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Background Population history, production system and within-breed selection pressure impacts the genome architecture resulting in reduced genetic diversity and increased frequency of runs of homozygosity islands. This study tested the hypothesis that production systems geared towards specific traits of importance or natural or artificial selection pressures influenced the occurrence and distribution of runs of homozygosity (ROH) in the South African sheep population. The Illumina OvineSNP50 BeadChip was used to genotype 400 sheep belonging to 13 breeds from South Africa representing mutton, pelt and mutton and wool dual-purpose breeds, including indigenous non-descript breeds that are reared by smallholder farmers. To get more insight into the autozygosity and distribution of ROH islands of South African breeds relative to global populations, 623 genotypes of sheep from worldwide populations were included in the analysis. Runs of homozygosity were computed at cut-offs of 1–6 Mb, 6–12 Mb, 12–24 Mb, 24–48 Mb and > 48 Mb, using the R package detectRUNS. The Golden Helix SVS program was used to investigate the ROH islands. Results A total of 121,399 ROH with mean number of ROH per animal per breed ranging from 800 (African White Dorper) to 15,097 (Australian Poll Dorset) were obtained. Analysis of the distribution of ROH according to their size showed that, for all breeds, the majority of the detected ROH were in the short (1–6 Mb) category (88.2%). Most animals had no ROH > 48 Mb. Of the South African breeds, the Nguni and the Blackhead Persian displayed high ROH based inbreeding (FROH) of 0.31 ± 0.05 and 0.31 ± 0.04, respectively. Highest incidence of common runs per SNP across breeds was observed on chromosome 10 with over 250 incidences of common ROHs. Mean proportion of SNPs per breed per ROH island ranged from 0.02 ± 0.15 (island ROH224 on chromosome 23) to 0.13 ± 0.29 (island ROH175 on chromosome 15). Seventeen (17) of the islands had SNPs observed in single populations (unique ROH islands). The MacArthur Merino (MCM) population had five unique ROH islands followed by Blackhead Persian and Nguni with three each whilst the South African Mutton Merino, SA Merino, White Vital Swakara, Karakul, Dorset Horn and Chinese Merino each had one unique ROH island. Genes within ROH islands were associated with predominantly metabolic and immune response traits and predomestic selection for traits such as presence or absence of horns. Conclusions Overall, the frequency and patterns of distribution of ROH observed in this study corresponds to the breed history and implied selection pressures exposed to the sheep populations under study.

In southern Africa, the Nguni cattle breed is classified as an indigenous and transboundary animal genetic resource that manifests unique adaptation abilities across distinct agroecological zones. The genetic integrity of various ecotypes is under potential threat due to both indiscriminate crossbreeding and uncontrolled inbreeding. The aim of this study was to assess the genetic diversity and autozygosity that exists both across countries (ES: eSwatini; SA: South Africa) and within-country (SA), between purebred stud animals (SA-S) and research herds (SA-R). Subsets of 96 ES, 96 SA-S and 96 SA-R genotyped for 40 930 common SNPs were used to study inbreeding, runs of homozygosity (ROH) and heterozygosity (ROHet) profiles as well as population structure. The highest proportion (0.513) of the 3 595 ROH was

Growth and carcass quality are economically important traits in goat production. This study investigated differentially expressed genes from the caprine pituitary gland transcriptome of South African indigenous goat breeds of varying growth performances and carcass quality parameters. Tissues were harvested from the pituitary gland of three South African Boer goats and three village ecotype goats all raised under similar conditions simulating intensive commercial production systems. Three additional tissues were harvested from village ecotype goats that were raised extensively on village farms. Between breed differences were investigated by comparing differential gene expression among three South African Boer and three village goats that were both raised under intensive commercial production system at a research farm. Within-breed differences were investigated by comparing differential gene expression among three village goats raised under extensive conditions (on-farm in Pella, S.A. village farming community) and three village goats raised under intensive commercial production system (at ARC research farm in Pretoria, South Africa. Total RNA was isolated from the pituitary gland of 36-week-old animals (n = 9) and sequenced individually in triplicates. An average of 28,298,512 trimmed, and quality-controlled reads/animal were mapped to the goat genome (Capra_hircus.ARS1.94) using HiSat2 software. Transcript assembly and quantification yielded 104 differentially expressed genes for village goats raised under extensive system and 62 for village goats raised under the intensive production system at the false discovery rate (FRD) of ≤0.05 and a fold change of ≥2. Growth-related genes such as POU3F4 and TSHZ1 were highly expressed within breeds raised under both production systems. Conversely, growth-related genes such as FGFR2 and SMPX genes were highly expressed between breeds raised under similar production systems. Ballgown analysis revealed a high expression of GH1 and IGF1 in the intensively raised compared to extensively raised goats. Both genes were also highly expressed in the village goats when compared to the Boer. The differential gene expression data provided insights into genes and molecular mechanisms associated with growth and growth development in goats.

