Doctoral Degrees (Genetics)

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Identification and remediation of student difficulties with quantitative genetics.
(2006) Hancock, Carolyn Elizabeth.; Anderson, Trevor Ryan.
Genetics has been identified as a subject area which many students find difficult to comprehend. The researcher, who is also a lecturer at the University of KwaZulu-Natal, had noted over a number of years that students find the field of quantitative genetics particularly challenging. The aim of this investigation was two-fold. Firstly, during the diagnostic phase of the investigation, to obtain empirical evidence on the nature of difficulties and alternative conceptions that may be experienced by some students in the context of quantitative genetics. Secondly, to develop, implement and assess an intervention during the remediation phase of the study which could address the identified difficulties and alternative conceptions. The research was conducted from a human constructivist perspective using an action research approach. A mixed-method, pragmatic paradigm was employed. The study was conducted at the University of KwaZulu-Natal over four years and involved third-year students studying introductory modules in quantitative genetics. Empirical evidence of students' conceptual frameworks, student difficulties and alternative conceptions was obtained during the diagnostic phase using five research instruments. These included: free-response probes, multiple-choice diagnostic tests, student-generated concept maps, a word association study and student interviews. Data were collected, at the start and completion of the modules, to ascertain the status of students' prior knowledge (prior knowledge concepts), and what they had learnt during the teaching of the module (quantitative genetics concepts). Student-generated concept maps and student interviews were used to determine whether students were able to integrate their knowledge and link key concepts of quantitative genetics. This initial analysis indicated that many students had difficulty integrating their knowledge of variance and heritability, and could not apply their knowledge of quantitative genetics to the solution of practical problems. Multiple-choice diagnostic tests and interviews with selected students were used to gather data on student difficulties and alternative conceptions. The results suggested that students held five primary difficulties or alternative conceptions with respect to prior knowledge concepts: (1) confusion between the terms variation and variance; (2) inappropriate association of heterozygosity with variation in a population; (3) inappropriate association of variation with change; (4) inappropriate association of equilibrium with inbred populations and with values of zero and one; and, (5) difficulty relating descriptive statistics to graphs of a normal distribution. Furthermore, three major difficulties were detected with respect to students understanding of quantitative genetics concepts: (1) students frequently confused individual and population measures such as breeding value and heritability; (2) students confused the terms heritability and inheritance; and, (3) students were not able to link descriptive statistics such as variance and heritability to histograms. Students found the concepts of variance and heritability to be particularly challenging. A synthesis of the results obtained from the diagnostic phase indicated that many of the difficulties and alternative conceptions noted were due to confusion between certain terms and topics and that students had difficulty with the construction and interpretation of histograms. These results were used to develop a model of the possible source of students' difficulties. It was hypothesized and found that the sequence in which concepts are introduced to students at many South African universities could be responsible for difficulties and alternative conceptions identified during the study, particularly the inappropriate association of terms or topics. An intervention was developed to address the identified difficulties and alternative conceptions. This intervention consisted of a series of computer-based tutorials and concept mapping exercises. The intervention was then implemented throughout a third year introductory module in quantitative genetics. The effectiveness of the intervention was assessed using the multiple-choice diagnostic tests and interview protocols developed during the diagnostic phase. The knowledge of the student group who participated in the intervention (test group) was compared against a student group from the previous year that had only been exposed to conventional teaching strategies (control group). t-tests, an analysis of covariance and a regression analysis all indicated that the intervention had been effective. Furthermore, an inductive analysis of the student responses indicted that most students understanding of the concepts of variance, heritability and histograms was greatly improved. The concept maps generated by students during the remediation phase, and data from the student interviews, provided an indication of the nature and extent of the conceptual change which had occurred during the teaching of the module. The results showed that most of the conceptual change could be classified as conceptual development or conceptual capture and not conceptual exchange. Furthermore, it seemed that conceptual change had occurred when considered from an epistemological, ontological and affective perspective, with most students indicating that they felt they had benefited from all aspects of the intervention. The findings of this research strongly suggest an urgent need to redesign quantitative genetics course curricula. Cognisance should be taken of both the sequence and the manner in which key concepts are taught in order to enhance students' understanding of this highly cognitively demanding area of genetics.
Association of genetic polymorphisms in select HIV-1 replication cofactors with susceptibility to HIV-1 infection and disease progression.
(2011) Madlala, Paradise Zamokuhle.; Ndung'u, Peter Thumbi.; Kormuth, Emil.
