Rouvay Roodt-Wilding

• PhD in Genetics
• Professor (Associate) at Stellenbosch University

Fruit surface cuticular waxes of grape berries are important in stress response and fruit quality. Despite extensive studies on the biosynthesis, regulation and composition of fruit surface waxes, knowledge of the compositional variation and genetic mechanisms underlying grape berry cuticular wax formation remains limited. This study aimed to chara...

Aquaculture in sub-Saharan African accounts for less than 2% of world aquaculture production. The use of unimproved species limits the growth of aquaculture. In order to increase production, there is a need to develop aquaculture species that show vigor and adapt to different culture conditions. A genetic improvement program for Oreochromis shiranu...

Introduction Aspalathus linearis (commonly known as rooibos) is endemic to the Cape Floristic Region of South Africa and is a popular herbal drink and skin phytotherapeutic ingredient, with health benefits derived primarily from its unique phenolic content. Several, seemingly habitat-specific ecotypes from the Cederberg (Western Cape) and Northern...

The Gempylidae (snake mackerels) family, belonging to the order Perciformes, consists of about 24 species described in 16 genera primarily distributed in tropical, subtropical, and temperate seas worldwide. Despite substantial research on this family utilizing morphological and molecular approaches, taxonomy categorization in this group has remaine...

This is the first report on the complete mitochondrial genome (mitogenome) of South African Thyrsites atun (Euphrasén, 1791) and its phylogenetic placement within the Gempylidae family. The complete mitogenome of snoek is 16,494 bp in length and comprises 2 rRNAs, 13 protein-coding genes, 22 tRNAs, and one control region. Gene order is similar to t...

Key message We present a high-density integrated map for grapevine, allowing refinement and improved understanding of the grapevine genome, while demonstrating the applicability of the Vitis18K SNP chip for linkage mapping. Abstract The improvement of grapevine through biotechnology requires identification of the molecular bases of target traits b...

Broadcast spawning animals often display differential parental contributions within aquaculture environments, which can influence offspring performance through a loss of genetic variation in cultured populations. This study aimed to assess the effect of different feeding regimes on reproductive performance of Tripneustes gratilla. To achieve this,...

Aquaculture practices can result in declines in the genetic diversity observed in progenitor natural populations, resulting in subsequent poor production output, particularly for broadcast spawning animals that frequently display differential parental contributions. This study aimed to assess the effect of different Tripneustes gratilla broodstock...

Aspalathus linearis (Burm. F.) R. Dahlgren (Fabaceae) or rooibos, is a strict endemic species, limited to areas of the Cederberg (Western Cape) and the southern Bokkeveld plateau (Northern Cape) in the greater Cape Floristic Region (CFR) of South Africa. Wild rooibos, unlike the cultivated type, is variable in morphology, biochemistry, ecology and...

The golden wildebeest, a colour variant of the blue wildebeest (Connochaetes taurinus taurinus), is one of the most common colour variant animals that South African game ranchers breed for. Based on pedigree records, the prevailing hypothesis is that the golden coat colour is an autosomal recessive trait. However, the genetic basis of the golden co...

Phenotypic plasticity in life-history traits in response to heterogeneous environments has been observed in a number of fishes. Conversely, genetic structure has recently been detected in even the most wide ranging pelagic teleost fish and shark species with massive dispersal potential, putting into question previous expectations of panmixia. Shall...

Blue wildebeest (Connochaetes taurinus taurinus) are economically important antelope that are widely utilised in the South African wildlife industry. However, very few genomic resources are available for blue wildebeest that can assist in breeding management and facilitate research. This study aimed to develop a set of genome-wide single nucleotide...

Aim The formation history of Africa's current river basins remains largely unknown. In order to date changes in landscape and climate, we studied the biogeography of the African freshwater fish with the largest natural distribution. We also validated biogeographical units. Location Continental Africa. Taxon Clarias gariepinus sl. Methods We inve...

Aim: The formation history of Africa's current river basins remains largely unknown. In order to date changes in landscape and climate, we studied the biogeography of the African freshwater fish with the largest natural distribution. We also validated biogeographical units. Location: Continental Africa. Taxon: Clarias gariepinus sl. Methods: We...