In this study, the genetic structure of indigenous Tswana and Swazi goats using the Illumina Goat50K SNP array was investigated. Two South African commercial goat breeds were included to investigate admixture with the indigenous populations in southern Africa. A total of 144 DNA samples including Boer goats (n = 24), Kalahari Red (n = 24), Swazi (n = 48), and Tswana goats (n = 48) were genotyped. Statistical analysis was performed using PLINK version 1.07. Genetic diversity, measured as expected heterozygosity, was estimated at 0.390, 0.398, 0.413, and 0.387 for Boer, Kalahari Red, Tswana, and Swazi goats, respectively. The individual inbreeding coefficient varied from 0.019 ± 0.05 to 0.011 ± 0.06 for the Tswana and Swazi goats, respectively. The Principal component analysis clustered the populations according to geographical origin and breed type. Linkage disequilibrium (LD) for shorter intervals (0–10 kb) ranged from 0.44 to 0.56 and commercial breeds had higher values. Effective population sizes decreased with generations and at the 13th generation ranged between 87 for Boer to 266 for Tswana goats. The Tswana population exhibited the highest level of genetic variation and effective population size, which holds potential for improved production in marginal regions. A national strategy is required to maintain genetic diversity in communal goat production systems through well-structured breeding and conservation programs.

The aim of this study was to use genome-wide SNP data to investigate phenotypic and genetic differences in resistance to Haemonchus contortus between resistant and susceptible South African Dohne Merino sheep. The participating farm (Wauldby) has a history of heavy H. contortus challenge and implemented a selection strategy for resistance to H. contortus in 2011. Faecal egg count (FEC), body condition scores (BCS) and Famacha© scores (FAM) were recorded annually on lambs from weaning in January until the end of June from 2011 to 2014. Animals with FAM scores of ≥ 2.5 or BCS scores

Simple Summary Ungulates are essential sources of food, labor, clothing, and transportation for humans. Due to their diverse habitats, ungulates have unique adaptive traits for survival. The availability of genomics resources has made it possible to identify genes associated with adaptations of ungulates to their respective environments. In this review, we document available ungulate genomics resources and genes associated with adaptive traits. Abstract Ungulates are a group of hoofed animals that have long interacted with humans as essential sources of food, labor, clothing, and transportation. These consist of domesticated, feral, and wild species raised in a wide range of habitats and biomes. Given the diverse and extreme environments inhabited by ungulates, unique adaptive traits are fundamental for fitness. The documentation of genes that underlie their genomic signatures of selection is crucial in this regard. The increasing availability of advanced sequencing technologies has seen the rapid growth of ungulate genomic resources, which offers an exceptional opportunity to understand their adaptive evolution. Here, we summarize the current knowledge on evolutionary genetic signatures underlying the adaptations of ungulates to different habitats.

A major obstacle in applying genomic selection (GS) to uniquely adapted local breeds in less-developed countries has been the cost of genotyping at high densities of single-nucleotide polymorphisms (SNP). Cost reduction can be achieved by imputing genotypes from lower to higher densities. Locally adapted breeds tend to be admixed and exhibit a high degree of genomic heterogeneity thus necessitating the optimization of SNP selection for downstream imputation. The aim of this study was to quantify the achievable imputation accuracy for a sample of 1,135 South African (SA) Drakensberger cattle using several custom-derived lower-density panels varying in both SNP density and how the SNP were selected. From a pool of 120,608 genotyped SNP, subsets of SNP were chosen (1) at random, (2) with even genomic dispersion, (3) by maximizing the mean minor allele frequency (MAF), (4) using a combined score of MAF and linkage disequilibrium (LD), (5) using a partitioning-around-medoids (PAM) algorithm, and finally (6) using a hierarchical LD-based clustering algorithm. Imputation accuracy to higher density improved as SNP density increased; animal-wise imputation accuracy defined as the within-animal correlation between the imputed and actual alleles ranged from 0.625 to 0.990 when 2,500 randomly selected SNP were chosen vs. a range of 0.918 to 0.999 when 50,000 randomly selected SNP were used. At a panel density of 10,000 SNP, the mean (standard deviation) animal-wise allele concordance rate was 0.976 (0.018) vs. 0.982 (0.014) when the worst (i.e., random) as opposed to the best (i.e., combination of MAF and LD) SNP selection strategy was employed. A difference of 0.071 units was observed between the mean correlation-based accuracy of imputed SNP categorized as low (0.01 < MAF ≤ 0.1) vs. high MAF (0.4 < MAF ≤ 0.5). Greater mean imputation accuracy was achieved for SNP located on autosomal extremes when these regions were populated with more SNP. The presented results suggested that genotype imputation can be a practical cost-saving strategy for indigenous breeds such as the SA Drakensberger. Based on the results, a genotyping panel consisting of ~10,000 SNP selected based on a combination of MAF and LD would suffice in achieving a

