Records management practices in selected municipalities in Limpopo province of South Africa.

Doctoral degree. University of KwaZulu-Natal, Pietermaritzburg.The high level of corruption and maladministration, lack of accountability and transparency in municipalities has become endemic and is a cause for concern in many municipalities of South Africa. The ability of any municipality to effectively perform its constitutional duties depends on the availability of relevant and comprehensive information from records. The poor state of records management in the government and public sectors in South Africa is a well-documented phenomenon. In considering poor records management practices in the public sector of South Africa, it is necessary to establish records management practices in municipalities. The purpose of this study was to examine records management practices in selected municipalities in the Limpopo Province of South Africa. The underlying principle of the study was that municipalities in South Africa are mandated by legislation to manage records systematically. The study sought to establish the current records management practices in the municipalities of the Limpopo Province, to establish the level of knowledge that staff members in municipalities have of records management, to identify the activities and strategies used to support records management practices and, finally, to identify the challenges faced by municipal officials in managing records. The Records Life Cycle and Records Continuum models were adopted in the study. Data were collected from 86 registry clerks using questionnaires and from five municipal managers and six records managers using interviews in the selected municipalities in the Limpopo Province using purposive sampling. The Statistical Package for the Social Sciences (SPSS) was used to analyse quantitative data to generate frequency counts, percentages, bar charts and tables while Thematic Content Analysis was used to analyse qualitative data. The ethical protocol of the University of KwaZulu-Natal was adhered to. The findings of the study revealed that paper-based records are the main formats of records created in municipalities in the Limpopo Province. The study further revealed that most of the municipal officials working with records in the selected municipalities in the Limpopo Province do not have formal qualifications in records management. It is evident from the findings of the study that while municipalities have records management policies, their employees, generally, are uninformed of their existence. The study recommends that records storage facilities in municipalities be improved to ensure that records are kept safe and conveniently accessible. Top management and political office bearers are encouraged to support effective and efficient records management practices in their municipalities. The study contributes to the body of knowledge on records management practices, especially in the context of the Limpopo Province.Author's Dedication on page vii

ENHANCING SERVICE DELIVERY THROUGH RECORDS MANAGEMENT IN MOGALE CITY LOCAL MUNICIPALITY

Records are essential to the efficient administration of municipalities and more critical to the facilitation of good governance, transparency and accountability. Despite this, the records management processes of many municipalities in South Africa have remained ineffective and inefficient. The study investigated the extent to which records management enhances service delivery in Mogale City Local Municipality. The objective was to determine how far sound records management goes in enhancing the public services, accountability, transparency and good governance. Through interviews and observations, it was revealed that the keeping of records was not attaining the intended goal of nurturing sound records management practices in Mogale City Local Municipality. The study sought to investigate how records management enhances service delivery in the Mogale City Local Municipality with a view to promoting good governance and efficiency in public service delivery. The study sought to address the following research questions: “What contribution, if any, does records management play in enhancing service delivery?”; “Are there any suitable standards and practices for records management activities in the MCLM?”; “To what extent does records management impact on transparency and accountability in Mogale City Local Municipality?” and “Identifying the benefits derived from records management in the municipality.” The study was underpinned by the record life-cycle and records continuum models. The literature reviewed was based on themes derived from the research questions, the underpinning models and broader areas of the study. The study adopted an interpretivist paradigm, which is associated with the qualitative research approach. The study adopted a single case study design and data were collected through the use of interviews and observation. The qualitative data collected were presented and analysed in narrative description. The findings of the study revealed that there is a positive correlation between records management and effective service delivery. In conclusion, it is evident that the future well-being and quality of basic service delivery depend on the ability of the MCLM to utilise records management strategic planning processes. Records contain information that will assist the municipality in determining the required resources, and moreover, in setting or improving service standards. The records management policy in the municipality must be adhered to and practiced consistently to ensure compliance and sound records management. This affirms the need for reformed records management strategies to enable administration efficiency and improved service delivery in the municipality.Information Scienc

