Genetics
Welcome to Stellenbosch University

Animal Genetics

​​​​​​​​​​​​​​​​​​​​​​​​There are currently two research groups involved with animal genetics studies:​

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


Conservation & Fisheries Management 

The South African coast is defined by variable biogeographical regions and oceanic currents that mould the rich biodiversity of each region. These unique environmental conditions influence the reproduction, adaptation and migration of the endemic fauna around the coast, which in turn has particular effects on the genetic composition of these animal populations. In the marine environment this wealth of biodiversity has become valuable as an economic commodity in both ecotourism and food security, it is therefore important to investigate species dynamics for long-term sustainable utilisation of wild resources. 

In particular, Dr Bester-van der Merwe has a specific interest in using genetic and genomic tools to understand the population variability and reproductive aspects of a number of cosmopolitan and endemic elasmobranch (shark, skates & rays) species. Elasmobranchs have come under threat due to fisheries activities, growing demand for shark products, and global climate change. Using genetic data, the robustness of shark populations can be determined to formulate recommendations for the effective management and exploitation of particular species within an ecosystems approach. 

Other projects in this research area includes a fishery project for swordfish in South Africa (Prof Roodt-Wilding), a global phylogeography and genetic diversity study of yellowtail (Prof Roodt-Wilding & Dr Bester-van der Merwe), genetic diversity studies of dusky and silver kob along the southern Africa coast (Prof Roodt-Wilding & Dr Bester-van der Merwe), a collaborative conservation project for crocodiles in Namibia (Dr Rhode) and a conservation project for freshwater fish in the Cape floristic region (Dr Rhode).​


Sustainable Animal Production

Animal production is a major contributor to the national agrarian economy and is a valuable source of animal protein for human consumption. With the rapid advancement of genomic technologies, it is now possible to expedite the genetic improvement of animals by unravelling the genetic architecture of complex traits and making direct correlations between genotype (molecular genetic variation) and phenotype (animal performance). However, globally there is still a substantial reliance on wild fisheries to fill this protein requirement. The dire state of the world's fisheries has led to the development of aquaculture, where aquatic animals are farmed in captivity to supply the market demand for seafood. In this manner, a sustainable and environmentally friendly source of animal protein could be established.

Dr Rhode is involved in various research projects that evaluates the genetic diversity in a number of aquatic animals with relevance to aquaculture in South Africa, including abalone, scallops, and dusky kob. These research projects investigate how patterns of genome-wide diversity changes over time as wild populations are brought under captivity. By understanding the micro-evolutionary processes that shape diversity during the initiation phases of domestication, optimal genetic management strategies can be formulated to increase production (including selective breeding of favourable traits) and simultaneously ensure the conservation of wild populations.

Dr Rhode is also currently managing a genetics programme for the commercial production of black soldier flies. The black soldier fly is an effective bioremedial species used to degrade organic waste. The fly larvae, in turn, makes a good fishmeal (protein) substitutes in animal feeds, hence creating a sustainable and recyclable system for animal production that is not reliant on wild fisheries.

Prof Roodt-Wilding and Dr Bester-van der Merwe are, respectively, involved in tilapia- and catfish breeding programmes for Malawi, and Prof Roodt-Wilding and Dr Rhode are currently initiating a genetic study for sea urchin culture in South Africa.

 

Agricultural Pest Diversity & Management

The southern reaches of the Western Cape province of South Africa, with its temperate Mediterranean climate is an important region for crop cultivation, especially for deciduous fruits, and is globally renowned. However, little is known about the habits and diversity of insects that regularly predate on economically important fruit trees, which complicates pest management strategies.

Dr van Asch has a particular interest in insect diversity as it relates to olive cultivation. Olive farming is a relatively new industry in South Africa and therefore it is important to identify and understand the various insect pests that might hamper orchard productivity and the expansion of the industry. Specifically, Dr van Asch aims to use genetic barcoding for species identification and further use other genetic markers to understand population structure and migration patterns of these insects. Species of interest include olive flies, olive flea beetles, olive lace bug and Braconid wasps (parasitoid wasps that may be used as biocontrol agents). The genetic data can be used to devise effective management strategies for pest control.​


Have a look under the Plant Genetics​ research page to find out more about the involvement of MBB in fruit crop molecular breeding.


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Systems Genetics Research Group

Principal investigators:
 Nathaniel W. McGregor, PhD
                                          Clint Rhode​​, PhD, PrSciNat
           
Laboratory managers: Sihle Mthethwa, MSc
                                         Jessica Vervalle, MSc
                                         
Postdoctoral researchers​: Tiro Tau, PhD
                                               Kevin O'Connell, PhD


The Systems Genetics group was co-founded by Drs McGregor and Rhode as a trans-disciplinary research enterprise to investigate complex biological phenomena with genetic underpinnings by integrating questions and methods of genetics with those of systems biology. In brief the group aims to understand the various genetic and environmental factors, as well as the interaction between these, to explain biological variation in form and function. The systems approach in particular seeks to elucidate how the flow of biological informa​tion from the genome, transcriptome, proteome, and metabolome to the broader phenome are interconnected and related as a singular biological system within the ecological and evolutionary context of organisms. As such, Dr Rhode has a primary interest in how evolutionary processes (e.g. the functional effects of selection, and migratory- and mating patterns) shape genomic diversity and by implication the genetic background of populations and the architecture of complex traits within and between populations. Whereas, Dr Rhode analyses the population, Dr McGregor focuses on individuals and why individuals within a population exhibits differential phenotypic expressions. He specifically looks at how heritable and non-heritable factors influence phenotypic development. By combining the two approaches, and by placing individual's genotypes into their evolutionary context, it is possible to gain a more refined understanding of the functionality and relationship between genotype and phenotype within a complex biological system. At present, the group's “flagship" project is investigating how the unique and complex history of the South African human population that consists of a “melting-pot" of ethnic and cultural groupings influence the development of phenotypes in complex traits, using mental health disorders as a model. Other potential projects include investigating the effects of domestication on novel animal species and complex traits of economic importance in biotechnological applications for bioremediation and aquaculture.​