In this study, we evaluated an admixed South African Simbra crossbred population, as well as the Brahman (Indicine) and Simmental (Taurine) ancestor populations to understand their genetic architecture and detect genomic regions showing signatures of selection. Animals were genotyped using the Illumina BovineLD v2 BeadChip (7K). Genomic structure analysis confirmed that the South African Simbra cattle have an admixed genome, composed of 5/8 Taurine and 3/8 Indicine, ensuring that the Simbra genome maintains favorable traits from both breeds. Genomic regions that have been targeted by selection were detected using the linkage disequilibrium-based methods iHS and Rsb. These analyses identified 10 candidate regions that are potentially under strong positive selection, containing genes implicated in cattle health and production (e.g., TRIM63, KCNA10, NCAM1, SMIM5, MIER3, and SLC24A4). These adaptive alleles likely contribute to the biological and cellular functions determining phenotype in the Simbra hybrid cattle breed. Our data suggested that these alleles were introgressed from the breed's original indicine and taurine ancestors. The Simbra breed thus possesses derived parental alleles that combine the superior traits of the founder Brahman and Simmental breeds. These regions and genes might represent good targets for ad-hoc physiological studies, selection of breeding material and eventually even gene editing, for improved traits in modern cattle breeds. This study represents an important step toward developing and improving strategies for selection and population breeding to ultimately contribute meaningfully to the beef production industry.

Genome-wide assessments of the genetic landscape of Farm Animal Genetic Resources (FAnGR) are key to developing sustainable breed improvements. Understanding the FAnGR adaptation to different environments and supporting their conservation programs from community initiative to national policymakers is very important. The objective of the study was to investigate the genetic diversity and population structure of communal indigenous goat populations from four provinces of South Africa. Communal indigenous goat populations from the Free State (FS) (n = 24), Gauteng (GP) (n = 28), Limpopo (LP) (n = 30), and North West (NW) (n = 35) provinces were genotyped using the Illumina Goats SNP50 BeadChip. An Illumina Goats SNP50 BeadChip data from commercial meat-type breeds: Boer (n = 33), Kalahari Red (n = 40), and Savanna (n = 31) was used in this study as reference populations. The Ho revealed that the genetic diversity of a population ranged between 0.39 &plusmn, 0.11 Ho in LP to 0.42 &plusmn, 0.09 Ho in NW. Analysis of molecular variance revealed variations of 3.39% (p &lt, 0.0001) and 90.64% among and within populations, respectively. The first two Principal Component Analyses (PCAs) revealed a unique Limpopo population separated from GP, FS, and NW communal indigenous goat populations with high levels of admixture with commercial goat populations. There were unique populations of Kalahari and Savanna that were observed and admixed individuals. Marker FST (Limpopo versus commercial goat populations) revealed 442 outlier single nucleotide polymorphisms (SNPs) across all chromosomes, and the SNP with the highest FST value (FST = 0.72, chromosome 8) was located on the UHRF2 gene. Population differentiation tests (PCAdapt) revealed PC2 as optimal and five outlier SNPs were detected on chromosomes 10, 15, 20, and 21. The study revealed that the SNPs identified by the first two principal components show high FST values in LP communal goat populations and allowed us to identify candidate genes which can be used in the development of breed selection programs to improve this unique LP population and other communal goat population of FS, GP, and NW, and find genetic factors contributing to the adaptation to harsh environments. Effective management and utilization of South African communal indigenous goat populations is important, and effort should be made to maintain unique genetic resources for conservation.

