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Addressing production challenges in goat production systems of South Africa: The genomics approach
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Functional traits have become increasingly important for efficient breeding schemes in the goat industry due to rising costs of production relative to product prices and consumers demanding healthy and nutritious food in addition to abiding to animal welfare standards. The challenges facing South African and other developing countries’ goat industries is in the implementation of cost-effective production systems for high quality meat and milk which is safe to the consumer from communal farming regions riddled by many production challenges. Genetic improvement for economically important traits such as growth, reproduction, health and product quality is currently based on convectional estimated breeding values. These methods have been practiced for several decades for breeds benefiting from efficient breeding schemes. South Africa is one of the few countries in the world that have successfully developed high producing commercialised goat breeds some of which have been adopted in other regions. Genetic progress using conventional genetic evaluations is however lengthy and based on a few traits. Molecular and genomic tools are increasingly being used for the detection and mapping of genes of economic importance in goats. Attention is turning to the simultaneous identification of genes for production and functional traits using whole genome sequence and genome-wide SNP data. South Africa has a rich genetic pool of feral, commercial, and indigenous non-descript goat populations to select from. Preliminary studies using the Illumina Goat SNP60K bead chip have revealed high genetic diversity and uniqueness of the South African goat breeds. The unique genomes of the different breeds and populations are a potential source of genetic variation, which could be useful for genetic improvement programs. Next generation sequencing and genotyping technologies present opportunities for genomic breeding schemes in the near future. This paper reviews current challenges faced by the goat industry in South Africa and worldwide. The feasibility of using second-generation genomic tools to improve traits of economic importance in the goat industry is discussed.
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... WGS studies done on the South African feral Tankwa goat revealed variants associated with cellular pathways, defense, and immunity [44]. SNPs that show a potential role in goat growth performance, diseases and adaptation processes have also been identified [44]. ...
... WGS studies done on the South African feral Tankwa goat revealed variants associated with cellular pathways, defense, and immunity [44]. SNPs that show a potential role in goat growth performance, diseases and adaptation processes have also been identified [44]. This technology has also been used in the identification of selection of signatures in important traits such as coat colour, growth, reproduction, and high-altitude adaptation in goats [45,46]. ...
... Whole genome sequencing has been very useful in the development of goat genomic studies especially in the sequencing of goat reference genomes. The first draft genome achieved through 11 WGS was from the female domestic goats Yunnan black goats with a genomic size of approximately 2.66 Gb [44]. This was followed by other goat genome sequences that have been successfully used in the identification of CNVs, SNPs and other genomic variants [44]. ...
Goat milk's medicinal properties and potential cosmetic and health benefits have prompted extensive scientific investigation into its therapeutic applications, particularly for human skin conditions like eczema and psoriasis. Genetic factors, including genes such as lactoferrin (LTF), lysozyme (LYZ), and β-casein (CSN2), play a crucial role in shaping milk composition and its effects on skin health. This review explores the utilization of genomic tools to elucidate the genomic profiles of dairy goat breeds and the medicinal properties of goat milk, particularly in addressing key skin diseases. Genetic determinants of milk composition, quality, nutritional quality, and functional properties such as the growth hormone receptor (GHR), butyrophilin (BTN1A1) and lactoglobulin (LGB) genes, facilitating targeted breeding strategies to enhance the production of bioactive compounds with dermatological relevance have been identified. Future genomic approaches should aim at exploring goat milk's immunomodulatory, antimicrobial, and antioxidant activities, offering potential applications in skin care formulations for managing inflammatory skin conditions. Furthermore, the integration of genomic data with functional studies can provide valuable insights into the therapeutic effects of goat’s milk and its derivatives in addressing skin diseases.
... In South Africa, there are over 6 million goats, and some of the breeds were commercialised and have gained international recognition; for example: Boer, Kalahari Red and Savanna goats. These goat breeds are known for their fast growth rate and good carcass quality [33,34]. The South African goat industry is dominated by three main products: meat (chevon), milk and fibre. ...