Oreochromis shiranus is an important cichlid both in capture fisheries and aquaculture. However, in Malawi, biomass yield for the species has declined. Sustainable strategies to increase in yield from capture fisheries and aquaculture would require sound knowledge of the population genetics of the species. In this study, 20 microsatellite markers d...

The abalone, Haliotis midae, is the most import aquaculture species in South Africa. Nonetheless, genetic improvement of the species is hindered by late maturity and long generational intervals. The application of marker assisted- and genomic selection is one strategy to accelerate genetic gains for production traits. However, with limited understa...

The ARC apple gene bank collection was genotyped for the fruit expressed gene ACS1, in which a short interspersed element (SINE) in the promoter is known, when homozygous, to correlate with delayed ethylene production. Primers were designed amplifying products less than 500 bp and 224 cultivars of domestic apple were analysed, 169 not previously ge...

Sea urchins, including Tripneustes gratilla, are susceptible to a disease known as bald sea urchin disease, which has the potential to lead to economic losses in this emerging aquaculture industry in South Africa. This disease is characterized by lesions that form on sea urchin exoskeletal surfaces. This study aimed to characterize the body surface...

Blush skin and flowering time are agronomic traits of interest to the Agricultural Research Council (ARC) Infruitec-Nietvoorbij pear breeding programme. The genetic control of these traits was investigated in the pear progeny derived from ‘Flamingo’ (blush cultivar) × ‘Abate Fetel’ (slightly blush) made up of 121 seedlings. Blush skin was scored ph...

Cyclopia species, fromwhich honeybush tea ismade, are endemic to the Fynbos Biome of South Africa. Despite its commercial importance, no molecular resources are available to characterise this genus. The polyploid nature of the genus furthermore complicates the use of molecularmarkers. The Agricultural Research Council (ARC) maintains a field gene b...

The collector sea urchin Tripneustes gratilla has been identified as a species with potential for aquaculture production in South Africa. The species’ roe is considered a culinary delicacy in Asia and Europe. However, T. gratilla remains genetically uncharacterised in South Africa. Therefore, the purpose of this study was to provide baseline geneti...

Cyclopia species, from which honeybush tea is made, are endemic to the Fynbos Biome of South Africa. Despite its commercial importance, no molecular resources are available to characterise this genus. The polyploid nature of the genus furthermore complicates the use of molecular markers. The Agricultural Research Council (ARC) maintains a field gen...

The tope shark (Galeorhinus galeus Linnaeus, 1758) is a temperate, coastal hound shark found in the Atlantic and Indo-Pacific oceans. In this study, the population structure of Galeorhinus galeus was determined across the entire Southern Hemisphere, where the species is heavily targeted by commercial fisheries, as well as locally, along the South A...

Regional and local sampling populations, collection site, sample numbers (N) and sampling year. (DOCX)

L (K) distributions using the “log probability of data” (Mean of LnP±1) approach prior to application of Evanno method (above) and Delta K analysis of the true number of clusters following the Evanno method (below) across the Southern Hemisphere (left) and across South African (right). (DOCX)

L (K) distributions using the “log probability of data” (Mean of LnP±1) approach prior to application of Evanno method (above) and Delta K analysis of the true number of clusters following the Evanno method (below) for the two main genetic clusters Group 1 (left) and Group 2 (right) identified using STRUCTURE. (DOCX)

Plots of the isolation-by-distance (IBD) analysis of the South African sampling populations showing regression linearized FST and geographic distance (R2 = 0.238, P = 0.1478). (DOCX)

Individual cluster membership of the Southern Hemisphere samples following hierarchical structure performed on the two main genetic clusters (Group 1 and Group 2) identified using STRUCTURE. (TIF)

The abalone, Haliotis midae, is an important aquaculture species in South Africa and the largest generator of revenue for the mariculture sector. Despite domestication of this species still being in the initial stages, significant differentiation has been observed between wild and cultured populations. The genetic consequences of founder effects ha...