Objective.Humans differ substantially with respect to susceptibility to human immunodeficiency virus type 1 (HIV-1) infection and disease progression. This heterogeneity is attributed to the interplay between the environment, viral diversity, immune response and host genetics. This study focused on host genetics. We studied the association of single nucleotide polymorphisms (SNPs) in peptidyl prolyl isomerase A (PPIA), transportin 3 (TNPO3) and PC4 or SFRS1 interacting protein 1 (PSIP1) genes with HIV-1 infection and disease progression. These genes code for Cyclophilin A (CypA), Transportin-SR2 (TRN-SR2) and Lens epithelium derived growth factor/p75 (LEDGF/p75) proteins respectively, which are all validated HIV replication cofactors in vitro. Methods. One SNP A1650G in the PPIA gene was genotyped in 168 HIV-1 negative and 47 acutely infected individuals using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). 6 intronic and 2 exonic haplotype tagging (ht) SNPs (rs13242262; rs2305325; rs11768572; rs1154330; rs35060568; rs8043; rs6957529; rs10229001) in the TNPO3 gene, 4 intronic ht SNPs (rs2277191, rs1033056, rs12339417 and rs10283923) and 1 exonic SNP (rs61744944, Q472L) in the PSIP1 gene were genotyped in 195 HIV-1 negative and 52 acutely infected individuals using TaqMan assays. The rs1154330, rs2277191, rs12339417 and rs61744944 were further genotyped in 403 chronically infected individuals. CypA and LEDGF/p75 messenger RNA (mRNA) expression levels in peripheral blood mononuclear cells (PBMCs) were quantified by real-time reverse transcriptase polymerase chain reaction (RT-PCR). The impact of the Q472L mutation on the interaction of LEDGF/p75 with HIV-1 integrase (IN) was measured by AlphaScreen. Results. The minor allele (G) of SNP A1650G (1650G) in the promoter region of PPIA was significantly associated with higher viral load (p<0.01), lower CD4+ T cell counts (p<0.01) and showed a possible association with rapid CD4+ T cell decline (p=0.05). The 1650G was further associated with higher CypA expression post HIV-1 infection. The minor allele (G) of rs1154330 in the intron region of TNPO3 was associated with faster HIV-1 acquisition (p<0.01), lower CD4+ T cell counts, higher viral load during primary infection (p<0.05) and rapid CD4+ T cells decline (p<0.01). The minor allele (A) of rs2277191 (rs2277191A) in the intron region of PSIP1 was more frequent among seropositives (p=0.06). Among individuals followed longitudinally, rs2277191A was associated with higher likelihood of HIV-1 acquisition (p=0.08) and rapid CD4+T cell decline (p=0.04) in the recently infected (primary infection) cohort. In contrast, the minor allele (C) of rs12339417 (rs12339417C) also in the intron region of PSIP1 was associated with higher CD4+ T cell counts during primary infection. The rs12339417C was also associated with slower rate of CD4+ T cell decline (p=0.02) and lower mRNA levels of LEDGF/p75 (p<0.01). Seroconverters had higher preinfection mRNA levels of LEDGF/p75 compared to nonseroconverters (p<0.01) and these levels decreased after HIV-1 infection (p=0.02). The Q472L mutation showed approximately 2-fold decrease in the association constant (Kd), suggesting stronger binding to HIV-1 integrase. Our findings demonstrate, for the first time, that genetic polymorphisms in the TNPO3 and PSIP1 genes may be associated with susceptibility to HIV-1 infection and the disease progression. These data provide in vivo evidence that TRN-SR2 and LEDGF/p75 are important host cofactors for HIV-1 replication. This is also the first study to show the association of genetic polymorphisms in the PPIA gene with disease outcome in a population (South African) with high burden of HIV-1 infection. Conclusions. Genetic variation in HIV-1 replication cofactors may be associated with disease outcome in a South African population. These data strongly support the role of these HIV replication cofactors in disease pathogenesis in vivo and suggest that these factors are possible targets for therapeutic interventions. However, these data will need to be replicated in larger cohorts to confirm the effect of these genetic variants. Further studies on how to target these factors in antiviral strategies are needed.
Breeding for disease resistance to the major foliar pathogens of dry beans (Phaseolus vulgaris) in South Africa.
(1994) Edington, Brian Ross.
