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

Basiese oorsig van vee-genomika

Stoettelers, produsente en veekundiges word deesdae links en regs met die term ‘genomika’ gekonfronteer. Terme soos dié word egter nie aldag goed verstaan nie en dikwels in die verkeerde konteks gebruik. In hierdie artikel verduidelik ek graag hierdie vakwoord en gee ’n bietjie agtergrond oor die algemene beginsels van vee-genomika.http://www.veeplaas.co.zaam2022Animal and Wildlife Science

Ouerskapbepaling deur DNS-toetsing

In Suid-Afrika is vleisbeesboerdery dikwels ekstensief van aard. Diere word oor groot oppervlakareas aangetref en dit bemoeilik akkurate waarneming en rekordhouding van parings. In kommersiële kuddes waar groep- en/of kuddeparings gedoen word en minder intense bestuursbeginsels somtyds toegepas word, is onbekende of verkeerde vaderskaptoekenning 'n groot probleem. Selfs in stoetboerdery, waar enkelparings en kunsmatige inseminasie (KI) algemeen toegepas word, word daar dikwels foute gemaak met die aantekening van veral vaderskap van nuwe kalfieshttp://reference.sabinet.co.za/sa_epublication/vp_stud?am201

Morphological characterisation of three indigenous Mozambican cattle populations

Information on phenotypic and morphometric variation is important in the characterisation of indigenous cattle breeds.  The objective of this study was to assess the morphological variation of the indigenous Angone, Landim, and Tete cattle breeds of Mozambique, kept under traditional management systems. These breeds are farmed mainly for meat and draught power, although they can produce some milk, especially the Landim. Data were collected through a survey of twenty-three villages in Maputo, Gaza, Inhambane (southern Mozambique), and Tete (central Mozambique) provinces. A total of 614 heads of adult animals including 140 Angone, 292 Landim, and 182 Tete were sampled.  The collected qualitative and quantitative data were examined using SPSS version 16. The dominant coat pattern was even (no spotting) (59.5 %), with black being the most common coat colour (51.5 %), followed by light brown (26.5 %). The three breeds showed morphological differentiation based on size, body weight, and horn shape. Landim males and females were significantly (p0.05) heavier than their Tete and Angone counterparts. Across breeds, the majority of cattle (95.2 %) had horns, and 66.9 % of these horns were curved. Individual assignment using discriminant function analysis revealed that 73.0 % of Landim, 77.4 % of Angone, and 59.9 % of Tete cattle were correctly assigned to their respective populations. Results from this study indicate a considerable phenotypic variation of Mozambican indigenous cattle and will assist in future improvement and conservation programs

Validation of the 50k Illumina goat SNP chip in the South African Angora goat

Tools for the genomic evaluation of goats have generally lagged behind those for other species. However, the recent availability of the goat SNP50 consortium bead chip has marked a positive change for this small ruminant species. Polymorphic loci can differ greatly between breeds of the same species. Exclusion of fibre-producing breeds, such as the Angora goat, during the development of this genotyping array necessitates the validation of SNPs included on the chip to allow for genomic applications that would accelerate genetic progress in mohair yield and quality. Forty eight unrelated Angora goats, displaying phenotypic variation in two important price-determining traits, namely fibre diameter and fleece weight, were genotyped with the goat SNP50 consortium bead chip. Results revealed that 46 983 SNP (88.1%) of the 53 347 called SNPs were polymorphic (MAF>0.05). After quality control, 3 960 SNP were filtered from further analysis for violating Hardy-Weinberg and call-rate parameter thresholds, leaving 43 759 (82%) of the 53 347 SNPs to be validated for downstream analysis. Observed and expected heterozygosity values of 0.365 and 0.370, respectively, were obtained for polymorphic SNPs. A total of 30 357 SNPs in linkage disequilibrium (LD) were removed to obtain a set of independent markers, resulting in a final SNP density of 1 SNP/ ~226 kb. Results indicate that the goat SNP50 bead chip was informative in the Angora goats that were studied, and should be useful in examining the underlying genetic variation.http://www.sasas.co.zaam201

Incorporating new technologies in breeding plans for South African goats in harsh environments

• Angora and meat producing goats play an important role in food security and sustainable livelihoods of livestock producers in South Africa. To maintain their role, it is important to select animals that can thrive in the harsh South African climate, especially under the envisioned climate change conditions. • Several phenotypes have been identified as selection criteria for adaptation. These include litter size at birth, litter size at weaning and litter weight at weaning (reproduction), weaning weight (growth), fecal egg counts, FAMACHA score, packed cell volume, tick counts, hair length, and coat type (endo- and ecto-parasite resistance) and coat type, coat thickness, color of skin and coat, rectal temperature (heat tolerance). Many of these phenotypic indicator traits have limitations such as low heritabilities or being difficult to measure. • The application of new technologies in breeding and selection is under-utilized in goats in general, and especially in South African goats. The use of validated causative mutations affecting traits relating to adaptation to harsh environments in selection programs would facilitate genetic progress in herds where phenotypic recording is challenging. • In addition, increased investments by various role players in applying new technology in the systematic collection of phenotypic indicator traits (especially for traits related to adaptation), can be used to improve the rate of animal improvement in the South African goat breeds.https://academic.oup.com/afam2024Animal and Wildlife SciencesSDG-02:Zero Hunge

Genetic Improvement in South African Livestock: Can Genomics Bridge the Gap Between the Developed and Developing Sectors?

