Genetic and phenotypic characterization of native fowl populations in South Africa

Native fowl populations in South Africa were characterized genetically and phenotypically. Four South African native populations, two dual-purpose breeds, and two populations from Mozambique and Botswana were included for genetic analysis. For phenotypic characterization, two commercial lines were also included as a benchmark. Twenty-three micro satellite markers were selected and tested to obtain genetic data for estimation of genetic variability and distance. Growth (weight gain) and egg production were included for phenotypic characterization. A relatively high (53% ¬64%) genetic variation was found among the populations, which suggests conservation as a genetic resource for future use. The lowest genetic variation (53%) was found for the Koekoek and Australorp populations, which are the two populations that were subjected to formal selection, while the highest variation was observed in the Naked Neck population (64%). The New Hampshire has often been included in upgrading programs and this is evident from the close relationship with both the Lebowa- Venda and Naked Neck fowls. Phenotypic trials indicated significant differences among the populations included for growth, carcass and egg production traits. The Koekoek and New Hampshire populations had the best performance for egg production and growth (weight gain) in the study. Genetic and phenotypic differences indicate that the populations can be distinguished as different breeds or groups of fowl. The results of this study may contribute to selection for improved performance for household food production, as well as conservation of the populations as a genetic resource.Thesis (PhD)--University of Pretoria, 2001.Animal and Wildlife Sciencesunrestricte

Strategies for the genetic improvement of South African Angora goats

Selection of Angora goats over the past decades has focused on traits related to fitness, body weight and fiber production. Research for genetic improvement of the Angora has been based on quantitative selection and more recently molecular technology has been applied. Although considerable progress has been made at increasing fine mohair production, the inability of Angora goats to survive sub-optimum conditions has become a concern. Selection emphasis on fibre production resulted in unthrifty animals and the South African (SA) Angora industry is still hampered by the loss of young goats. DNA marker information assists conventional selection by increasing selection accuracy, improving the rate of genetic improvement and leading to a better understanding of the physiological background of traits. The genetic diversity of the SA Angora goat breed was estimated and an improved linkage map was recently developed. The extensive production systems in South Africa pose a challenge for pedigree integrity, and a microsatellite panel was constructed for parentage verification. Selection for quantitative trait loci (QTL) will lead to increased genetic progress and offers the opportunity to improve understanding of and exploit phenotypic variation. Putative QTL associated with fleece and growth traits have been identified in the South African Angora goat population. The current goat SNP chip does not include any fibre-producing goat breed, and this chip is currently being verified in the SA Angora goat population, in conjunction with the sequencing of certain keratin genes.http://www.elsevier.com/locate/smallrumreshb201

Parentage verification of South African Angora goats, using microsatellite markers

South African Angora goats are farmed under extensive production systems in relatively large herds. As a result, breeders make use of group and flock-mating systems that limit accurate parentage recording and selection efficiency. In this study the aim was to refine a panel of microsatellite markers suitable for parentage verification in South African Angora goats. The markers were first evaluated based on the number of alleles, allele frequency, PIC, HE, HO and individual exclusion probability, and secondly as part of a panel. Eighteen markers were tested in 192 South African Angora goats representing different family structures with known and unknown parent information. The final set of microsatellite markers, with the strongest exclusion and the least number of microsatellite markers, consisted of 14 microsatellite markers namely BM1258, BM1329, BM1818, BM7160, CSRD247, HSC, INRA63, INRABERN192, MCM527, OarFCB48, SRCRSP5, SRCRSP8, SRCRSP9 and SRCRSP24. This panel had a combined first-parent exclusion probability of 99.7% and it was possible to perform parental identification in a test family.http://www.sasas.co.zanf201

A perspective on the impact of reproductive technologies on food production in Africa

Africa for the largest part is still regarded as part of the developing world and has a history of political instability, natural disasters, floods and droughts that all had an effect on the development of livestock production systems and the potential application of biotechnologies. It is expected that the human population in sub Saharan Africa will experience a growth of 1.2 % per year over the next 30 years. There is therefore pressure to increase sustainable productivity of livestock. Reproductive technologies such as Artificial Insemination in Africa were driven primarily by the need to control or prevent venereal diseases like Trichomoniases and Campylobacter fetus venerealis in cattle. Reproductive biotechnology had a limited impact in Africa due to several factors including a lack of infrastructure and animal recording systems, clear breeding objectives and continuously changing production systems and markets. Africa has a large variety of genetic resources adapted to the diverse environment and production systems and biotechnology should be applied within this context for an increase in food production.http://www.springer.comseries/55842015-06-30hb201