Consumption of food that is contaminated by microorganisms, chemicals, and toxins may lead to significant morbidity and mortality, which has negative socioeconomic and public health implications. Monitoring and surveillance of microbial diversity along the food value chain is a key component for hazard identification and evaluation of potential pathogen risks from farm to the consumer. The aim of this study was to determine the microbial diversity in meat and meat products from different enterprises and meat types in South Africa. Samples (n = 2017) were analyzed for Yersinia enterocolitica, Salmonella species, Listeria monocytogenes, Campylobacter jejuni, Campylobacter coli, Staphylococcus aureus, Clostridium perfringens, Bacillus cereus, and Clostridium botulinum using culture-based methods. PCR was used for confirmation of selected pathogens. Of the 2017 samples analyzed, microbial ecology was assessed for selected subsamples where next generation sequencing had been conducted, followed by the application of computational methods to reconstruct individual genomes from the respective sample (metagenomics). With the exception of Clostridium botulinum, selective culture-dependent methods revealed that samples were contaminated with at least one of the tested foodborne pathogens. The data from metagenomics analysis revealed the presence of diverse bacteria, viruses, and fungi. The analyses provide evidence of diverse and highly variable microbial communities in products of animal origin, which is important for food safety, food labeling, biosecurity, and shelf life limiting spoilage by microorganisms.

The Beef Genomics Program (BGP) and the Red Meat Research and Development Trust of South Africa (RMRDT-SA) and financial assistance of the National Research Foundation (NRF).

A population structure study was performed in South African ovine populations using the OvineSNP50 beadchip. Blood samples were obtained from 295 sheep of which 172 had been identified as smallholder Dorpers, 4 smallholder White Dorpers, 46 purebred Dorpers, 26 purebred South African Mutton Merinos and 47 purebred Namaqua Afrikaners. Blood from the latter three breeds were obtained from a resource flock maintained on the Nortier research farm. Genetic diversity was estimated using allelic richness (A r), observed heterozygosity (H o), expected heterozygosity (H e) and inbreeding coefficient (F). Population structure analysis was performed using fastSTRUCTURE to determine the breed composition of each genotyped individual. The Namaqua Afrikaner had the lowest H e of 0.280 ± 0.18 while the H e of smallholder Dorper, Dorper and South African Mutton Merino did not differ and were 0.364 ± 0.13, 0.332 ± 0.16 and 0.329 ± 0.17, respectively. The average inbreeding coefficient was highest for the pure breeds, Namaqua Afrikaner, Dorper and South African Mutton Merino compared to the average inbreeding coefficient for the smallholder Dorper population. The smallholder Dorper were introgressed with Namaqua Afrikaner, South African Mutton Merino and White Dorpers. Similarly, the smallholder Dorper population was more genetically diverse than the purebred Dorper, South African Mutton Merino and Namaqua Afrikaner from the research farm. The higher genetic diversity among the smallholder sheep may be advantageous for their fitness and can be used to facilitate selective breeding.

South African indigenous goat populations are renowned for their adaptability to local agro-ecological conditions and suitability for low input production systems. This is particularly important in a country where a majority of the goats are kept under marginalized communal production systems. Adaptation of animal genotypes to the environment is central to the coping of local livestock populations to changing climatic and production objectives and is a key parameter to use in conservation and improvement programs. South Africa has successfully developed world-renowned commercial meat breeds, the Boer, Kalahari Red and Savanna, all from the non-descript indigenous goat populations. In addition, South Africa has a feral Tankwa goat population that is found in the Northern Cape province. Despite its success stories and unique goat populations, majority of the South African goats are non-descript indigenous veld goats whose genetic diversity is yet to be fully characterized and harnessed. Advances in genomics and population genetics have led to substantial progress in identifying local genetic adaptation of livestock species. Landscape genomics merges the competing effects of production system, geographical, and environment landscapes with adaptive variation. The review gives an overview of current knowledge on the South African indigenous goat genetic resources and the major goat production systems across the different agro-ecological zones of the country. The review then explores the opportunities and potential of landscape genomic methods and how they can complement traditional phenotypic and genetic characterization approaches. The factors that make it feasible to undertake a landscape genomics analysis for South African livestock such as goats are discussed. The developments in genomics and statistical genomics and the opportunities they bring to goat landscape genomics research is presented.