... The South African goat industry is dominated by three main products: meat (chevon), milk and fibre. Goat meat production contributed R 3.6 billion to the South African economy between 2001 and 2011 [33]. ...
The following are aspects were discussed in this chapter: Domestication of goats – checking on when the goats were first domesticated and for what purposes; Current goat industry - looking on the contribution of goats economically; Conservation of domestic animal diversity - looking on the importance of conserving indigenous animals since some of them are under threat of extinction; Male goat fertility – discussing male fertility indicators; Characterisation approaches - different approaches to be followed when characterising indigenous species; and Phenotypic and genetic characterisation of indigenous goats.
... Even though goat meat is rich in nutrients, the sensory attributes of goat meat are less desirable compared to meat sourced from other species [9]. Thus, goat meat consumption and retail availability in South Africa still fall behind other countries [10]. In terms of red meat in general, cattle are regarded as a priority over goats due to the multipurpose uses, marketing and other positive associations with the meat as opposed to goat meat [8]. ...
Although goat meat is a nutritious and sustainable Animal Food Source (AFS), it is not commonly preferred as an AFS in sub-Saharan Africa even though goats thrive in the region. To explore the potential of promoting goat meat consumption among young adults in KwaZulu-Natal, South Africa, an experimental study was conducted involving the development, nutrient analysis and microbial testing of two goat meat products through a series of recipe development trials. This study aimed to use food processing techniques to improve the sensory qualities of goat meat (texture and aroma) in value-added products. Goat meat patties and sausages were developed and evaluated for consumer acceptance using Check-All-That-Apply (CATA) food action rating scale and paired preference testing (n=100). Results from the nutrient analysis showed that both the patty (31.57g/100g) and the sausage (26.88g/100g) were high in protein. The total fat content for each sample was less than 10g per 100g portion.The coliform counts for both samples were very low and well within the acceptable range. The yeast and mould counts were very low, and total bacterial counts were low and within an acceptable range. The CATA test revealed the most frequently selected term used to describe the sensory attributes were ‘smoky’ for aroma (82%, 55%), ‘brownish-grey’ for appearance (68%, 80%), ‘meaty’ for flavour (92%, 86%), and ‘tender’ for texture (59%, 51%) for the goat meat patty and sausage, respectively. Participants showed a more positive attitude towards purchasing and consuming the goat meat patty (96%) than the goat meat sausage (88%). Both products received positive sensory feedback. However, the majority of the participants preferred the goat meat patty (66%) over the sausage (34%). The findings suggest that promoting goat meat consumption in South Africa can be achieved through the introduction of value-added convenience products like the goat meat patties and sausages developed in this study. Key words: Goat meat, goat meat patty, sausages, young adults, consumer acceptance
... South Africa contributes to almost 10% of the southern African goat population (Mohlatlole et al., 2015) with approximately 5.62 million goats distributed throughout nine provinces. The Limpopo province carries 17% of the national flock size and is ranked second after the Eastern Cape Province with 39% (DAFF, 2016). ...
Principal component analysis (PCA) is a vital statistical technique for defining the morphological structure of livestock but has not been used in South African Kalahari Red goats. Thirteen morphometric traits and eleven body indices from two hundred and ninety-six (296) South African Kalahari Red goats (269 does and 27 bucks) aged 2-3 years were used to define morphological structure using PCA. The coefficient of determination (R 2), root mean square error (RMSE), Akaike's information criterion (AIC), Mallows' Cp-statistic (Cp), and coefficient of variation (CV) were used to select the best fit model. Body weight was correlated with all morphometric traits in both sexes. The first two principal components explained 87.31% of the variation in measurements from male goats and 62.32% of the trait variation in the females. The inclusion of head length, body length, canon circumference, rump length, rump width, body condition score, wither height, and rump height increased the accuracy to 98% with smaller RMSE (2.42), AIC (55.35), Cp (10.00), and CV (3.98), and the use of PC1 and PC2 included 94% of the variation (RMSE, 3.62; AIC, 72.26; Cp, 3.00; CV, 5.94 in males). In females, the inclusion of all morphometric traits included 87% of the variation (RMSE, 2.93; AIC, 590.63; Cp, 13.00; CV 5.87). The use of PC1 and PC2 included 82% of the variation (RMSE, 3.41; AIC, 663.60; Cp, 3.00; CV, 6.84). PCA can therefore be used in breeding programs to define the morphological structure of South African Kalahari Red goats with a severe reduction in the number of morphometric traits to be recorded.