The South African abalone (Haliotis midae) is a gastropod mollusc of economic importance. In recent years natural populations have come under considerable pressure due to overharvesting and ecological shifts. The spatial genetic structure of H. midae has been determined; however there has not been a temporal assessment of abalone population dynamic...

The study investigated the global and regional phylogeography of the yellowtail kingfish Seriola lalandi by examining genetic diversity and population genetic structure of this species at inter- and intra-ocean level and on a regional scale. DNA fragments of two mitochondrial genes, cytochrome b (Cytb) and cytochrome c oxidase subunit I (COI) and o...

Next generation sequencing platforms have recently been used to rapidly characterize transcriptome sequences from a number of non-model organisms. The present study compares two of the most frequently used platforms, the Roche 454-pyrosequencing and the Illumina sequencing-by-synthesis (SBS), on the same RNA sample obtained from an intertidal gastr...

Aquatic animal diseases are one of the most important limitations to the growth of aquaculture. miRNAs represent an important class of small ncRNAs able to modulate host immune and stress responses. In Mollusca, a large phylum of invertebrates, miRNAs have been identified in several species. The current preliminary study identified known miRNAs fro...

The South African abalone is a gastropod mollusc of economic importance. In recent years natural populations have come under considerable pressure due to natural and anthropogenic factors. The spatial genetic structure of abalone has been determined; however the degree to which adaptive evolutionary processes vs. neutral mechanisms maintain this po...

The sensitivity of abalone Haliotis midae larvae to low levels of toxicants was used to conduct a laboratory- scale experiment to determine the possibility of using chemical containment to prevent the escape of larvae from land-based culture systems, thereby reducing the environmental impact of farming operations. The cryoprotective agent, dimethyl...

Relatively rapid and cost-effective genotyping using the OvineSNP50 chip holds great promise for the South African sheep industry and research partners. However, SNP ascertainment bias may influence inferences from the genotyping results of South African sheep breeds. Therefore, samples from Dorper, Namaqua Afrikaner (NA), South African Merino (SA...

The population genetic structure and demographics of the common smoothhound shark Mustelus mustelus were investigated across 2 major oceanographic barriers along the southern African coastline: the Angola-Benguela Front and the Indian/Atlantic boundary. Population genetic structure was inferred using multilocus data generated from 8 microsatellite...

Prior knowledge of the genetic diversity, extent of linkage disequilibrium (LD) and population structure is necessary to determine the sample size and number of SNPs necessary to ensure sufficient power of detection in genome-wide association studies (GWAS) and genomic prediction. The OvineSNP50 chip was used to genotype Dorper, Namaqua Afrikaner (...

Morphological identification and molecular data (mtDNA COI) were used to resolve the taxonomic identity of a non-native freshwater shrimp in the Cape Floristic Region (CFR) of South Africa and to evaluate levels of genetic diversity and differentiation in the species' core natural distribution. The species was morphologically and genetically identi...

South Africa’s demersal sharks are threatened by over-exploitation, lack of species-specific catch data and non-cohesive fishing regulations. Two of the species most affected by fisheries are the common smoothhound (Mustelus mustelus) and the tope shark (Galeorhinus galeus) for which regional population structure is largely unknown. In this study,...

South Africa’s demersal sharks are threatened by over-exploitation, lack of species-specific catch data and non-cohesive fishing regulations. Two of the species most affected by fisheries are the common smoothhound (Mustelus mustelus) and the tope shark (Galeorhinus galeus) for which regional population structure is largely unknown. In this study,...

South Africa’s demersal sharks are threatened by over-exploitation, lack of species-specific catch data and non-cohesive fishing regulations. Two of the species most affected by fisheries are the common smoothhound (Mustelus mustelus) and the tope shark (Galeorhinus galeus) for which regional population structure is largely unknown. In this study,...

The abalone, Haliotis midae, is an important aquaculture species in South Africa and the largest generator of revenue for the mariculture sector. Despite domestication of this species still being in the initial stages, significant differentiation has been observed between wild and cultured populations. The genetic consequences of founder effects, i...