Frequency of the malignant hyperthermia gene in the South African pig industry

Porcine stress syndrome (PSS) is a genetic disorder caused by a recessive mutation in the halothane (HAL) gene and results in sudden death of pigs when placed under stress during transport and pre-slaughtering conditions. Animals that are affected by this mutation tend to develop pale, soft and exudative (PSE) meat, which results in an economic loss. In South Africa, the frequency of the number of carriers (Nn) and recessive (nn) pigs has increased by 21% to 30% from 2000 to 2003. This study aims to determine the prevalence of the malignant hyperthermia (MH) gene in breeding boars at nucleus or seed-stock level, and the prevalence at commercial abattoirs across the South African pig industry. Results indicate a low number of carriers (Nn = 17) and recessive (nn = 1) pigs at seed-stock level. For commercial abattoirs, 96.4% of the pigs tested did not carry the mutation. The low incidence of the MH mutation from breeding stock should eliminate a contributory factor to PSE meat in South Africa. Transport over long distances to abattoirs may ultimately have an effect on pork obtained even from non-carriers of the MH mutation.http://www.sasas.co.zahb201

Genetic diversity of South African dairy goats for genetic management and improvement

The dairy goatindustry is a small, butimportant role player in the South African agricultural sector. The limited number of animals representing the three main breeds (Saanen, British Alpine and Toggenburg) has raised concerns over the genetic diversity of these animals and the impact on their genetic management. In this study, 240 dairy goats representing three breeds were genotyped with 25 microsatellite markers. Sufficientlevels of genetic diversity were observed in all the breeds, with observed heterozygosity values exceeding 60%. A slight population differentiation was indicated by the low FST values across and within the populations. This was confirmed by the AMOVA analyses with most of the variation shown within populations (91.7%). Negative FIS values in the three breeds indicated limited inbreeding. Population structure analyses revealed six distinct groups, with the Saanen population clustering into three sub-groups. The Toggenburg and British Alpine breeds formed their own separate cluster, with a last cluster formed by animals from all three pure-bred populations, indicating high levels of admixture. These results caution farmers against uncontrolled crossbreeding practices and recommend routine evaluation of genetic diversity.This work is based on the research supported in part by a number of grants from the National Research Foundation of South Africa (UID: 78566 (NRF RISP grant for the ABI3500)).http://www.elsevier.com/locate/smallrumreshb2017Animal and Wildlife Science

Identification of novel variants for KAP 1.1, KAP 8.1 and KAP 13.3 in South African goats

The yield and quality of animal fibres such as mohair, cashmere and cashgora are primarily influenced by the expression of various keratin associated protein genes, such as KAP 1.1, KAP 8.1, and KAP 13.3. Recent developments in molecular genetics provide the opportunity to characterize KAP genes at a base-pair level, which can lead to improved selection and genetic progress in mohair fibre production. PCR and sequencing technology was used to identify and characterize KAP 1.1, KAP 8.1, and KAP 13.3 in 108 goats, representing the South African Angora, Boer and Angora x Boer goat populations. The three genes showed varying degrees of polymorphism with between 4 and 18 alleles identified per locus. Some discrepancies in the current gene sequence of KAP 1.1 were discovered. Nineteen novel variants were identified in total, seven for KAP 1.1, one for KAP 8.1 and eleven for KAP 13.3. Observed heterozygosity values closely matched expected heterozygosity values, with Boer goats consistently having the lowest levels of expected and observed heterozygosity (approximately 0.5) for all three of the genes. The greatest variation for each gene existed between the Angora and Boer goat breeds, with FST values of 0.28, 0.13, and 0.24 for KAP 1.1, 8.1, and 13.3 respectively. Predominant alleles differed between the various populations, indicating the need for further research into possible allelic and fibre quality associations.http://www.elsevier.com/locate/smallrumres2018-04-30hj2017Animal and Wildlife Science

Gene expression profiles of the small intestine of village chickens from an Ascaridia galli infested environment

