The Development and Genetic Improvement of South African Goats

South Africa has a thriving goat industry, consisting of fiber, meat and dairy‐producing goat breeds. These animals play an important role in terms of food security, socioeconomic welfare and cultural well‐being. The South African goat industry is differentiated into a formal, commercial market with niche products such as mohair, chevon and goat’s cheeses versus the informal, mainly meat‐producing sector serving communal and smallholder farmers. Exotic and locally improved breeds, i.e., Angora, Saanen and Boer goats mainly serve the commercial industries, whereas the unimproved veld goat populations are well adapted in the resource‐poor environments. Genetic improvement has historically been limited to the commercial breeds, but poor participation in animal recording and improvement schemes have resulted in slow genetic progress, with the exception of the Angora goat. Molecular research has opened up new possibilities for genetic characterization, preservation and utilization of the unique genetic resources retained by these animals

The Tankwa Karoo National Park feral goat population:A unique genetic resource

The feral goats from Tankwa Karoo National Park in the Northern Cape, South Africa, constitute a potentially unique goat population, which dates back to the early 1900s, but is now at risk of extinction. A total of 66 feral goats from Tankwa Park and former Tankwa goats, now kept on a private farm were genotyped, using eight microsatellite markers. The data were compared with genotypic data of selected commercial breeds (Angora, Boer and Saanen dairy goats). Analysis of population structure using Bayesian and frequency-based methods suggests some uniqueness in the Tankwa populations. This uniqueness may reflect decades of random drift, but could also reflect alleles for adaptation to a harsh environment resulting from natural selection. These results are the first for the Tankwa goat and provide essential information for compiling a strategy for conservation and breeding of this genetic resource.http://www.sasas.co.za/hb201

Capitalizing on the Potential of South African Indigenous Beef Cattle Breeds: A Review

Cattle populations arrived in Southern Africa almost 2000 years ago, brought by farming communities migrating southwards. For centuries, cattle have been an integral component of livestock production to meet the animal protein needs of a growing population and they are also important in many cultural and religious events, as repositories of wealth and signifiers of social status. Selection within these cattle populations led to the development of breeds such as the Nguni, Afrikaner and Drakensberger that are well adapted to the local production environment. Genetic information has been generated for most of these populations, providing new insights into their ancestry and indicating moderate levels of diversity and relatively low inbreeding. Indigenous cattle breeds are present in both the well-developed commercial sector as well as the developing South African livestock sector. These breeds have been included in several research studies, mostly focusing on their production and adaptive potential. Genetic improvement of the local cattle populations and breeds, which are often more resilient to local environmental conditions, has the potential to improve the productivity of the small-scale production developing sector and contribute to the alleviation of poverty

Novel Insights into the Bovine Polled Phenotype and Horn Ontogenesis in Bovidae

Despite massive research efforts, the molecular etiology of bovine polledness and the developmental pathways involved in horn ontogenesis are still poorly understood. In a recent article, we provided evidence for the existence of at least two different alleles at the Polled locus and identified candidate mutations for each of them. None of these mutations was located in known coding or regulatory regions, thus adding to the complexity of understanding the molecular basis of polledness. We confirm previous results here and exhaustively identify the causative mutation for the Celtic allele (PC) and four candidate mutations for the Friesian allele (PF). We describe a previously unreported eyelash-and-eyelid phenotype associated with regular polledness, and present unique histological and gene expression data on bovine horn bud differentiation in fetuses affected by three different horn defect syndromes, as well as in wild-type controls. We propose the ectopic expression of a lincRNA in PC/p horn buds as a probable cause of horn bud agenesis. In addition, we provide evidence for an involvement of OLIG2, FOXL2 and RXFP2 in horn bud differentiation, and draw a first link between bovine, ovine and caprine Polled loci. Our results represent a first and important step in understanding the genetic pathways and key process involved in horn bud differentiation in Bovidae

Understanding beef cattle production practices and associated factors constraining performance: A survey of smallholder farmers in South Africa

