Plant Genetics

There are currently four research groups involved with plant genetics studies:

Cereal Genomics
Molecular Breeding & Biodiversity
The Plant Breeding Laboratory (SU-PBL)
Vitis Laboratory

Principal Investigator: Anna-Maria Botha-Oberholster, PhD
Laboratory manager: Francois Burger, MSc

Postdoctoral researcher: Anandi Bierman , PhD

Russian wheat aphid resistance
Research in the Cereal Genome programme focuses on the elucidation of the underlying genetic mechanisms involved in host-pest interactions by making use of genomic tools. Understanding defence mechanisms in the wheat host and how Diuraphis noxia (commonly known as the Russian wheat aphid, RWA) biotypes develop are therefore pivotal to our research. Whether recognition occurs non-specifically or specifically (via aphid effector proteins), plants activate a suite of defensive syndromes. It is these aphid associated molecular patterns (AAMPs) elicited in the host, that is of particular interest. Two distinct biochemical pathways are key mediators, depending on the type of invader: wounding during insect herbivory initiates responses mostly mediated by jasmonic acid (JA)/ethylene (ET), whereas microbial pathogens initiate salicylic acid (SA) associated responses such as the hypersensitive response (HR). During HR, affected cells are flooded with toxic chemical compounds (e.g., H₂O₂), often resulting in programmed cell death at the site of infection. Aphid recognition seems to stimulate both SA and JA/ET mediated defence responses. Recognition and signalling are key processes determining the effectiveness of host defence. The RWA being a phloem feeding and sucking insect produces salivary compounds. These compounds may be the most important eliciting factors involved in the onset of plant defence. Several compounds have recently been suggested as eliciting agents, and we know now that the eliciting agent passed from the RWA in the plant is a proteinaceous compound. These salivary proteins, and the responses of the host to these compounds, are currently under investigation. The research team is also studying the development of RWA biotypes and has developed a "hyper virulent" RWA mutant biotype (known as SAM), which is being used as the genetic model organism in our studies. Recently, the team sequenced the genomes of global RWA populations utilizing several different NextGen Sequencing platforms, and released the first draft D. noxia genome in 2014. International collaborators on the RWA genome sequence initiative included: Prof. Nora LV Lapitan (Colorado State University, USA); Prof. C. Mike Smith (Kansas State University, USA); Dr. Gary Puterka (USDA, Stillwater, USA); Dr. Mustapha El-Bouhssini (ICARDA), Dr. Anna Maria Castro (Argentina); and Prof. Martina Zurovcova (Czech Republic). To further our understanding of the host-pest interaction, we have also sequenced chromosomes 7DS and 7DL from ditelosomic lines of wheat using NextGen Sequencing technology, and analyses of this data is currently underway.

Water quality and food security

Since South Africa is a water scarce country, conservation of our water resources are of the utmost importance, thus motivating our involvement in research on drought tolerance in plants, as well as other issues related to water quality and plant health. Specific interests include the effects of heavy and trace metal pollutants on plant stress, associated production of reactive oxygen species, and genotoxicity. This initiative is strongly supported through our collaboration with the research team of Dr. Paul J. Oberholster at the CSIR: Natural Resources and the Environment, South Africa.

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Molecular Breeding & Biodiversity (MBB)

Principal investigators: Rouvay Roodt-Wilding, PhD
Aletta Bester-van der Merwe, PhD
Clint Rhode, PhD, PrSciNat
Barbara van Asch, PhD

Laboratory managers: Jessica Vervalle, MSc
Sihle Mthethwa, MSc

The MBB-group has a primary disciplinary foundation in molecular population- and -quantitative genetics. As such, the group maintains a diverse research portfolio investigating how various micro-evolutionary processes (natural and anthropogenic) influence the genetic composition of animal- and plant populations. This has further implications for understanding how genetic variation relates to the development of phenotypic variation. In order to answer such questions the MBB-group builds on the theoretical tenets of the modern evolutionary synthesis of biology and employs the latest technologies in molecular and genome science, including molecular marker- and next generation DNA sequence technologies. The MBB-group's research has wide implications for both fundamental biology and applied bioscience. Currently the group has four thematic research areas that correspond with the research interests and expertise of the principal investigators, and are aligned with national imperatives for growing the knowledge base for a sustainable and productive bio-economy.

Fruit Crop Molecular Breeding
The temperate Mediterranean climate of the southern Cape is an important, and globally renowned, region for crop cultivation, especially deciduous fruits and grapevine in South Africa. Traditional plant breeding relies on phenotypic selection and hybridisation techniques. These methods are slow and require considerable effort in practice. With the rapid advancement of genomic technologies, it is now possible to accelerate the genetic improvement of crops through marker assisted selection making direct correlations between molecular genetic variation at quantitative trait loci (QTL) and variation in traits of commercial value.
Prof Roodt-Wilding has an interest in the application of molecular marker technologies for identifying the molecular determinants of complex traits and marker assisted selection in fruit tree breeding programmes. In collaboration with the Agricultural Research Council (ARC), Prof Roodt-Wilding is managing various research projects that entail gene mapping of traits related to fruit colour, flavour, and aroma in pears, grapevine, plums, peaches and apricots. Molecular markers are also used for DNA fingerprinting of various fruit germplasm banks and the genetic characterisation of indigenous species such as honeybush. The results of these studies inform plant breeders on the optimal strategies for breeding for enhanced traits and the management of genetic resources for the various species.
Dr Bester-van der Merwe, also in collaboration with the ARC, is investigating the genetic mechanisms underlying the dwarf trait in apples.