... According to Stonehavenstud [4], this breed is commonly known for its rapid growth, moderately high milk production and excellent mothering ability. Mohlatlole et al. [5] highlighted that this breed has a large body frame and underwent strict selection for larger carcasses and rapid growth. The live body weight of an animal is very crucial since it helps farmers manage their livestock during selection, feeding and medical dosages [6][7][8]. ...
The Savanna goat breed is an indigenous goat breed in South Africa that is reared for meat production. Live body weight is an important tool for livestock management, selection and feeding. The use of multivariate adaptive regression splines (MARS) to predict the live body weight of Savanna goats remains poorly understood. The study was conducted to investigate the influence of linear body measurements on the body weight of Savanna goats using MARS. In total, 173 Savanna goats between the ages of two and five years were used to collect body weight (BW), body length (BL), heart girth (HG), rump height (RH) and withers height (WH). MARS was used as a data mining algorithm for data analysis. The best predictive model was achieved from the training dataset with the highest coefficient of determination and Pearson’s correlation coefficient (0.959 and 0.961), respectively. BW was influenced positively when WH > 63 cm and HG >100 cm with a coefficient of 0.51 and 2.71, respectively. The interaction of WH > 63 cm and BL < 75 cm, WH < 68 cm and HG < 100 cm with a coefficient of 0.28 and 0.02 had a positive influence on Savanna goat BW, while male goats had a negative influence (−4.57). The findings of the study suggest that MARS can be used to estimate the BW in Savanna goats. This finding will be helpful to farmers in the selection of breeding stock and precision in the day-to-day activities such as feeding, marketing and veterinary services.
... Together with their crosses, these ecotypes have evolved to adapt to predominantly agro-ecological conditions [9]. These adaptive traits are important for climate change and make goats an important animal resource that needs to be prioritized for conservation for future food security in changing environments [10]. South African communal farming is disadvantaged by herds with fewer animals and a low flock density per population [11]. ...
Goats were amongst the first livestock to be domesticated more than 10,000 years ago for their meat, milk, skin, and fiber. They were introduced to Southern Africa by migrating nations from Central Africa to the south. Due to local adaptation to the different agro-ecological zones and selection, indigenous goats are identified as ecotypes within the indigenous veld goat breed. Their ability to thrive in a resource-limited production system and in challenging environmental conditions makes them valuable animal resources for small-scale and emerging farmers. They play important roles in household agriculture and cultural activities as well as in poverty alleviation. Studies have described the phenotypic and genetic variations in indigenous goats, targeting the major goat-producing regions and the breeds of South Africa. In turn, information is restricted to certain breeds and regions, and the experimental design is often not adequate to inform the conservation status and priorities in changing environments. Advances in genomics technologies have availed more opportunities for the assessment of the biodiversity, demographic histories, and detection regions associated with local adaptation. These technologies are essential for breeding and conservation strategies for sustainable production for food security. This review focuses on the status of indigenous goats in South Africa and the application of genomics technologies for characterization, with emphasis on prioritization for conservation and sustainable utilization.
... It is therefore a necessity to improve the breeding practices to increase and sustain communal goat breeds, to meet the demands of the human population (Semakula et al., 2010). South Africa is one of the countries with a lot of communal areas with untapped diversity in the production of goats (Mohlatlole et al. 2015), which has the potential to improve the communal farmers' socio-economic status while affecting their livelihoods (Semakula et al. 2010). Several studies have been conducted to identify the socio-economic status and breeding practices of goat farmers (Debraj et al., 2011;Mahto et al., 2014;Sabapara, 2016;Oumer et al., 2020), However, no study has been conducted to identify the socio-economic status and breeding practices at Madiga village, Limpopo province. ...
