-based diagnostic protocol for the viruses of grapevine, in support of the South African Wine Grape Certification Scheme.

    All citrus planting is pre-immunized with mild strain populations of CTV prior to release from the CIP. While this protects the plant from infection by severe forms of CTV in the majority of instances, on some occasions severe symptoms are still found, especially in the case of Grapefruit. The plant Virology group are busy with studies where the strains present in greenhouse maintained pre-immunizing CTV populations and field planted, pre-immunized Citrus trees with various symptoms are being characterised, pure sources of CTV strains are isolated, and factors affecting strain dynamics are assessed.

    Citrus greening disease has been reduced to manageable levels through stringent vector control strategies and rouging, but remains a problem in the cooler citrus production areas of South Africa. The perpetuation of the disease in spite of stringent rouging may be due to the presence of hosts other than citrus, which may serve as reservoirs of the disease. The Plant Virology group are investigating the possibility that other hosts of the bacteria exist with the initial emphasis is being placed on evaluating indigenous Rutaceous species. 

    The plant virology group research is funded primarily by the wine grape industry (Winetech) and by the Citrus Growers Association through Citrus Research International, and collaborates with numerous role-players regarding these projects including ARC, Vititec, Vergelegen Wines, University of Florida, New Zealand Wine, University of Victoria and the USDA-ARS

    Contact details:

    Prof Gerhard Pietersen

    ARC-Plant Protection Research Institute
    c/o Dept. of Microbiology & Plant Pathology
    Room 9-21, New Agriculture Building
    Lunnon Street           
    University of Pretoria
    0002 PRETORIA
    South Africa
    Tel: +27-12-420-3265 (University of Pretoria)
    Tel: +27-12-808-8196 (ARC-PPRI)
  • Cassava Biotechnology Programme, Wits University

    4th Apr 2014

    Cassava mosaic disease (CMD) causes devastating losses to cassava on the sub-Saharan African continent. CMD is caused by several distinct geminivirus species, including ACMV, EACMV and SACMV, which are transmitted by the whitefly Bemisia tabaci.  Cassava brown streak disease (CBSD) has also recently escalated and is now also a major problem in cassava in eastern and southern African countries, but to date has not been reported in SA. CBSD is caused by two distinct ipomoviruses.

    Cassava research in our laboratory focuses on five main areas:

    1.       Development of virus resistance to CMD

    This project is the genetic engineering of virus resistance into cassava using RNA silencing as the induced mechanism. Different hairpin constructs have been made and transformed into cassava, and we are testing these for efficacy against SACMV, EACMV and ACMV.

    2.       Characterization of cassava geminivirus and whitefly diversity

    This project involves both discovery and molecular characterization of new and existing geminiviruses in cassava in South Africa and Mozambique.

    3.       Sub-viral agents associated with geminiviruses

    Several sub-viral agents have been associated with geminiviruses, and these are known to modify disease. Amongst these are beta- and alpha-satellites, and defective interfering DNAs.  Our laboratory is also looking at discovery, characterization and function of these agents in infected cassava .

    4.       Functional genomics of geminivirus-cassava host interactions

    This project involves next-generation sequencing and functional genomics techniques to examine global interactions between South African cassava mosaic virus (SACMV) and host plants (natural host cassava as well as experimental hosts, Arabidopsis and Nicotiana benthamiana).   Transcriptome studies provide information on potential genes involved in susceptibility and resistance in cassava and model hosts, while small RNAs (miRNA and siRNA) data provides clues as to epigenetic mechanisms involved in host responses to SACMV infection.  Resuts from this can be used in future to devise strategies for developing natural resistance.

    5.       Cassava brown streak disease

    I am involved with collaborators and PG students outside of SA as CBSD does not occur in SA.  Many of these projects are funded by Bill Gates Foundation and I collaborate with MARI in Tanzania, and Danforth Plant Center in the US.  I have four PhD students working on aspects of virus diversity; virus evolution and virus resistance (transgenic cassava) in Tanzania, Malawi, Uganda and Mozambique.

  • Development of Genomics Resources for Molecular Breeding of Drought Tolerance in Cassava

    4th Apr 2014

    Cassava is an important root crop in unfavourable environments in poor areas of developing countries. As cassava is often cultivated in dry areas, research towards improvement of drought tolerance in cassava is needed. In order to accelerate the advance of genetic improvement of cassava, genomic resources must be made available to the community. A genome sequencing project for cassava has already been initiated at the U.S. D.O.E. Joint Genome Institute (JGI) in Maryland, USA. A partially inbred cultivar generated at CIAT has been selected for genomic sequencing to avoid the problem of heterozygosity.

    The CGIAR Generation Challenge Programme has provided funding for a project aimed at developing a panel of single nucleotide polymorphism (SNP) markers on a genome-wide basis to localize favourable alleles in existing mapping populations, generated from contrasting drought tolerance genotypes. For this purpose, a bacterial artificial chromosome (BAC) library from the same genotype being sequenced at JGI is being fingerprinted. A set of minimally overlapping clones or minimal tiling path (MTP) will be selected and the ends of all BAC clones in the MTP will be sequenced for SNP discovery.