Resistances to bean common mosaic virus, halo, common and Ascochyta blight, angular leaf spot, anthracnose and rust pathogens of beans in South Africa were combined by reverse dichotomous crossing. Full resistance to Uromyces appendiculatus from Carioca 80 was conditioned by a single dominant gene. Partially dominant resistance to Phaeoisariopsis griseola was conditioned by a single gene in Carioca 80 and two genes in PAl 127. Differences in aggressiveness of isolates of Phoma exigua var. exigua were found. Different levels of Ascochyta blight resistance were found in the glasshouse, but field testing showed little difference after flowering. Inoculations of differential cultivars indicated the presence of at least eight races of U. appendiculatus and the a-Brazil race of Colletotrichum lindemuthianum . Inoculations of the old set of halo blight differential cultivars identified races 1 and 2. Forty-five lines with partial resistance to rust were obtained by recurrent selection. Very highly significant differences were noted between ratings of percentage leaf area affected by rust and yield of 23 cultivars planted in field trials. Significant genotype x environment interaction was noted for rust ratings. Ratings at different dates within a trial were correlated with one another, showing few ratings are required per trial, and a correlation of -0.678 between yield and rust rating was found. Inheritance of partial resistance and improved yield of eight cultivars crossed in a full diallel was mostly due to additive effects but non-additive effects were also very highly significant. Reciprocal effects were not significant for yield and rust ratings. Genotype x environment interactions were significant for rust ratings and yield. High estimates of narrow-sense heritability for rust resistance were obtained. No relationship between resistance and time to flowering, pustule size, leaf hairs and stomata was found. Latent periods in unifoliate leaves did not correlate with resistance but a closer match was found in the fourth trifoliate leaves. Inoculations with three additional single-pustule isolates of the 23 parent cultivars indicated the cultivars had similar levels of resistance. Ring necrosis was found in nine cultivars or crosses with them. The ring reaction was conditioned by a single dominant gene and possibly by the epistatic interaction of two dominant genes in Carioca 80. Differences in symptom severity in plants derived from Epicure indicated the possibility of additional gene interaction.
The development of a white clover for use in the eastern high potential areas of South Africa.
(1988) Smith, Albert.; Reusch, J. Dieter H.
The problems associated with the use of white clover in pastures in the eastern high potential areas of South Africa i.e. high P requirements, low tolerance to high Al levels and low pH in the soil as well as a limited survival time of approximately 30 months, were identified and found to be related to the inadequate root system of white clover cultivars. During the improvement programme cultivars available on the world market were introduced and evaluated under dryland conditions. Selections were made from these introductions on the basis of root conformation in high AI, low pH soils, their response to grazing and induced moisture stress. A laboratory technique for the improvement of Al tolerance was developed and the tolerance of white clover plants to high levels of Al was improved but due to the complexity of pasture plant improvement it was decided that the selection for tolerance to Al could be more effectively carried out in the field. The effectiveness of vesicular arbuscular mycorrhizas as phosphate gatherers indicated that local strains of mycorrhizas combined as effectively with white clover as the imported strains. As no seed production of white clover is undertaken in South Africa guidelines for local seed production were also established. As a result of the improvement programme, Trifolium repens cv. DUSI was developed as an open pollinated synthetic variety, based on thirty eight selected mother lines. DUSI has a greater tolerance to high AI, low pH, low P in the soil and due to an improved root system with a high percentage of secondary taproots produces better under dryland conditions and has a longer stand life than any of the cultivars of white clover available on the local market. Plant Breeders Rights were obtained for cv. DUSI and the cultivar was inscribed on the South African variety list. Limited amounts of Breeders seed have been made available to the South African Forage Seed Association for commercial seed production.
Genetic/epigenetic determinants in chemokines and chemokine receptor genes that influence HIV susceptibility in a cohort of high-risk women from South Africa.
(2010) Ramsuran, Veron.; Ndung'u, Peter Thumbi.; Ahuja, Sunil K.; Kormuth, Emil.
No abstract available.
'n Ontleding van die genetiese bydrae van KI-bulle tot die samestelling van die Friesras in Suid-Afrika.
(1978) Cilliers, Barend.; Weyers, W. H.
No abstract available.
Systematics and phylogeography of the Cape Parrot (Poicephalus robustus)
Coetzer, Willem Gabriël.; Willows-Munro, Sandi.; Downs, Colleen Thelma.; Perrin, Michael Richard.
Abstract available from the print/hard copy.
A comparative socio-economic impact analysis of the 2010 Comrades Marathon on the cities of Durban and Pietermaritzburg.
(2015) Maharajh, Ashok.; Van Heerden, Johan.