The study was conducted to investigate the socioeconomic status and breeding practices used by goat farmers in Madiga village, Limpopo Province, South Africa. A total of 26 goat farmers out of 54 were randomly selected and given well-structured questionnaires. The Chi-square test was used for data analysis. The results showed that age was highly significantly affected (P < 0.01) by gender, with a high number of males less than 30 years and 30-50. The results also showed that the purpose of keeping the goats was significantly affected (P < 0.05) by gender. The results indicated that there is no significant (P > 0.05) variation between selection criteria (growth rate, coat color, conformation, and others) amongst the male and female farmers and the selection criteria values: 2 (15.4%), 5 (38.5%), 4 (30.8%), 2 (15.4%) and 3 (23.1%), 5 (38.5%), 1 (7.7%), 4 (30.8%), respectively. The present study suggests the importance of growth rate, skin color, conformation, and others in the selection of goat breeding in Madiga village. However, the selection of traits for breeding was not different amongst the male and female farmers. Developing a community-based breeding program will benefit both male and female farmers.
Simple Summary
To explore the genomic variations associated with goats’ body conformation traits, we performed a genome-wide association study (GWAS) on Tashi goats. We assessed eight body conformation traits in 155 Tashi goats and performed whole-genome sequencing on 100 of them. We obtained 1676.4 Gb of raw data and identified 11,257,923 qualified single nucleotide polymorphisms (SNPs). GWAS revealed 109, 20, 52, 14, 62, 51, 70, and 7 SNPs significantly associated with body height, body length, chest depth, chest width, chest girth, rump width, rump height, and cannon bone circumference, respectively. We annotated 183 genes based on the significant SNPs’ physical locations. Notably, several SNPs have been identified multiple times in two regions, chr.10:25988403-26102739 and chr.11:88216493-89250659, where candidate genes such as FNTB, CHURC1, and RNF144 could be crucial for goat body conformation traits. Our findings offer significant insights into body conformation and support the use of molecular breeding in meat goats.
Abstract
Identifying genetic markers of economically valuable traits has practical benefits for the meat goat industry. To better understand the genomic variations influencing body conformation traits, a genome-wide association study was performed on Tashi goats, an indigenous Chinese goat breed. A total of 155 Tashi goats were phenotyped for eight body conformation traits: body height, body length, chest depth, chest width, chest girth, rump width, rump height, and cannon bone circumference. Then, 100 Tashi goats were randomly selected for whole-genome sequencing and genotyped. We obtained 1676.4 Gb of raw data with an average sequencing depth of 6.2X. Clean reads were aligned to the ARS1.2 reference genome, and 11,257,923 single nucleotide polymorphisms (SNPs) were identified. The structure analysis showed that these Tashi goats were almost not genetically related. The 109, 20, 52, 14, 62, 51, 70, and 7 SNPs were significantly associated with body height, body length, chest depth, chest width, chest girth, rump width, rump height, and cannon bone circumference. Within the ±500 kb region of significant SNPs, 183 genes were annotated. The most significantly enriched KEGG pathway was “olfactory transduction”, and the most significantly enriched gene ontology (GO) terms were “cellular process”, “cellular anatomical entity”, and “molecular transducer activity”. Interestingly, we found several SNPs on chromosomes 10 and 11 that have been identified multiple times for all eight body conformation traits located in two fragments (114 kb and 1.03 Mb). In chr.10:25988403-26102739, the six SNPs were tightly linked, the TACTAG genotype was the highest at 91.8%, and the FNTB (Farnesyltransferase, CAAX Box Beta) and CHURC1 (Churchill Domain Containing 1) genes were located. In chr.11:88216493-89250659, ten SNPs were identified with several dependent linkage disequilibrium (LD) blocks, and seven related genes were annotated, but no significant SNP was located in them. Our results provide valuable biological information for improving growth performance with practical applications for genomic selection in goats.