Have a look under the Animal Genetics research page to find out more about the involvement of MBB in conservation & fisheries management, sustainable animal production and agricultural pest diversity & management.
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The Plant Breeding Laboratory (SU-PBL)

Principal investigator: Willem Botes

Laboratory manager: Aletta Ellis

The Plant breeding laboratory (PBL) is situated on Welgevallen experimental farm. The PBL consists of a modern molecular genetics laboratory, quality evaluation laboratory, glasshouses and several growth chambers. The research focus of the PBL is small grain cereals, and at present the PBL conducts a industry funded wheat pre-breeding program and a (semi-commercial) triticale breeding program.

Wheat pre-breeding program
One of the most effective ways to achieve the introduction of existing and/or novel resistance genes into a breeding program is by a structured process of pre-breeding. Since 2002 a pre-breeding program based on a male sterility mediated marker assisted recurrent selection (MS-MARS) scheme has been developed and implemented at the PBL utilizing a base population derived from local germplasm and resistance genes that are commonly being utilised by international breeding programs. Genes are pyramided in order to produce advanced lines with a broad spectrum resistance to leaf rust, stem rust and stripe rust, and are annually distributed as a rust resistance nursery to wheat breeding programs in South Africa.

Triticale breeding program

Triticale is a man-made hybrid between wheat and rye, and has been grown commercially in the Western Cape for the past three decades. The PBL conducts, the only triticale breeding program in South Africa, both public and private, and indeed on the African continent. Triticale is highly adapted to stresses (biotic and abiotic), and thrive on marginal soils with minimum input (e.g. low fertiliser requirements for instance). During the past few years the PBL has regularly released new commercial cultivars under licensing agreements through private partners, i.e. "AgBeacon" of which Agricol is the licensee in the Western Cape.

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The Vitis Laboratory

Principal Investigators: Johan Burger, PhD

Hano Maree, PhD

Laboratory manager: Mandi Engelbrecht, MSc

Postdoctoral researchers: Manuela Campa, PhD

Marike Visser, PhD

The Vitis laboratory is a multi-disciplinary research group that mainly focus on the study of plant-pathogen interactions between woody perennial plants such as grapevine, citrus and pome fruit and their most important viral pathogens. To do this we utilise a range of molecular techniques from the basic to the cutting edge.
Current plant virus and virus-like projects within the group include the study of Aster yellows phytoplasma (AY) and Grapevine leafroll-associated virus 3 (GLRaV-3), Grapevine rupestris-associated virus (GRSPaV) and Citrus tristeza virus (CTV) molecular variants and their interaction with different cultivars using diverse next-generation sequencing approaches such as sRNA-Seq, dsRNA-Seq and RNA-Seq. Within the group NGS technology is also used to characterise the virome and microbiome of individual plants through dsRNA-Seq and targeted amplicon sequencing. The use of NGS as a diagnostic for high-throughput unbiased simultaneous detection of all possible viral pathogens is being developed. Additionally, we are also constructing grapevine Ampelovirus infectious clones that, if successful, would give us the tools to make great advances in our understanding of the plant-pathogen interactions of this important virus genus.
The Vitis laboratory also embarked on a genome-sequencing project in which the Vitis vinifera cv. Pinotage, the only locally bred wine grape cultivar, will be sequenced. This ambitious long-term project has only been made possible by the advances in NGS technology in the last few years.
The Vitis laboratory is applying lessons learn in plant virology to the medical field. Currently we are studying the sRNA profiles in Mycobacterium tuberculosis (TB) patients blood serum for the purpose of developing biomarker assays that could be used for early diagnosis. We are also venturing into the field of Nanotechnology with a project that aims to use the unique properties of a plant virus to function as a biological nanoparticle that could be targeted to cancer cells for visualisation and treatment of prostate cancer.

Vironostix (Miss Mandi Engelbrecht) is the extension arm of the Vitis laboratory offering virus diagnostics on crops and ornamental plants using the latest RT-PCR assays.

Funders:
The Vitis laboratory receives funding from the following organisations: National Research Foundation (NRF), Wine industry network of expertise and technology (Winetech), Technology and Human Resources for Industry Programme (THRIP), Medical Research Council (MRC), Citrus Research International (CRI) and the Pinotage association (PA).

Current collaborators:
Dr Jasper Rees, Agricultural Research Council, Biotechnology Platform
Ms Glynnis Cook, Citrus Research International
Dr Shane Murray, Centre for Genomic and Proteomic Research (CPGR)
Prof Gerhard Walzl, Stellenbosch University (Tygerberg) Immunology Department
Dr Katharina Ronacher Stellenbosch University (Tygerberg) Immunology Department
Prof Nicole Steinmetz, Case Western Reserve University, USA
Prof Ed Rybicki, Molecular and Celular Biology, University of Cape Town
Dr Ann Meyers, Molecular and Celular Biology, University of Cape Town
Prof Massimo Delladone, University of Verona, Italy

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Plant Genetics

Water quality and food security

Fruit Crop Molecular Breeding

Wheat pre-breeding program

​Triticale breeding program​

Funders:

Current collaborators:

Triticale breeding program