Nematodes of the genus Ascaridia are known to infect many species of birds and result in fatal diseases. A. galli damages the intestinal mucosa of chickens leading to blood loss, secondary infection and occasionally the obstruction of small intestines due to high worm burden. This study investigated the gene expression profiles in chickens from two different provinces of South Africa naturally exposed to A. galli infestations and tested either positive or negative for the parasite. The study further investigated gene expression profiles of the A. galli infected duodenum, jejunum and ileum tissues of the small intestines. The A. galli positive intestines displayed hypertrophy of the intestinal villi with accumulation of inflammatory cells and necrosis of the crypts of Lieberkühn glands, lesions that were absent in the uninfected intestines. Total RNA isolated from small intestines of infected and non-infected intestines was sequenced using Illumina HiSeq technology to generate up to 23,856,130 reads. Between any two-way comparisons of the intestines, 277 and 190 transcripts were significantly expressed in Limpopo and KwaZulu-Natal (KZN) chickens, respectively. Gene ontology analysis of the differentially expressed genes (DEGs) revealed an enrichment of genes reported to function in the immune response, defense response, inflammatory response and cell signalling genes. T cell receptor signalling pathways and arachidonic acid metabolism pathways were among the most significantly impacted pathways. Overall, the study provided insights into adaptative mechanisms for chickens extensively raised in parasite infected environments.Tthe Agricultural Research Council-BTP and the NRF under the Zambia/south Africa bilateral Research Program. Dr Malatji received an NRF-DST Professional Development Program research fellowship and University of Pretoria postgraduate support bursary.https://www.journals.elsevier.com/veterinary-parasitology-xpm2020Animal and Wildlife Science

Residual feed intake as selection tool in South African Bonsmara cattle

In South African Bonsmara cattle, feed conversion ratio (FCR) is mostly used as a measure of feed efficiency in selection programs but has the disadvantage of being a ratio trait and unfavourably correlated to weight and mature size. Residual feed intake (RFI) overcomes both these disadvantages. The purpose of this study was to evaluate RFI as a potential trait in a selection programme by determining its correlations with growth related traits as well as other efficiency traits. Data of 5981 Bonsmara bulls that participated in centralised growth tests was analysed. In this study, RFI was calculated within contemporary groups of more than ten animals. The h2 for RFI, FCR and KR were 0.27±0.02, 0.23±0.02 and 0.18±0.02 respectively. The genetic correlation between RFI and FCR, and RFI and KR were 0.65±0.04 and 0.12±0.07 respectively. Correlations approaching zero were estimated between RFI and shoulder height (SH), body length (BL), scrotal circumference (SC), average daily gain (ADG), weaning weight (WW) and metabolic mid-weight (MMW), and a strong correlation of 0.79±0.03 with daily feed intake (DFI). This study shows sufficient genetic variation for RFI to be considered by the Bonsmara breed as a measure of feed efficiency and confirms its independence from growth and size traits.http://www.elsevier.com/locate/livscihb201

SNP-based genetic diversity of South African commercial dairy and fibre goat breeds

Goats (Capra aegagrus hircus) have not been a prioritized livestock species with regards to molecular research. The genetic characterization of commercial South African (SA) goat breeds should contribute to improving the management of available animal genetic resources. The aim of this study was to investigate genetic diversity within and among SA commercial goat breeds utilizing the 50k goat beadchip. 88 goats originating from four breeds (dairy: British Alpine, Saanen, Toggenburg; fibre: Angora) were genotyped with the goat SNP50 beadchip. Average MAF values ranged from 0.25 for the Angora to 0.29 for the Saanen, with 46 983 and 50 368 polymorphic SNPs obtained for the respective breeds. Observed heterozygosity values ranged from 0.365 for the Angora to 0.431 for the Toggenburg breed. Linkage disequilibrium (LD) estimation revealed average r2 values of 0.12 and 0.15 for dairy and fibre breeds, respectively. LD decay was shown to occur after a distance interval of 20-40kb and 40-60kb for dairy and Angora breeds, respectively. Principal component analysis (PCA) produced clusters corresponding to the different production types (dairy and fibre). The Angora, British Alpine and Saanen breeds showed high proportions of membership to respective inferred ancestral populations with ADMIXTURE (97%, 84% and 92%, respectively). The results obtained in this study indicated genetic uniformity within dairy and fibre goats due to productionspecific trait selection. Sufficient levels of genetic variation was, however, observed to allow genetic progress for SA commercial goat breeds pending the improved management of these goat genetic resources.UP Genomics Research Institute.http://www.elsevier.com/locate/smallrumres2017-03-31hb2016Animal and Wildlife Science