Recent global meat consumption trends report an increase in goat meat consumption as a protein source; however, consumption is not popular in South Africa. Despite goat meat being a nutritious and sustainable source, the willingness to consume goat meat as an acceptable protein source among young adults is not known. The study aims to explore factors that may prevent goat meat consumption and determine the potential for goat meat consumption among young adults from a rural and urban university in KwaZulu-Natal, South Africa. An online meat consumption survey was developed and disseminated through email to students (n=416). Goat meat consumption by young adults was reported to be mainly due to cultural practices. Although most of the participants consumed goat meat, the frequency of consumption was lower than that of chicken, beef and pork. Key barriers to goat meat consumption included a lack of availability, unappealing aroma and allergies. The findings indicated the potential to promote goat meat availability at retail outlets in South Africa, specifically through value-added convenience products. An integrated approach, including consumer education and the increasing availability of goat meat and value-added products, will improve the consumption of this sustainable and nutritious protein source.
Abstract
Saanen and South African Indigenous goats were crossbred, and all three types were compared in terms of productivity, milk production and diseases. Clinical mastitis occurred in the herd at a moderate level (28 cases of clinical mastitis, including peracute outbreaks in six years). Peracute cases resulted in deaths, or loss of an udder half. The main organism identified was Staphylococcus epidermidis, infecting 109 of the 1032 udder halves sampled (10.6%). The other bacteria were few (27 of 1032 udder half samples: 2.6%), primarily of Staphylococcus aureus (23 of 27 colonies: 85%). Pasteurella haemolytica and Streptococcus sp. were each identified once, and Escherichia coli twice. Somatic Cell Counts (SCC) were an unreliable indication of subclinical mastitis. Abscesses were not a major problem (up to ten cases a year). Dystocia, and the resultant metritis, occurred in only 11 cases in a six year period. Squamous cell carcinoma developed on the udders of half of the 24 pure Saanens from the fourth lactation onwards, and they were culled. No cases were reported in the Crossbred goats. Adequate shade resolved the problem. Foot problems occurred when hoofs had not been trimmed regularly. Serious eye infections seldom occurred. Six cases of adult goats with pneumonia were recorded. Caprine arthritis encephalitis (CAEV) was not recorded, and appears not to exist in South Africa. Internal parasites were not a significant problem in adult goats. Lice were the only external parasites in the penned goats. Indigenous goats appeared to be resistant to tick infestation.
Mortality increased as the goats became older, and as the size of the herd increased. The rates of 10% for Saanens and 15% for Crossbreds were high, compared to that for the Indigenous goats of 4%. The most important causes of death were mastitis, ketosis and pneumonia. Pneumonia was diagnosed as the cause of death for five adult goats. Few cases of dystocia were recorded, but some goats were lost as a result of uterine infections and peritonitis. Pregnancy toxaemia, and ketosis occurred because of increased demand for energy late in gestation. Plastic bags in the rumen caused deaths of Indigenous goats in the veld paddocks. Only two cases of heartwater were recorded during this period (1988 to 1994).
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.
The development of molecular biological techniques has created new possibilities for the selection and genetic improvement of livestock. The discovery of the PCR had a major impact on the research of eukaryotic genomes and contributed to the development and application of various DNA markers. DNA markers have already found wide application in parentage verification, individual identification and control of genetic disorders. The ultimate use of DNA markers would be to identify quantitative trait loci (QTL) in order to practice genotypic selection. This paper reviews DNA markers (RAPD, DFP, RFLP AFLP, minisatellites, microsatellites, SNP) and provides a brief overview of the current application of these markers in animal breeding.