Sport has always been a significant component of society but is now becoming an increasingly significant component of the economy. Recent years have seen the staging of hallmark and mega-events in sport as increasingly important in the development of a tourist product centered on large cities (Jones, 2001). Studies that assess the impact of hallmark and mega-events often focus on the economic impact of the host economy. Such events are often rationalised as an economic initiative of the host governing authority. This study aspires to estimate the economic and social impacts of a large one-day international sporting event viz. the 2010 Comrades Marathon on the economies of two cities viz. Pietermaritzburg and Durban. A secondary objective is to demonstrate the value of such a major sporting event to the regional and provincial governments as well as formal and informal businesses in the said cities. This study also addresses the social impact of the event on the residents and communities in KwaZulu-Natal. According to Matheson (2006) the role of sports in a society such as South Africa in driving the developmental agenda cannot be over-emphasised. He stated that sporting events do not only play an important economic role but are also useful catalysts in forging social cohesion and nation building. This study also seeks to investigate the socio-economic impact of the 2010 FIFA World Cup that was hosted in South Africa on the Comrades Marathon. Durban was one of the nine cities that hosted games whilst Pietermaritzburg was utilised as a training venue by one of the international teams. It is important to note that the first World Cup match was played eleven days after the Comrades Marathon was run. The study also seeks to investigate the regional origins of visitors to the event and the relationship between the visitors both national and international and the expenditure generated at the event. Durban and Pietermaritzburg like other key cities in the world are and will increasingly be confronted by two vital and related challenges. Firstly, there is need to successfully compete in a universal economy characterised by increased competition and globalisation. Secondly, there is need to eliminate poverty and address issues of inequality and marginalisation. Thus, the Comrades Marathon, as a hallmark sporting event, can be seen as a primary driver to create jobs and contribute to competitiveness. The organisation of major sporting events is a crucial time in the lives of large cities. It provides them with an opportunity to promote themselves, their energy and creativity and, increasingly, their competitiveness. However, it also involves exchanging experiences in this field so as to control the effects, minimise possible risks and guarantee positive results as far as possible. Measuring the effect of an event on the development of a city is a complex and demanding task. This exercise spreads over a variety of different spheres viz. the economy, society, tourism, public finance, organisation capacity, infrastructures, public confidence and international reputation. Much of the analysis in this study was undertaken using a questionnaire survey to interview the key interest groups at the registration venues in both the cities prior to the event and on race day at the finish venue in Durban. The data collected was then analysed using a specialist statistical software package viz. SPSS to calculate the additional expenditure in the host cities. In certain instances, face-to-face interviews were employed to collect the data. The questionnaire requested data on places of residence, the age, gender, occupations, income, spending patterns, features of the cities, unsavoury incidents experienced and the types of activities that the population found attractive. The population comprised of foreign runners and supporters, domestic runners and supporters that reside in other provinces of South Africa, residents of the cities, stall holders at the registration venues, representatives of the sponsors of the event, the organizer of the Bonitas Comrades Experience, vendors, the organisers of the event and representatives of selected shopping malls and hotels in the cities. A truly great sports event is an event where the impact and spin-offs for all those involved viz. the organisers, the community within which the event takes place, the participants and possibly the government, is a positive one when clear benefit is acquired from the event. The Statistical Package for the Social Sciences (SPSS) was used to analyse the data collected. The Chi-Square Test and the Analysis of Variance were applied in this study. The chi-square test was used to determine whether there is a significant difference between the expected frequencies and the observed frequencies in one or more categories. The ANOVA (Analysis of Variance) was used to analyse the differences between group means and their associated procedures. It provides a statistical test of whether or not the means of several groups are equal and is useful in comparing/testing three or more means i.e. groups or variables for statistical significance. The p-value of 0.001 that was computed revealed that there was a significant difference in terms of the racial groups amongst the respondents who resided in Durban and Pietermaritzburg. This can be attributed to the substantial increase in the number of participants and their supporters and family members that arrived in the cities because of the aggressive marketing campaign that the CMA had conducted both internationally and nationally and the fact that the 2010 FIFA World Cup was hosted by South Africa. The p-value regarding the income earned by the respondents was calculated to be 0.001 which showed that there was a significant difference in the income of the respondents who visited the registration venues in Durban and Pietermaritzburg. The p-value of 0.8 revealed that there was no significant difference in the age categories of the respondents that resided in both the cities. A p-value of 0.001 confirmed that there was a significant difference in the items the respondents purchased in the cities. The p-value of 0.20 verified that there was no significant difference in the various types of accommodation establishments that the respondents utilized in both cities. The p-value of 0.001 indicated that there was a significant difference in the duration of stay of the respondents who resided in Durban and those who resided in