Accounting for population admixture in genomic evaluations

Genomic evaluations of animals in multi-breed and admixed populations tend to ignore the population structure and assume that these populations are homogeneous, which may lead to limited success in the application of this technology. The objective of this thesis was to develop approaches for accounting for the admixed structure of the Nordic Red dairy cattle (RDC) and furthermore, investigate the predictive ability of these methods in the estimation of genomic enhanced breeding values. The Nordic RDC population is a composite of the Finnish Ayrshire, Swedish Red, Norwegian Red, Danish Red, and their crosses with other breeds. The study was carried out using individual breed proportions derived from the pedigree to define the base breeds, dense marker genotypes and phenotypes of progeny tested bulls with reliabilities from traditional evaluations close to one. Two approaches were developed: (1) the multi-trait random regression model, which accounts for the interactions between marker effects and base breed origin of alleles, (2) the adjusted genomic relationship matrices by allele frequencies (AF) estimated within breeds versus across breeds, estimated from the currently genotyped versus the base (founding) population. Then, the predictive ability of genomic relationships accounted for breed composition was investigated in genomic evaluations with GBLUP of genotyped animals only, and GBLUP of both genotyped and ungenotyped animals (single-step GBLUP). Information in all evaluation models were weighted by the reliability of the phenotype (i.e., bull or cow deregressed breeding value). The validation of genomic evaluations for all models was assessed as the regression of phenotype on direct estimated genomic values or genomic enhanced breeding values. Gains in validation reliabilities were 2 and 3% for milk and protein, respectively, and -1% using the multi-trait random regression model in comparison to GBLUP model that assumed a homogeneous population. The use of AF within breeds greatly reduced differences in additive genomic relationship coefficients between populations, when assessed both across and within sub-populations. This was more evident and closer to pedigree relationships when breed-wise AF were estimated from the base population. Whereas the use of AF across breeds increased genomic relationships, especially for individuals that were originating from populations that were further from the mean population AF across breeds. Accounting for the population structure with breed-wise AF also, relaxed assumptions when incorporating pedigree-based relationships for single-step GBLUP. This advantage however, was not achieved in genomic evaluations. The validation reliabilities between GBLUP with breed-wise AF and GBLUP with AF across breed were generally similar at 33% for milk and protein and 43% for fat. The validation reliabilities increased to 37%, 40% and 47% for milk, protein and fat, respectively, but were similar irrespective of AF used to compute genomic relationships in single-step GBLUP. The improvement in at least 5% for all traits with single-step GBLUP shows the benefit of utilizing all the available information into genomic evaluations. From the methods developed, it was concluded that accounting for the population structure overall had marginal advantage in the predictive ability of genomic evaluations. However, as genomic selection is becoming a dominant tool, biased evaluations in multi-breeds from ignoring differences between breeds is clearly to be feared. Therefore, a more reasonable and cautious approach for integrating genomic information in multi-breeds would be from single-step evaluations that utilize cow performance record as phenotype and genomic relationships accounted for varying AF between the breeds founder populations.Genomisen tiedon käyttö eläinten valinnassa (genominen valinta) on tehostanut lypsylehmien jalostusta. Tärkeimmät syyt jalostuksen tehostumiseen ovat arvosteluvarmuuden paraneminen varsinkin nuorilla eläimillä sekä lyhentynyt sukupolvien välinen aika. Genomisen valinnan avulla voidaan saavuttaa jopa 70% arvosteluvarmuus tuotosominaisuuksien suhteen Holstein-rotuisilla eläimillä ilman eläimen omaa tai jälkeläisten tuotoksia. Myös pohjoismaisella punaisella rodulla genomisen valinnan arvosteluvarmuus on kohtuullisen hyvä, mutta sitä on rajoittanut rodulle ominainen useasta eri alkuperästä johtuva populaatiorakenne. Pohjoismainen punainen rotu koostuu alkuperäisistä suomalaisista Ayshirestä, ruotsalaisesta, tanskalaisesta ja norjalaisesta punaisesta rodusta sekä niiden eriasteista risteytyksistä myös muiden kuin pohjoismaisten rotujen kanssa. Tutkimuksen tavoitteena oli kehittää menetelmiä, joilla pohjoismaisen punaisen rodun populaatiorakenne voitaisiin ottaa huomioon genomisessa valinnassa sekä tutkia näiden menetelmien arvosteluvarmuutta. Käytetty aineisto sisälsi sukupuutiedot, joiden avulla kullekin eläimelle voitiin laskea sen rotusuhteet (kuinka monta prosenttia eläimen perimästä on peräisin esim. Ayshirestä ja ruotsalaisesta punaisesta jne.) ja määrittää sen pääasiallinen rotualkuperä. Aineisto sisälsi myös keinosiemennyssonnien jalostusarvot ja genotyypit (SNP, pistemutaatiomerkki). Tutkimuksessa kehitettiin kaksi rotualkuperän huomioivaa menetelmää genomiseen valintaan. Ensimmäinen menetelmä oli ns. monen ominaisuuden satunnaisregressiomalli (menetelmä 1), jossa kullekin eläimelle laskettiin genominen jalostusarvo huomioimalla eläimen rotualkuperä. Toisessa testattavassa menetelmässä (menetelmä 2) eläinten väliset sukulaisuudet laskettiin SNP genotyyppien perusteella (genominen sukulaisuusmatriisi) kuitenkin niin, että sukulaisuuksien laskennassa käytettiin rotukohtaisia alleelifrekvenssejä sen sijaan, että olisi käytetty rotujen yli laskettuja alleelifrekvenssejä. Menetelmällä 2 laskettiin genomiset jalostusarvot joko ainoastaan genotyypitetyille sonneille tai samanaikaisesti populaation kaikille eläimille. Menetelmien antamaa arvosteluvarmuutta verrattiin vastaaviin menetelmiin, joissa populaation rakennetta ei huomioitu. Menetelmän 1 antama arvosteluvarmuus oli keskimäärin 2% parempi maitotuotoksen, 3% parempi valkuaistuotoksen ja 1% huonompi rasvatuotoksen suhteen kuin menetelmällä, jossa populaation rakennetta ei huomioitu. Rotukohtaisten alleelifrekvenssien huomioiminen genomisen sukulaisuusmatriisin muodostamisessa (menetelmä 2) ei parantanut arvosteluvarmuutta verrattaessa menetelmään, jossa niitä ei huomioitu. Sen sijaan genomisten jalostusarvojen laskeminen populaation kaikille eläimillä samanaikaisesti antoi keskimäärin 5% paremman arvosteluvarmuuden kuin tilanne, jossa genomiset jalostusarvot laskettiin vain genotyypitetyille sonneille. Yhteenvetona voidaan todeta, että populaatiorakenteen huomioiminen genomisten jalostusarvojen laskennassa tuo vain pienen parannuksen arvosteluvarmuuteen. Sen sijaan genomisten jalostusarvojen laskeminen populaation kaikille eläimille samanaikaisesti on suositeltavaa