The major advancements in molecular technology over the past decades led to the discovery of DNA-markers, sequencing and genome mapping of farm animal species. New avenues were created for identifying major genes, genetic defects, quantitative trait loci (QTL) and ultimately applying genomic selection (GS) in livestock. The identification of specific regions of interest that affect quantitative traits aimed to incorporate markers linked to QTL into breeding programs by using marker assisted selection (MAS). Most QTL explained only a small proportion of the genetic variation for a trait with limited impact on genetic improvement. Single nucleotide polymorphism (SNP) markers created the possibility to genotype cattle in a single assay with hundreds of thousands of SNPs, providing sufficient genomic information to incorporate into breeding value estimation. Genomic selection is based on the principle of associating many genetic markers with phenotypic performance. A large database of genotyped animals with relevant phenotypes pertinent to a production system is therefore required. South Africa has a long history of animal recording for dairy and beef cattle. The challenge for implementation of GS would be the establishment of breed-specific training populations. Training populations should be genotyped using a high density SNP panel, and the most appropriate genomic prediction algorithm determined. The suitability of commercially available genotyping platforms to South African populations should be established. The aim of this review is to provide an overview of the developments that occurred over the past two decades to lay the foundation for genomic selection with special reference to application in the South African beef and dairy cattle industry.
The success of Genome Wide Association Studies in the discovery of sequence variation linked to complex traits in humans has increased interest in high throughput SNP genotyping assays in livestock species. Primary goals are QTL detection and genomic selection. The purpose here was design of a 50-60,000 SNP chip for goats. The success of a moderate density SNP assay depends on reliable bioinformatic SNP detection procedures, the technological success rate of the SNP design, even spacing of SNPs on the genome and selection of Minor Allele Frequencies (MAF) suitable to use in diverse breeds. Through the federation of three SNP discovery projects consolidated as the International Goat Genome Consortium, we have identified approximately twelve million high quality SNP variants in the goat genome stored in a database together with their biological and technical characteristics. These SNPs were identified within and between six breeds (meat, milk and mixed): Alpine, Boer, Creole, Katjang, Saanen and Savanna, comprising a total of 97 animals. Whole genome and Reduced Representation Library sequences were aligned on >10 kb scaffolds of the de novo goat genome assembly. The 60,000 selected SNPs, evenly spaced on the goat genome, were submitted for oligo manufacturing (Illumina, Inc) and published in dbSNP along with flanking sequences and map position on goat assemblies (i.e. scaffolds and pseudo-chromosomes), sheep genome V2 and cattle UMD3.1 assembly. Ten breeds were then used to validate the SNP content and 52,295 loci could be successfully genotyped and used to generate a final cluster file. The combined strategy of using mainly whole genome Next Generation Sequencing and mapping on a contig genome assembly, complemented with Illumina design tools proved to be efficient in producing this GoatSNP50 chip. Advances in use of molecular markers are expected to accelerate goat genomic studies in coming years.
The aim of the study was to investigate the milk potential of Saanen, British Alpine and Toggenburg dairy goats does under extensive nutritional management. Saanen produced more milk (1.45 kg day(-1)) than the two other breeds. Toggenburg produced the least amount of milk (0.56 kg). All breeds produced less than their reported production under improved management regimes. The Toggenburg and the British Alpine least expressed their genetic potential for milk production under extensive nutritional and management scheme. However, the milk yield from these temperate breeds under extensive management system was still much higher than the reported milk production of indigenous goats. Milk from the British Alpine had the highest protein content while the least milk protein content was found in the Toggenburg breed. Fat content was highest in the Toggenburg milk followed by the British Alpine, with the least amount of fat found in the Saanen milk. Milk yield, protein and fat contents were influenced by stage of lactation, season and parity. Milk yield declined with lactation stage.
In this paper we use the accelerometer of a smart phone to design and implement a fall monitor with GPS function for the user. We not only analyze the change of acceleration but also analyze the six typical actions of humans. These are going upstairs, going downstairs, standing up, sitting down, running and jumping. Then we compare the six actions with the characteristics of a fall. These are weightlessness, impact, immobility and overturning of the body. Our design is based on an open source system platform and the accelerometer in the smart phone. If there has been a fall motion our design provides the GPS functionality to obtain the location of the user and draws the help path on both the smart phones and the computers of his family, friends or help center immediately.