Farm practices of beef cattle smallholders in South Africa are characterized by poor management  practices with limited advisory services. This study aimed to assess current beef cattle farming practices and limiting factors for improved beef production in South African smallholder farmers. A questionnaire was administered to 460 individual smallholder farmers purposively selected from seven provinces of South Africa (SA). The questionnaire captured information on demographics and farm profiles, constraints on production, marketing, ecological and reproduction management. Frequency procedure and logistic regression were used for data analysis. The majority of farmers were males (77%), fully committed to cattle farming (92%) and participated in informal markets (61%). Farmers constraints included extreme weather events, disease outbreaks, lack of access to information on farm management, supply of cattle nutrition and fair market pricing. The majority (93%) of farmers had no knowledge on body condition scoring (BCS) prior breeding and recorded inter-calving periods of two years (77%). Only 17% of farmers kept calving records and 80%  practices culling of old cows. The regression model revealed that lack of information and understanding of farm business, and information communicated by government were among the dominating factors associated with the constraints. The study confirmed the need to enhance the approach of farm information dissemination and skills transfer to mitigate farming challenges and improve productivity. Policy makers may ensure adoption of farm information chains through more implementations of open platforms such as farmer's schools and farmers days

Understanding the underlying genetic mechanisms for age at first calving, inter-calving period and scrotal circumference in Bonsmara cattle

peer-reviewedBackground Reproduction is a key feature of the sustainability of a species and thus represents an important component in livestock genetic improvement programs. Most reproductive traits are lowly heritable. In order to gain a better understanding of the underlying genetic basis of these traits, a genome-wide association was conducted for age at first calving (AFC), first inter-calving period (ICP) and scrotal circumference (SC) within the South African Bonsmara breed. Phenotypes and genotypes (120,692 single nucleotide polymorphisms (SNPs) post editing) were available on 7,128 South African Bonsmara cattle; the association analyses were undertaken using linear mixed models. Results Genomic restricted maximum likelihood analysis of the 7,128 SA Bonsmara cattle yielded genomic heritability’s of 0.183 (SE = 0.021) for AFC, 0.207 (SE = 0.022) for ICP and 0.209 (SE = 0.019) for SC. A total of 16, 23 and 51 suggestive (P ≤ 4 × 10-6) SNPs were associated with AFC, ICP and SC, while 11, 11 and 44 significant (P ≤ 4 × 10-7) SNPs were associated with AFC, ICP and SC respectively. A total of 11 quantitative trait loci (QTL) and 11 candidate genes were co-located with these associated SNPs for AFC, with 10 QTL harbouring 11 candidate genes for ICP and 41 QTL containing 40 candidate genes for SC. The QTL identified were close to genes previously associated with carcass, fertility, growth and milk-related traits. The biological pathways influenced by these genes include carbohydrate catabolic processes, cellular development, iron homeostasis, lipid metabolism and storage, immune response, ovarian follicle development and the regulation of DNA transcription and RNA translation. Conclusions This was the first attempt to study the underlying polymorphisms associated with reproduction in South African beef cattle. Genes previously reported in cattle breeds for numerous traits bar AFC, ICP or SC were detected in this study. Over 20 different genes have not been previously reported in beef cattle populations and may have been associated due to the unique genetic composite background of the SA Bonsmara breed

Genetic Diversity and Population Structure in South African, French and Argentinian Angora Goats from Genome-Wide SNP Data.

The Angora goat populations in Argentina (AR), France (FR) and South Africa (SA) have been kept geographically and genetically distinct. Due to country-specific selection and breeding strategies, there is a need to characterize the populations on a genetic level. In this study we analysed genetic variability of Angora goats from three distinct geographical regions using the standardized 50k Goat SNP Chip. A total of 104 goats (AR: 30; FR: 26; SA: 48) were genotyped. Heterozygosity values as well as inbreeding coefficients across all autosomes per population were calculated. Diversity, as measured by expected heterozygosity (HE) ranged from 0.371 in the SA population to 0.397 in the AR population. The SA goats were the only population with a positive average inbreeding coefficient value of 0.009. After merging the three datasets, standard QC and LD-pruning, 15 105 SNPs remained for further analyses. Principal component and clustering analyses were used to visualize individual relationships within and between populations. All SA Angora goats were separated from the others and formed a well-defined, unique cluster, while outliers were identified in the FR and AR breeds. Apparent admixture between the AR and FR populations was observed, while both these populations showed signs of having some common ancestry with the SA goats. LD averaged over adjacent loci within the three populations per chromosome were calculated. The highest LD values estimated across populations were observed in the shorter intervals across populations. The Ne for the Angora breed was estimated to be 149 animals ten generations ago indicating a declining trend. Results confirmed that geographic isolation and different selection strategies caused genetic distinctiveness between the populations