Evaluation of female fertility in dairy cattle enterprises – A review

The aim of this article was to review the state of fertility of female dairy cattle in South Africa and to compare it with international efforts at improving fertility. Fertility in dairy cows is defined as the ability to conceive from first insemination soon after calving and to carry the calf full term to calving. It is one of the main profit drivers in the dairy industry and is a complex trait that is influenced by the environment, genetics, and their interaction. Generally, there has been a decline in dairy cow fertility across breeds worldwide because of intense selection for milk yield, milk components, and body conformation traits. In addition, most fertility traits are negatively correlated to milk production traits. Milk production has been the focal point of selection programmes as it is linked directly to the profitability of the dairy enterprise. The low heritability of fertility traits is one of the factors that discouraged efforts to include fertility in genetic evaluations. However, owing to its economic importance, female fertility was later included in the breeding objectives for dairy cattle in several countries. Although most fertility traits are heritable to a low degree, some additive genetic variability can be exploited

Investigation of effects of three candidate genes on leg action and fat deposition traits in pigs

Data from 188 sows were used in the current study to examine the effects of high mobility group AT-hook1 (HMGA1), transcription factor 7-like-2 (TCF7L2) and insulin-like growth factor binding protein 3 (IGFBP3) genes on leg action and fat deposition traits, and further to explore the possible relationships between these genes on both traits. The candidate genes used in the study are known for their roles in fat deposition and growth. Overall leg action was scored on a scale of 1 (good movement) to 9 (leg weakness). Fatness traits included 10th rib backfat (BF10), adjusted 10th rib backfat to 125 kg (adjBF10) and last rib backfat (last BF), measured by ultrasonic imaging approach. The association analyses between single nucleotide polymorphisms (SNPs) and traits were performed using PROC MIXED procedures of SAS. The results showed that the associations between HMGA1, TCF7L2 and IGFBP3 genotypes with fat deposition traits were mostly suggestive in this limited data set. Leg action was also suggestively associated with IGFBP3 gene effects but was not associated with HMGA1 and TCF7L2 genes. Thus, IGFBP3 AA homozygote individuals tended to have had better movements (5.40), and were fatter when compared to GG homozygotes (5.84). The results from this study suggest a possible association between the IGFBP3 gene effects on both leg action and fatness. Therefore, further studies must be carried out in several populations, and using larger data to demonstrate these results conclusively

Across breed multi-trait random regression genomic predictions in the Nordic Red dairy cattle

Current genomic prediction equations, when carried out in multiple populations with admixed structures ignore structure and assume these populations are uniform. The observed reliabilities of direct genomic breeding values (DGV) for unproven bulls in these populations so far have been low. The current study evaluated reliabilities of DGV in selection candidates using multi-trait random regression model which account for interactions between marker effects and breed of origin in the admixed Nordic Red dairy cattle. Our breed-specific model used breed proportions (BP) as random predictors and deregressed proofs of estimated breeding values (DRP) as response variables weighted by approximated reliability of DRP. Reliabilities were explored as squared correlation between DRP and DGV, weighted by the mean reliability of DRP. Estimated reliabilities were low for milk (0.32) and protein (0.32) and slightly higher (0.42) for fat. Observed reliabilities were similar to those estimated assuming homogenous structure. The Nordic Red cattle is admixed but closely related, thus, the model under investigation may have been unable to differentiate additive genetic effects by breed of origin with a medium dense marker dataNon peer reviewe