South Africa (SA) holds a unique position on the African continent with a rich diversity in terms of available livestock resources, vegetation, climatic regions and cultures. The livestock sector has been characterized by a dual system of a highly developed commercial sector using modern technology vs. a developing sector including emerging and smallholder farmers. Emerging farmers typically aim to join the commercial sector, but lag behind with regard to the use of modern genetic technologies, while smallholder farmers use traditional practices aimed at subsistence. Several factors influence potential application of genomics by the livestock industries, which include available research funding, socio-economic constraints and extension services. State funded Beef and Dairy genomic programs have been established with the aim of building reference populations for genomic selection with most of the potential beneficiaries in the well-developed commercial sector. The structure of the beef, dairy and small stock industries is fragmented and the outcomes of selection strategies are not perceived as an advantage by the processing industry or the consumer. The indigenous and local composites represent approximately 40% of the total beef and sheep populations and present valuable genetic resources. Genomic research has mostly provided insight on genetic biodiversity of these resources, with limited attention to novel phenotypes associated with adaptation or disease tolerance. Genetic improvement of livestock through genomic technology needs to address the role of adapted breeds in challenging environments, increasing reproductive and growth efficiency. National animal recording schemes contributed significantly to progress in the developed sector with regard to genetic evaluations and estimated breeding values (EBV) as a selection tool over the past three decades. The challenge remains on moving the focus to novel traits for increasing efficiency and addressing welfare and environmental issues. Genetic research programs are required that will be directed to bridge the gap between the elite breeders and the developing livestock sector. The aim of this review was to provide a perspective on the dichotomy in the South African livestock sector arguing that a realistic approach to the use of genomics in beef, dairy and small stock is required to ensure sustainable long term genetic progress

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

A homozygosity-based investigation of the South African feral Tankwa goat population

The Tankwa goat is a known feral goat landrace that originated in the Karoo region of South Africa. These goats are able to thrive with no managerial intervention, and prosper in the harsh, arid conditions that characterizes their natural habitat. This study aimed to use a ROH-approach to describe the Tankwa goat in terms of autozygosity and to identify possible signatures of selection. Genome-wide SNP data for 360 Tankwa goats were used to calculate diversity statistics, detect runs of homozygosity and estimate individual genetic inbreeding coefficients. SNP genotypes of 48 Angora and 40 Dairy individuals were compared using the FST approach to detect signatures of selection. Relatively low minor allele frequency (0.249), and high linkage disequilibrium (r2 = 0.469) levels were estimated for the Tankwa population, with moderate levels of heterozygosity (HE = 0.368; HO = 0.367). The results for both the detected runs of homozygosity and inbreeding estimate, indicates an ancient origin of inbreeding for the Tankwa goats with low levels of autozygosity. Signatures of selection were identified in 50 SNPs, of which 0.1% was considered significant. A total of 49 genes were identified that may possibly be significant in various biological pathways. Three of these genes, namely GJB2, GJB6 and GJA3 on CHI12, were previously associated with adaptation to heat and drought resistance in other breeds. Genes GJB2 and GJB6 are known to be linked to the sensory perception of sound, while GJA3 and OPA3 are linked to visual perception. These genes could play an important role in the survival of an individual existing in a harsh environment in terms of foraging and evading predators. Understanding the genetic background of these genes, as well as the metabolic pathways that they control, could assist in further investigating production efficiency of domesticated species in a climate change environment.The Department of Agriculture, Environmental Affairs, Rural Development and Land Reform.https://www.elsevier.com/locate/smallrumresAnimal and Wildlife SciencesSDG-02:Zero HungerSDG-15:Life on lan

Smallholder Goat Production in Southern Africa: A Review

Goats play a crucial role in improved livelihoods and food security in Africa. Indigenous and locally developed types exhibit a wide range of phenotypic diversity, but are commonly well adapted to the harsh environment in which they need to survive and produce. They have various functions in communities in developing countries, from providing food security to being a liquid form of cash and playing a role in ceremonial occasions. The Southern African goat population exceeds 35 million animals, most of which are kept in small-scale traditional production systems in communal areas. These traditional production systems are characterised by informal, lowly-skilled labour, small numbers of animals and limited resources. Most goats are part of mixed crop-livestock systems, where different livestock species and crop farming compliment one another. The productivity and offtake from these animals are relatively low. Some goats form part of agropastoral production systems, with marginally higher management and resource inputs. Both of these systems are dependent on a high degree of variability where the keepers/farmers can exploit various resources as and when necessary. Goats possess a range of adaptive mechanisms that enable them to deal with harsh and challenging environments, making them the ideal species for use in these production systems. This chapter aims to provide background information on the current smallholder management practices of goat keepers in Southern Africa