Overfishing has led to the collapse of many marine fish stocks along the South African coast, particularly species characterised by predictable distribution patterns and vulnerable life-history traits. Dusky kob (Argyrosomus japonicus) is an estuarine-dependent sciaenid fish that has been severely depleted by overfishing and is currently managed by...

Molluscs predominately use the cellular defence system as the primary mechanism of defence against pathogenic infection, in which haemocytes play a pivotal role. Haliotis midae is a commercially important South African species that it is susceptible to bacterial pathogens, fungal and yeast infections in the farming environment. The current study ai...

This study describes the successful implementation of a modified cetyltrimethyl ammonium bromide (CTAB) protocol to isolate genomic DNA and amplify 14 microsatellite markers from fertilized eggs and larvae of an emerging South African farmed marine fish species, the dusky kob Argyrosomus japonicus. To test and validate the efficiency of this method...

Exploitation through direct and indirect fisheries has caused a drastic decline of shark populations over the last few decades. Similar to the rest of the world, Southern Africa's diverse chondrichthyan fauna (sharks, skates and chimeras) is experiencing high fishing pressures brought on by the current demand for shark related products. Integrated...

The abalone, Haliotis midae, is an important aquaculture species in South Africa. The species is still largely undomesticated; however there is increasing interest in the development of genetically superior strains for production traits. Abalone aquaculture, therefore, provides a model system to study the initial genetic effects of domestication on...

Abalone aquaculture represents the primary generator of revenue within the South African mariculture sector. However, a number of opportunities for improvement within the industry remain, particularly with regards to the genetic improvement of cultured stock. To this aim, the initial stage of a breeding programme, employing quantitative breeding te...

The South African scallop, Pecten sulcicostatus, has been identified to have potential commercial value as a species for aquaculture, however, little is known of the genetic constitution of these mollusc populations along the South African coast; furthermore until now, no genetic resources were available for this species. Non-destructive DNA extrac...

Hybridization between fish species can play a significant role in evolutionary processes and can influence management and conservation planning, however, this phenomenon has been widely understudied, especially in marine organisms. The distribution limits of two sciaenid species (silver kob, Argyrosomus inodorus, and dusky kob, A. japonicus) partly...

Background Similarly to the rest of the world, southern Africa’s diverse chondrichthyan fauna is currently experiencing high fishing pressures from direct and non-direct fisheries to satisfy market demands for shark products such as fins and meat. In this study, the development of microsatellite markers through cross-species amplification of primer...

A South African Merino sheep flock has been divergently selected for more than 8 generations for the ability of ewes to rear multiple offspring. Selection has resulted in a High line and a Low line that differ markedly in their reproductive output. The causative mutations and/or quantitative trait loci responsible for the difference in reproductive...

Haliotis midae is South Africa's most important aquaculture species. The reproduction cycle is currently not closed as many farms rely on wild-caught broodstock for seed production. However, there is an increasing interest in genetic improvement in commercial stocks, with a growing number of producers implementing selective breeding strategies. Hig...

In this study, effective gamete concentrations, egg viability, and fertilization volumes were evaluated for Haliotis midae (L.). Sperm concentrations between 5 × 103 and 5 × 104 mL−1 (p > 0.05) consistently resulted in high hatch-out rates (96 ± 1%). At concentrations higher than 5 × 105 mL−1, hatch-out rates decreased to 69 ± 7% (p −1 resulted in...

The abalone, Haliotis midae, is currently the primary mariculture species of South Africa. There is increasing interest to genetically improve the species for production traits. A combination of classical breeding and molecular breeding has been advocated for a number of aquaculture species. Various methods have been developed in order to identify...

Haliotis midae is one of the most valuable commercial abalone species in the world, but is highly vulnerable, due to exploitation, habitat destruction and predation. In order to preserve wild and cultured stocks, genetic management and improvement of the species has become crucial. Fundamental to this is the availability and employment of molecular...

Identifying genomic regions that may be under selection is important for elucidating the genetic architecture of complex phenotypes underlying adaptation to heterogeneous environments. A population genomic approach, using a classical neutrality test and various Fst-outlier detection methods was employed to evaluate genome-wide polymorphism data in...