Pietermaritzburg. The findings of this study revealed that a grand total of R130 978 314 was new income that was generated by the participants, their families and friends. This amount comprised of R110 340 612 that was generated in Durban and R20 637 702 in Pietermaritzburg. A closer examination of the amount generated in Durban showed that R93 397 920 was the average daily expenditure of the participants, their families and friends and that R16 942 692 was the expenditure spent on accommodation. The findings also revealed that of the total amount spent in Pietermaritzburg the sum of R16 283 266 was the average daily expenditure by the participants, their families and friends and R4 354 436 represented the expenditure spent by the afore-mentioned on accommodation. This bodes well for the event, the organisers and the Cities of Durban and Pietermaritzburg. It must also be noted that the Comrades Marathon also brings additional intangible benefits for the local and South African fraternity. The event is also likely to have significant yet unquantifiable benefits for the local economy by presenting Durban and Pietermaritzburg in a positive light to the South African television audience and to its potential participants and their supporters. In addition to the quantifiable impacts related to the Comrades Marathon that was previously discussed, the event also engendered significant intangible benefits to the communities of Durban and Pietermaritzburg in terms of lifestyle improvements. Examples of the intangible benefits are: • significant national and international exposure for the cities as sport fans who enjoyed their visits to the cities may return later thereby raising future tourist revenues • enhancing community pride, self-image, exposure, reputation and prestige associated with hosting a world-famous event and in this way creating a climate of optimism • enhancing the national and international image of the cities so that they become world-class cities and travel destinations • enhancing economic growth and ancillary private sector development spurred on by the operations and activities associated with the Comrades Marathon • providing assets in the cities e.g. the International Convention Centre (ICC) in Durban that can augment their world-class attractions, accommodations and international airport • increase in tourism • promoting the cultural diversity of the population in terms of race, ethnicity and religion • motivate the community to develop active healthy lifestyles and in so doing reduce absenteeism and increase productivity in the work place Furthermore, there is escalating evidence that the media coverage of the race has improved. Gerretsen (2006) reported that Tourism KZN confirmed that the race was viewed by millions because of the television coverage. It is envisaged that television viewers might decide to take a trip to the city at some time in the future based on what they see during the broadcast of the event. This is an exceptional way to showcase the province’s scenic beauty and the warmth and hospitality of its inhabitants. The potential of the Comrades Marathon to attract more visitors and for the visitors to stay longer is indicated by the number of visitors who expressed an interest in existing activities and/or attractions which are related to sport and recreation. The Comrades Marathon is an excellent example of a hallmark sporting event that attracts “outsiders” to the region and the cities. These tourists thus generate “new money” into the economies of the cities and the province.
Landscape genomic approach to investigate genetic adaptation in South African indigenous goat populations.
(2016) Mdladla, Khanyisile.; Dzomba, Edgar Farai.; Muchadeyi, Farai Catherine.
Abstract available in PDF file.
Investigating floral choice in bees (megachilidae) using pollen metabarcoding.
(2017) Gous, Annemarie.; Willows-Munro, Sandi.; Swanevelder, Dirk Z.H.; Eardley, Connal Desmond.
Interactions between plants and their pollinators are often poorly understood, specifically in a species-diverse country such as South Africa. Traditional methods of studying plant-pollinator interactions are time-consuming and imprecise. This study aimed to develop a technique that uses genetic analyses to identify pollen provenance directly from bees (Megachilidae) housed in a historic collection and to apply this technique to investigate floral choice differences in species of megachilid bees from three regionally important areas in South Africa: the Succulent Karoo, Savanna, and a widespread group, with bees occurring throughout the country. To develop the technique to accurately identify provenance, pollen was sampled from Megachile venusta specimens in the collection. Three DNA barcode regions were amplified and sequenced on an Illumina MiSeq instrument: the internal transcribed spacer 1 (ITS1) and internal transcribed spacer 2 (ITS2) regions, and the ribulose-1,5-biphosphate carboxylase (rbcL) gene. Sequenced reads were compared to sequence reference databases that were generated by extracting sequence and taxonomic data from GenBank. ITS2 reads were also compared to an established ITS2 database for Viridiplantae. More diverse plant classifications were obtained with ITS2 compared to ITS1. Amplification and sequencing of rbcL was inconsistent on pollen sampled from historic specimens. To study how floral choice differed in three South African regions, ITS2 was sequenced on Illumina HiSeq and MiSeq from pollen sampled from two different bee species from each region. Sequence reads were compared to the previously published ITS2 sequence reference database. Generalised linear models (GLM) indicated that the mean number of both plant families and species varied significantly between bee species. No significant effect of the time since bee collection was found. Taxon identifications were only confidently interpreted on family-level due to very limited local plant representation in sequence reference databases. DNA metabarcoding of mixed-origin pollen samples provided a faster, more accurate method of determining pollen provenance, without the need for expert palynologists. The use of historic collections to sample pollen directly from pollinators provided additional value to these collections. Sampling pollen from historic collections can also provide the spatial and temporal scales for investigations into changes in plant community structure or pollinator floral choice in the face of global climate change.