Salmonellosis is an infectious zoonotic disease of socio-economic importance worldwide. Food animals with subclinical infection as well as farm effluents are usually the sources of contaminated meat, eggs and milk, which cause diarrhoea and systemic infections in humans. The indiscriminate use of antibiotics to curb salmonellosis in both animals and humans has contributed to the emergence and spread of drug-resistant bacteria among both pathogenic and commensal organisms. The aim of the study was therefore to determine the presence, serovar distribution and antimicrobial resistance profiles of Salmonella isolated from domestic livestock species in South Africa. For this purpose,1069 rectal and cloacal swabs were collected from pigs (n = 322), chickens (n = 286) and goats (n = 461) from smallholder farms in Limpopo, Eastern Cape, Northern Cape, North West and KwaZulu Natal provinces of South Africa. The frequency of occurrence of Salmonella per animal species was highest in pigs (5.90%; n = 19), followed by chickens (3.15%; n = 9) and goats had the lowest proportion of 0.43% (n = 2). Nine Salmonella serovars were obtained including S. Techimani, a serovar that was not previously observed in South African animals. Six isolates were assigned to Salmonella II. Some of the Salmonella were untypable (n = 6). All Salmonella isolates were sensitive to cefotaxime, enrofloxacin, florphenicol and polymyxin B. Most of the Salmonella isolates were resistant to at least one antimicrobial (n = 20; 66.7%) and resistance was predominant towards trimethoprim (n = 11; 36.7%), followed by ampicillin (n = 5; 16.7%), oxytetracycline (n = 3; 10%), and kanamycin (n = 1; 3.3%). The results illustrate the presence of diverse and rare Salmonella serovars that were not previously isolated from animals in South Africa. The pattern of development of antibiotic resistance should be monitored and followed-up. The occurrence of elevated trimethoprim resistant Salmonella in South African food animals could lead to the emergence and distribution of drug resistant salmonellosis in human beings.

Highlights • The transcriptome of chickens from parasite infested environment was sequenced. • Different genes were reported between A. galli infected and non-infected chickens. • Upregulated immune and inflammatory response genes are associated with fighting parasites. • T cell receptor signalling and arachidonic acid metabolism pathways were impacted. • Different segments of the intestines differed in gene expression and associated pathways., 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.

South Africa has a diverse array of phenotypically distinct and locally adapted sheep breeds that have been developed for different production systems ranging from mutton to wool and pelt, and some dual-purpose and nondescript breeds kept by smallholder farmers. This study investigated genetic diversity, population genetic structure and divergence between South African sheep breeds in order to gain an insight into breed history and genomic architecture aligned to breeding goals and production systems. The Illumina OvineSNP50 BeadChip was used to genotype 400 sheep belonging to 14 breeds representing mutton, pelt and mutton and wool dual-purpose breeds. Nguni sheep were included as a representative of indigenous nondescript breeds that are reared by smallholder farmers. Seeking a clearer understanding of the genetic diversity of South African breeds relative to global populations, 623 genotypes of sheep from worldwide populations were included in the analysis. These sheep breeds included six African, two Asian and eight European breeds. Across breeds, genetic diversity ranged from observed heterozygosity (H0 ) = 0.26 ± 0.02 in Namaqua Afrikaner to H0 = 0.38 ± 0.01 in Dohne Merino. The overall mean H0 was 0.35 ± 0.04. The African and Asian populations were the most inbred populations with FIS ranging from 0.17 ± 0.05 in Grey Swakara and Ronderib Afrikaner sheep to 0.34 ± 0.07 in the Namaqua Afrikaner. The South African Dohne Merino (FIS = 0.03 ± 0.01), SA Merino (FIS = 0.05 ± 0.04) and Afrino (FIS = 0.09 ± 0.02) and other global Merino-derived breeds were the least inbred. The first principal component explained 27.7% of the variation and separated the fat- and rump-tailed sheep (i.e. Swakara, Nguni, Blackhead Persian, Ethiopian Menzi, Meatmaster) from the Merino and Merino-derived breeds and the Dorset Horn. The second principal component separated the Merino and Merino-derived breeds from the English breed of Dorset Horn. Overall, South African indigenous breeds clustered together with indigenous breeds from other African and Asian countries. The optimal admixture cluster (K = 20) revealed various sources of within- and amongst-breed genomic variation associated with production purpose, adaptation and history of the breeds. The Blackhead Persian, Nguni and Namaqua Afrikaner breeds differed significantly from other breeds, particularly with the South African Mutton Merino and Dorset Horn. Breed-differentiating SNPs were observed within genomic regions associated with growth, adaptation and reproduction. Genes such as RAB44, associated with growth and meat/carcass traits, differentiated the Blackhead Persian from the Dorset Horn and South African Mutton Merino. The MAP2 and HRAS genes, which are associated with immune traits involving Toll-like receptors and Chemokine signalling pathways, differentiated the Nguni from the Dorset Horn. The current results give insight into the current status of the sheep genetic resources of South Africa relative to the global sheep population, highlighting both genetic similarities as well as divergence associated with production systems, geographical distribution and local adaptation.