The South African abalone Haliotis midae Linnaeus is the most important aquaculture species in South Africa. Marker-assisted selection is envisioned to play an integral part of the genetic improvement program of abalone, and therefore the generation of linkage maps for quantitative trait loci analyses are necessary. This study reports on a first-ge...

This study reports the first classification of cytological structures in developing gonads of cultivated Haliotis midae. Gonad tissue from animals ranging from 6-48 mo of age was evaluated histologically. The process of oogenesis was divided into 9 distinct stages according to the size and histological structures of each cell type, whereas spermato...

The dusky kob (Argyrosomus japonicus) is a large, estuarine-dependent sciaenid fish that has been severely depleted in South African waters and that, in recent years, has received considerable attention from the local fish farming industry. Discovery and application of appropriate molecular markers is necessary to improve the understanding of wild...

The marine family Haliotidae (Mollusca: Gastropoda) includes approximately 56 extant abalone species found worldwide. None of these species are globally distributed while four areas of endemism (temperate Australia, South Africa, New Zealand and North Pacific) have been recognized. Phylogenetic relationships of 18 abalone species including five Sou...

Farming of Haliotis midae is the most lucrative aquaculture venture in South Africa. The genome of this species needs to be studied to assist in selective breeding programs aimed at increasing overall yield, and molecular markers will be required to attain this goal. We identified and characterized 82 polymorphic microsatellite loci by using repeat...

Identifying genomic regions that may be under selection is vital for elucidating the genetic architecture of complex phenotypes underlying adaptation to heterogeneous environments. A population genomic approach, using a classical neutrality test and various Fst-outlier detection methods were employed to evaluate genome-wide polymorphism data in ord...

Haliotis midae is the only commercially important abalone species in South Africa with a high international demand. Since the closure of the commercial fishery, for conservational purposes, emphasis has shifted to aquaculture. Currently, abalone culture is the largest aquaculture sector in South Africa in terms of tonnage and revenue. With regards...

Abalone culture is South Africa’s largest aquaculture sector in terms of revenue. Nonetheless, the industry is in its formative years and much scope remains for refinement and regulation of production practices. It is important to manage genetic diversity in terms of the particular breeding objectives pursued by respective facilities: selective bre...

Fluorescent molecules have revolutionized the field of molecular biology and biotechnology, and could be of benefit to research conducted on economically important haliotid species (abalone) for applications such as protein analysis, cell metabolism studies, fluorescence resonance energy transfer, cell imaging, and reporter genes for gene transfer....

Abalone production is the largest aquaculture sector in South Africa. Although, currently, production is based on an open system, due to increasing demand for abalone products focus have been placed on the development of genetically superior domesticated strains for enhanced production traits. Phenotypic selection is the backbone of classical breed...

Haliotis midae is the only commercially important abalone species in South Africa and in recent years the demand for this species has increased steadily. Since the fishery is unable to supply this demand, emphasis has shifted to aquaculture and at present it is South Africa’s largest aquaculture sector in terms of revenue. Nonetheless, much scope r...

Abalone culture is South Africa's largest aquaculture sector in terms of revenue. Nonetheless, the industry is in its formative years and much scope remains for refinement and regulation of production practices. It is important to manage genetic diversity in terms of the particular breeding objectives pursued by respective facilities: selective bre...

The South African Abalone, commonly known as perlemoen, is a marine gastropod mollusc with considerable economic value as its production is the country’s largest aquaculture sector. Abalone is in a unique position as efforts to conserve natural populations and endeavours to create a genetically superior strain for production will run concurrently....

Recent studies have shown the non-random distribution of microsatellite motifs between genomic regions within a particular species. This study investigates such microsatellite distributions in the genome of the economically important abalone Haliotis midae, via a bioinformatic survey. In particular, the association of specific repeat motifs to codi...

Recent studies have shown the non-random distribution of microsatellite motifs between genomic regions within a particular species. This study investigates such microsatellite distributions in the genome of the economically important abalone Haliotis midae, via a bioinformatic survey. In particular, the association of specific repeat motifs to codi...