Quantification of the thioredoxin system.
(2017) Letrisha, Padayachee.; Pillay, Che Sobashkar.
Abstract available in PDF file.
DNA metabarcoding of zooplankton enhances community-level analyses of connectivity in a marine pelagic environment.
(2021) Govender, Ashrenee.; Willows-Munro, Sandi.; Groeneveld, Johan Conrad.; Singh, Sohana.
Zooplankton are abundant and diverse marine organisms that form ecologically important communities in marine pelagic ecosystems. They are well-suited for biomonitoring of ecosystem health and changes in biodiversity because their community structure and biomass respond rapidly to environmental variation. Biomonitoring of zooplankton communities using traditional morphology-based species identification methods is labor-intensive due to their cryptic morphology, high diversity and small body size. Fast-developing molecular techniques such as DNA metabarcoding (large-scale, high-throughput DNA sequencing of targeted gene regions to simultaneously identify multiple species present in samples) may provide higher resolution, accurate, faster and more cost-effective biomonitoring tools. The primary objectives of this dissertation were to develop and test a novel DNA metabarcoding approach for biomonitoring of marine zooplankton over the continental shelf of eastern South Africa. Novel taxon-specific DNA mini-barcode primers were designed to increase species identification rates of selected taxa. Artificially assembled mock communities with known composition and relative abundances were then used in an experimental setup to test detection rates and the accuracy of designed and published primers. The DNA metabarcoding protocol was then used to assess connectivity among zooplankton communities over the narrow KwaZulu-Natal continental shelf. Plankton tow nets were used to sample cross-shelf transects at three sites (uThukela, Durban and Aliwal), which are strongly influenced by the Agulhas Current but differ in shelf width, seafloor substrate and benthic habitat structures. Connectivity network analysis detected distinct clustering of zooplankton communities associated with each transect. The hypothesis that a dynamic ocean current regime associated with the offshore Agulhas Current (nearby and flowing parallel to the shelf-edge) would result in similar well-mixed alongshore zooplankton communities was rejected. A strong benthicpelagic coupling effect was inferred based on the species composition of planktonic larvae and benthic adults occurring at the respective transects. This dissertation provides a refined and novel method for biomonitoring of marine pelagic environments in coastal waters, based on taxonspecific DNA metabarcoding of zooplankton communities. The approach is well-suited to measuring the long-term effects of climate change on marine pelagic ecosystems and ocean productivity.
Gene expression profiling of South African indigenous goat breeds using RNA-seq technologies in search of genes associated with growth and carcass quality traits.
(2020) Ncube, Keabetswe Tebogo.; Muchadeyi, Farai Catherine.; Dzomba, Edgar Farai.
Abstract available in pdf.
Genome-wide characterization of South African pig breeds.
(2022) Hlongwane, Nompilo Lucia.; Muchadeyi, Farai Catherine.; Dzomba, Edgar Dzomba.