    In the mean time, SSR markers in the parents of the mapping populations are to be tested to estimate the level of polymorphism. The genome-wide SNP marker set that this project will deliver will allow identification of quantitative trait loci (QTL) associated with drought tolerance by high-throughput genotyping of validated SNPs.

    As cassava is a close relative of castor bean, whose genome has been sequenced, once the genome sequence and fingerprint map of cassava are released, it will be possible to conduct comparative analyses within the Euphorbiaceae family. This kind of information will facilitate the elucidation of the evolutionary history and domestication of cassava.

    Furthermore, the availability of a fingerprint map and the genome sequence for one genotype of cassava will open the door for genome-wide diversity studies using other cultivated or wild cassava varieties in comparison with the reference genome. Next-generation sequencing technologies will make it affordable to re-sequence different cassava genomes and take full advantage of the broad genetic diversity of cassava for breeding and crop improvement.

    This international project is being led by Dr Pablo Rabinowicz of the University of Maryland, involves the University of California, as well as two ACGT partner institutions, the University of Pretoria (Prof Zander Myburg) and University of the Witwatersrand (Prof Chrissie Rey). South African involvement was facilitated through the ACGT’s standing as a consortium member of the Generation Challenge Programme.

  • Plant Barcoding

    Plant Barcoding
    4th May 2012

    University of Johannesburg Team helps to “barcode” the world’s plants

    An international team of 52 scientists working in 10 countries, including botanists from the University of Johannesburg (UJ), has concluded a four year effort to agree on a standard ‘plant DNA barcode’ to provide the foundation for the widespread use of DNA technologies to identify plants. Dr Michele van der Bank is the lead investigator of the project at UJ. The University is also playing a leading role in Africa as the continent’s representative for the new TreeBOL initiative (DNA barcoding of all the trees of the world). Michelle van der Bank and Olivier Maurin are heading the regional working group for Africa. Their aim is to facilitate the transfer of precise and reliable information between the continent’s tree collections and the rest of the world, and also to build capacity in Africa.

    DNA barcoding has been widely used to identify animal species since its invention five years ago. It provides an efficient means by which many undescribed species that exist on earth can be discovered. This discovery is important because understanding biodiversity is crucial to long-term human existence on the planet.

    However, its use for plants was delayed because of the complex nature of plant genetics and finding the right stretch of plant DNA. Previously, scientists had difficulties in reaching a consensus on which DNA region, or indeed how many regions, to use. For the first time, the botanists involved in evaluating plant barcoding regions have pooled their data to agree on a standardised approach. This involved comparing the performance of the seven leading candidate DNA barcoding regions on a common set of samples.

    The primary application of the methodology will be the identification of the many species in the world’s biodiversity hotspots where a shortage of specialists hinders conservation efforts. Other applications include identifying illegal trade in endangered species, identifying invasive organisms, poisonous species and fragmentary material in forensic investigations. The technique will work on minute amounts of tissue and can be used on fragments of plant material, small seedlings, and in some cases digested or processed samples. The methodology will also be used immediately in global projects such as Tree-BOL which aims to build the DNA barcode database for all the species of trees of the world – many of which are of economic and conservation importance.

    During the past two years UJ has collected approximately 80% of the tree species of southern Africa, which forms part of the TreeBOL Africa project and has also set up several collaborated projects with researchers in Africa. One of many barcoding projects currently at UJ is the barcoding of protected timber and traded trees in Africa to assist custom officials at our ports/borders. Dr van der Bank`s team has completed the barcoding project for all trees and shrubs of the Kruger National Park. They are using the standardized protocol for plants to barcode all these species and are adding it onto the BOLD (Barcode of Life Database) database.

    For more information, contact Prof Michelle van der Bank, Tel: +27 11 559 2495, Fax: +27 11 559 2411

  • Forest Molecular Genetics

    24th Apr 2012

    The Forest Molecular Genetics (FMG) Programme is an academic research programme in the Department of Genetics at the University of Pretoria. This Programme is part of the research portfolio of the Forestry and Agricultural Biotechnology Institute (FABI) and is hosted in the Forest Molecular Genetics Laboratory in the Department of Genetics. The FMG-programme is headed by Prof Zander Myburg.

    The FMG programme makes use of various high-throughput technologies to investigate the molecular genetics of xylem development in fast-growing Eucalyptus and tropical pine tree species (e.g. Pinus patula). Focus areas of the programme include: gene discovery and functional genetics research (e.g. transcriptomics, metabolomics, wood microchemistry, plant transformation, yeast-1-hybrid and yeast-2-hybrid analyses); allele discovery (e.g. allele cloning, sequencing and SNP detection); and the development of molecular breeding tools for genetic improvement of targeted forest tree species (e.g. SSR and SNP marker analysis). We also employ the herbaceous model plant, Arabidopsis thaliana, as a platform for the functional genetic analysis of candidate wood formation genes discovered in trees.

    The majority of research activities in the FMG programme are funded as part of a joint research venture of the University of Pretoria, Sappi Forests and Mondi Business Paper South Africa. Additional financial support is provided by the Technology and Human Resources for Industry Programme (THRIP), the National Research Foundation of South Africa (NRF) and the Department of Science and Technology (DST).

    For more information, contact Zander Myburg (zander.myburg[at]
    Tel: +27 12 420 4945, Fax: +27 12 420 3947