The slow growth rate of Haliotis midae impedes the optimal commercial production of this most profitable South African aquaculture species. To date, no comprehensive effort has been made to identify genes associated with growth variation in farmed H. midae. The aim of this study was therefore to investigate growth variation in H. midae and to ident...

Over the past two decades, the South African abalone (Haliotis midae), has been under serious threat mainly due to overexploitation. To assure successful management and conservation of wild stocks, the consideration of species-specific evolutionary and population dynamic aspects is critical. In this study, eight microsatellites and 12 single nucleo...

Top BLAST matches from NCBI NR database. BLAST results against the Genbank non-redundant (NR) protein database for all the contigs with a cut-off E-value of 10-3 are shown.

Transcripts related to disease resistance. Overview of potential disease resistance-related sequences identified from H. midae cDNA library according to the GO, KOG and PFAM functional description.

Primer sequences for SSR loci. Information of each SSR where primer pairs were designed. Repeat motif, number of repeats, sequences of forward and reverse primer and melting temperature are reported.

Contigs file. Fasta file of the 22,271 sequences assembled de novo.

SSRs discovery. Fasta file of the 181 sequences where 420 primer pairs were designed.

SNPs discovery. The information on the SNPs found in the contigs with coverage ≥100× are reported.

Worldwide, the genus Haliotis is represented by 56 extant species and several of these are commercially cultured. Among the six abalone species found in South Africa, Haliotis midae is the only aquacultured species. Despite its economic importance, genomic sequence resources for H. midae, and for abalone in general, are still scarce. Next generatio...

The genome size of the abalone Haliotis midae was determined using flow cytometry and calculated relative to the known genome size of the rainbow trout (Oncorhynchus mykiss). The C value for H. midae was estimated to be 1.43 pg, which is smaller in comparison with other abalone species with the same number of chromosomes (2n = 36), namely H. corrug...

Clarias gariepinus, a catfish species widely distributed in Africa including South Africa, is naturally absent from the Western Cape and the coastal Eastern Cape provinces. Because of its potential as an aquaculture species it has been widely used in aquaculture ventures in South Africa, specifically a stock known as Dutch catfish, a domesticated s...

The abalone, Haliotis midae, is the most valuable commodity in South African aquaculture. The increasing demand for marine shellfish has stimulated research on the biology and physiology of target species in order to improve knowledge on growth, nutritional requirements and pathogen identification. The slow growth rate and long generation time of a...

Background: Analysis of the rates of non-synonymous vs. synonymous substitutions (w = d N /d S) in the kappa casein (CSN3) genes of Bovidae has provided evidence that positive selection has accelerated amino acid divergence of this protein. 1 The goat CSN3 gene is extraordinarily polymorphic, with sixteen alleles identified to date. 2 A significant...

Abstract The establishment and evaluation of family lines using pedigree information provides an advanced understanding of the variability that exists for complex, economically valuable traits and is a necessary step in the execution of an effective breeding programme. The aim of this study was to assign parentage to mass-spawned Haliotis midae juv...

Cryopreservation could provide stock quantities of embryos for transgenic research. This study aimed to determine the least toxic cryoprotective agent for Haliotis midae embryos. They were exposed for 30min to concentrations varying from 5% to 20% of the following cryopreservatives: methanol (MET), polyethylene glycol (PEG), dimethyl sulfoxide (ME(...

In this study, we describe the first set of SNP markers for the South African abalone, Haliotis midae. A cDNA library was constructed from which ESTs were selected for the screening of SNPs. The observed frequency of SNPs in this species was estimated at one every 185 bp. When characterized in wild-caught abalone, the minor allele frequencies and F...

Haliotis midae is an important species within the fisheries industry of South Africa, with an output of almost 750 tonnes in 2005 (Loubser 2005). H. midae has been cultured in captive conditions since 1981 (Genade et al. 1985, 1988), but the first real effort to establish commercial abalone farms was made in 1990 by industrial and academic institut...

Despite the widespread distribution of the genus Haliotis, chromosome numbers are only known for a small subset of species. In South Africa, no chromosome studies have been conducted on any of the five species occurring in the region. This study is the first report for Haliotis midae, the largest and only economically important species in South Afr...