South African pig production is dominated by the commercial sector with a small portion of the smallholder farmers. With an expected increase in pork consumption, commercial breeds such the Large White, South African Landrace and Duroc comes with proven growth potential. On the other hand, indigenous breeds like Kolbroek and Windsnyer have low growth potential, although they are well adapted to the hardy and harsh conditions of South Africa. Village pigs kept by communal farmers have potential to provide food security and assists in poverty alleviation. The free-roaming Warthogs, Bush Pigs and Wild Boars that are found in the villages and in national parks and zoos could be a contribution to the pig genetic resource of South Africa. However, the possibility of interactions of domestic and wild pigs is there and could be a concern to the pork industry, with potential challenges of indiscriminate crossbreeding and introgression. In addition, the zoos are home to some exotic and wild populations such as the Vietnamese Potbelly and Warthogs. Genetic diversity, history and relationships of pigs found in South Africa is poorly understood. Pigs are currently understudied in South Africa resulting in a poor understanding of (i) the genetic diversity and how it is distributed within and among breeds and populations, (ii) the effect of the current production systems on the genetic diversity and threat to populations that has a potential to cause inbreeding and extinction and (iii) the interactions within and between domestic and wild pig populations. This lack of research and information is to the detriment of the species and the pig sector and makes it difficult to implement successful genetic improvement programs further predisposing the unimproved and indigenous pig populations to genetic loss and risk of extinction. This study aimed to close the information gap through genomic characterisation of the pig populations that are within the borders of South Africa. The study sampled broadly from domestic pig populations consisting of villages (Mopani, Capricorn, Alfred Nzo and O.R. Tambo), commercial (Large White, South African Landrace and Duroc), indigenous (Kolbroek and Windsnyer) and Vietnamese Potbelly representing Asian ancestry and wild pig populations consisting of Wild Boars, Warthogs and Bush Pigs. The pigs were sampled from diverse production systems consisting of intensive, semi-intensive and free-range/scavenging as well as pigs in national parks and zoos. The Illumina Porcine SNP60K was used to genotype the pigs generating 62 163 genome-wide SNPs that were analysed to infer of a number of genomic parameters that included (i) within and between population genetic diversity and population structure, (ii) linkage disequilibrium, haplotype blocks and effective population size, (iii) population history, gene flow and introgression and finally (iv) genomic signatures of selection within and between populations. Genetic diversity levels ranged from 0.204 ± 0.151 forWarthog to 0.371 ± 0.126 for Capricorn village pigs. Clustering of South African populations was comparable to the genetic cluster using the worldwide genotypes from a deposited database. There were four major clusters consisting of (i) Duroc, (ii) Vietnamese Potbelly, (iii) Bush Pigs and Warthogs and (iv) a large cluster of commercial Large White and South African Landrace, indigenous Kolbroek and Windsnyer and village pigs of Mopani, Capricorn, Alfred Nzo and, O.R. Tambo (villages) as well as Wild Boar populations. The PCA clustering which included the global populations also displayed four clusters. Bush Pigs and Warthogs clustered together while the Durocs formed a separate cluster. The Vietnamese Potbelly clustered with Chinese populations. The South African villages, worldwide village dataset, Wild Boars, South African indigenous and all the Large Whites and Landraces constituted one major cluster. Admixture based population structure had K = 10 as the optimal which made up of eight distinct clusters of the Warthogs and Bush Pigs; Wild Boars; Vietnamese Potbelly; Kolbroek; Windsnyer; Large White; South African Landrace and Duroc, as well as admixed clusters of Alfred Nzo together with O.R. Tambo (Eastern Cape Province) and Mopani and Capricorn (Limpopo Province). Clustering of populations also depicted the production systems the pigs are reared under. Generally, the effective population sizes of all pig populations have been on the decrease since 12 to 22 generations ago. The effective population sizes of indigenous and commercial breeds were lower compared to that of village populations. Overall, linkage disequilibrium and haplotype blocks results reflected the differences between breeds and production systems. Average LD ranged from 0.18±0.22 for Mopani to 0.40±0.36 for Kolbroek. Most populations (Alfred Nzo, Mopani, South African Landrace, Duroc and Windsnyer) had a high LD on chromosome 14. The highest mean correlation was observed at 1 kb between Duroc and Large White at r = 0.79±0.73. A total of 23 969 haplotypes were observed across populations with Duroc having the highest number of haplotype blocks of 3 402 while Alfred Nzo had the least at 1 350. Duroc pigs had the most unique haplotype blocks 2 513 and associated QTLs 562. Mopani shared the most haplotype blocks with 10 other populations while Mopani and Capricorn shared the most (963) haplotypes. Three haplotype blocks were shared across populations and the corresponding genes were associated with carcass quality and growth, immune response, fertility, and milk production. There was a total of 910 genomic regions with high LD (LD > 0.80) and most QTLs were concentrated on chromosome 7 at 236.
Genetic prediction of feed efficiency in South African Holstein cattle.
(2023) Madilindi, Matome Andrias.; Banga , Cuthbert Baldwin.; Zishiri, Oliver Tendayi.