Genome-wide identification of breed-informative single-nucleotide polymorphisms in three South African indigenous cattle breeds

Access to genotyping assays enables the identification of informative markers that discriminate between cattle breeds. Identification of these markers can assist in breed assignment, improvement and conservation. The objective of this study was to identify breed informative markers to discriminate between three South African indigenous cattle breeds. Data from BovineSNP50 and GeneSeek Genomic Profiler (GGP-80K) assays were generated for Afrikaner, Drakensberger and Nguni, and were analysed for their genetic differentiation. Hereford and Angus were included as outgroups. Breeds were differentiated using principal component analysis (PCA). Single-nucleotide polymorphisms (SNPs) within the breeds were determined when minor allele frequency (MAF) was ≥ 0.05. Breed-specific SNPs were identified using Reynolds Fst and extended Lewontin and Krakauer's (FLK) statistics. These SNPs were validated using three African breeds, namely N’Dama, Kuri and Zebu from Madagascar. PCA discriminated among the breeds. A larger number of polymorphic SNPs was detected in Drakensberger (73%) than in Afrikaner (56%) and Nguni (65%). No substantial numbers of informative SNPs (Fst ≥ 0.6) were identified among indigenous breeds. Eleven SNPs were validated as discriminating the indigenous breeds from other African breeds. This is because the SNPs on BovineSNP50 and GGP-80K assays were ascertained as being common in European taurine breeds. Lower MAF and SNP informativeness observed in this study limits the application of these assays in breed assignment, and could have other implications for genome-wide studies in South African indigenous breeds. Sequencing should therefore be considered to discover new SNPs that are common among indigenous South African breeds and also SNPs that discriminate among these indigenous breeds

Genomic technologies for food security : a review of challenges and opportunities in Southern Africa

The Southern African Development Community (SADC) region includes 15 member states which all face growing population numbers and a possible protein shortage within the next 20 years. Although these countries have a wealth of livestock genetic resources and mostly are quite agriculturally dependent, there exist clear limitations and challenges regarding animal recording, genetic improvement, production efficiency and the implementation of new technologies, such as genomic selection (GS). Genomic selection incorporates genomic information with phenotypic information (breeding values) to derive genomic estimated breeding values (GEBV) and leads to an increased rate of genetic improvement. The countries within the SADC region are in several stages of development with regard to agriculture and infrastructural development and this limits the implementation of advanced technologies. The establishing of reference populations seems beyond the capacity of most of these countries at present, mainly in terms of financial viability, infrastructural support and national cohesion. Genomic technology however holds potential for the introgression of favourable genes in resource-poor livestock production systems and traceability of livestock products. Furthermore,identification of traits associated with adaptability and disease resistance and unique products would contribute to food security on various levels. This review discusses interventions that may mitigate constraints, and proposes key research areas needed for addressing the limitations mentioned.Cape Wools SA, the Western Cape Agricultural Research Trust, the Technology and Human Resources for Industry Programme.http://www.elsevier.com/locate/foodres2016-10-31hb201

Gene-set enrichment analysis of selective sweeps reveals phenotypic traits in Nguni cattle

Adaptation of animals to different environments is typically associated with structural and functional genomic variations. High throughput SNP genotyping and next-generation sequencing (NGS) have made it possible to study positive selection footprints and adaptation traits. Nguni is a small frame-size breed, mostly horned, and well known for being adapted to diverse South African environmental conditions. This study used previously identified selective sweeps to perform functional analysis of genes related to phenotypic characteristics in Nguni. Two hundred and sixty-four candidate selective sweeps were used for gene-set enrichment analysis in molecular functional categories (KEGG pathways) using the database for annotation, visualization, and integrated discovery (DAVID). In total, 107 genes were identified across all the chromosomes with 74 genes associated with eight phenotype queries, including fat content, milk production, walking ability, heat tolerance, meat production, reproduction, and bone and muscle development. Gene CRHR2 was associated with meat quality (juiciness and flavour). The IRAK3 gene was associated with decreased body size, feed intake and fatness in cattle, and CARD15 with disease resistance. Gene annotation using phenotype queries identified four genes (SPI, YWHAZ, RGS4, and RGS5) that were associated with myometrial relaxation in cattle. Genes such as NOD2 and IL21R were associated with inflammatory bowel diseases in cattle, whereas CPLS gene was associated with fat content. These genes are important to the phenotypic and adaptive characteristics present in South African Nguni cattle and hold potential for selection for traits of economic importance.The Red Meat Research and Development of South Africa (RMRDSA) and the National Research Foundation (NRF).http://www.sasas.co.zaam2022Animal and Wildlife Science