Feed efficiency is a trait of outstanding importance in dairy cattle; however, it is difficult and expensive to measure and, therefore, not easy to improve through selection. The current study investigated the possibility of predicting the genetic merit for feed efficiency, in South African Holstein cattle, using routinely recorded easy-to-measure traits. The first two objectives were mainly to develop and validate models to predict dry matter intake (DMI) and gross feed efficiency (GFE) using milk production traits and live weight (LW). Data consisted of 30 daily measurements of DMI, milk yield (MY), energy-corrected milk (ECM), butterfat yield (BFY), protein yield (PROY), lactose yield (LACY), butterfat percent (BFP), protein percent (PROP), lactose percent (LACP), and 25 daily LW records of a group of 100 first-parity Holstein cows, fed a total mixed ration. Similar measurements were also collected from a group of 110 multiparous Holstein cows, in lactations 2 to 6. Gross feed efficiency was calculated as kg ECM divided by kg DMI. Forward stepwise regression analyses were performed to develop the models, using the PROC REG procedure of the Statistical Analysis System (SAS) software. Within-herd validation of the models for robustness and accuracy, was subsequently conducted by performing regression analyses between actual and predicted DMI and GFE records. The developed models reliably predicted daily DMI (kg/day) and GFE from milk, butterfat yield and/or live weight, with accuracies ranging from 66 to 98%. Validation of the best model to predict DMI, for first-parity cows, yielded a fairly moderate R2 value (0.49) and a low root mean square error (RMSE) (1.46 kg/day), while the best prediction model for GFE yielded a fairly high R2 value (0.64) and a low RMSE (0.13). The best prediction model for GFE, for multiparous cows, had a fairly moderate R2 value (0.54) and a low RMSE (0.06), upon validation, suggesting reasonable robustness and accuracy. The developed models, therefore, present an opportunity to easily generate large quantities of phenotypic data on individual cow DMI and GFE, at a relatively low cost, which can be used to achieve accurate selection for feed efficiency. The third objective was, essentially, to assess the extent of genetic variability for the predicted traits, in order to evaluate their utility as selection criteria for feed efficiency. First, repeatability animal models were used to estimate genetic parameters for predicted gross feed efficiency (pGFE) and its relationship with energy-corrected milk (ECM) in the first three parities, using the ASReml software. Data of 11,068 test-day milk production records on 1,575 Holstein cows that calved between 2009 and 2019, were used. Predicted gross feed efficiency was calculated using the models developed in the first two objectives. Heritability estimates for pGFE ranged from 0.09 ± 0.04 in mid lactation to 0.18 ± 0.05 in late lactation. Estimates were moderate for primiparous (0.21 ± 0.05) and low for multiparous (0.10 ± 0.04) cows. Repeatability and heritability estimates across all lactations were 0.37 ± 0.03 and 0.14 ± 0.03, respectively. Genetic correlations between pGFE in different stages of lactation ranged from 0.87 ± 0.24 (early and mid) to 0.97 ± 0.28 (early and late), whereas a strong genetic correlation (0.90 ± 0.03) was obtained between pGFE and ECM, across all lactations. The average genetic merit for pGFE, across all lactations, increased at a marginal rate of 0.0058 per year, for cows born during the period 2007 to 2017. The low to moderate heritability estimates for pGFE suggest potential for genetic improvement of the trait through selection, albeit with a modest accuracy of selection. The high genetic correlation of pGFE with ECM may, however, assist to improve accuracy of selection for feed efficiency by including both traits in multi-trait analyses. Due to the scarcity of information on the genetic variation exhibited by predicted dry matter intake (pDMI) from milk components, further genetic analyses were undertaken. Such analyses were important to determine whether pDMI could be a useful selection criterion for feed efficiency in dairy cattle. These analyses under the third objective involved estimation of heritabilities, repeatabilities and genetic correlations among predicted dry matter intake and gross feed efficiency, by repeatability animal models. Data consisted of 440,062 test-day records of 62,695 cows, in the first three parities, that calved between 2009 and 2019. Predicted dry matter intake was generated from milk yield data, using the developed prediction model, and pGFE was derived as kg ECM divided by kg pDMI. Heritability estimates ranged from 0.05 ± 0.02 for pGFE in mid lactation to 0.13 ± 0.03 for pDMI in late lactation. Estimates of heritability across parities were 0.08 ± 0.02 and 0.13 ± 0.02 for pGFE and pDMI, respectively. Corresponding estimates of repeatability across parities were 0.26 ± 0.01 and 0.41 ± 0.01 for pGFE and pDMI, respectively. Genetic correlations between pDMI and pGFE were moderate and negative in early (-0.42 ± 0.24) and mid lactation (-0.20 ± 0.24), and low and positive in late lactation (0.05 ± 0.17). The genetic correlation between pDMI and pGFE decreased with increase in parity, from 0.26 ± 0.16 to -0.09 ± 0.17. The low heritability estimates for pDMI and pGFE indicate low accuracy of selection for these traits in South African Holstein cattle. This can, however, be improved through multi-trait analyses including traits with which they are correlated. Results of the current research pave the way for achieving genetic improvement in feed efficiency in the South African Holstein cattle population. This can go a long way towards the development of a more profitable and environmentally sustainable dairy industry. Higher rates of genetic change can be attained through genomic selection, by using the predicted phenotypes to identify genes or markers associated with feed efficiency.

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