The South African beef cattle population is heterogeneous and consists of a variety of breeds, production systems and breeding goals. Indigenous cattle breeds are uniquely adapted to their native surroundings, necessitating conservation of these breeds as usable genetic resources to sustain efficient production of beef. Current projections indicate positive growth in human population size, with parallel growth in nutritional demand, in the midst of intensifying environmental conditions. Sanga cattle, therefore, are invaluable assets to the South African beef industry. Modern genomic methodologies allow for an extensive insight into the genome architecture of local breeds. The evolution of these methodologies has also provided opportunities to incorporate deoxyribonucleic acid (DNA) information into breed improvement programs in the form of genomic selection (GS). Certain challenges, such as the high cost of generating adequate numbers of dense genotypic profiles and the introduction of ascertainment bias when non-commercial breeds are genotyped with commercial single nucleotide polymorphism (SNP) panels, have caused a lag in progress on the genomics front in South Africa. Genotype imputation is a statistical method that infers unavailable or missing genotypic data based on shared haplotypes within a population using a population or breed representative reference sample. Genotypes are generated in silico , providing an animal with genotypic information for SNP markers that were not genotyped, based on predictive model-based algorithms. The validation of this method for indigenous breeds will enable the development of cost-effective low-density bead chips, allowing more animals to be genotyped, and imputation to high-density information. The improvement in SNP densities, at lower cost, will allow enhanced power in genome-wide association studies (GWAS) and genomic estimated breeding value (GEBV)-based selection for these breeds. To fully reap the benefits of this methodology, however, will require the setting up of accurate and reliable frameworks that are optimized for its application in Sanga breeds. This review paper aims, first, to identify the challenges that have been impeding genomic applications for Sanga cattle and second, to outline the advantages that a method such as genotype imputation might provide. Keywords: breed improvement, developing countries, indigenous breeds, genomics

The sustainability of goat farming in marginal areas of southern Africa depends on local breeds that are adapted to specific agro-ecological conditions. Unimproved non-descript goats are the main genetic resources used for the development of commercial meat-type breeds of South Africa. Little is known about genetic diversity and the genetics of adaptation of these indigenous goat populations. This study investigated the genetic diversity, population structure and breed relations, linkage disequilibrium, effective population size and persistence of gametic phase in goat populations of South Africa. Three locally developed meat-type breeds of the Boer (n = 33), Savanna (n = 31), Kalahari Red (n = 40), a feral breed of Tankwa (n = 25) and unimproved non-descript village ecotypes (n = 110) from four goat-producing provinces of the Eastern Cape, KwaZulu-Natal, Limpopo and North West were assessed using the Illumina Goat 50K SNP Bead Chip assay. The proportion of SNPs with minor allele frequencies0.05 ranged from 84.22% in the Tankwa to 97.58% in the Xhosa ecotype, with a mean of 0.32 ± 0.13 across populations. Principal components analysis, admixture and pairwise FST identified Tankwa as a genetically distinct population and supported clustering of the populations according to their historical origins. Genome-wide FST identified 101 markers potentially under positive selection in the Tankwa. Average linkage disequilibrium was highest in the Tankwa (r(2) = 0.25 ± 0.26) and lowest in the village ecotypes (r(2) range = 0.09 ± 0.12 to 0.11 ± 0.14). We observed an effective population size of150 for all populations 13 generations ago. The estimated correlations for all breed pairs were lower than 0.80 at marker distances100 kb with the exception of those in Savanna and Tswana populations. This study highlights the high level of genetic diversity in South African indigenous goats as well as the utility of the genome-wide SNP marker panels in genetic studies of these populations.

The present study investigated the seroprevalence of antibodies to Ehrlichia ruminantium and the associated risk factors in goats from five different farming provinces of South Africa. Sera collected from 686 goats of the commercial meat type (n=179), mohair type (n=9), non-descript indigenous goats from Eastern Cape (n=56), KwaZulu-Natal (n=209), Limpopo (n=111), North West (n=61) and Northern Cape (n=11) provinces and a feral Tankwa goat (n=50) were tested for the presence of immunoglobulin G (IgG) antibodies to antigens of E. ruminantium using the indirect fluorescent-antibody test (IFAT). Fifty two percent of these goats had ticks. The overall seroprevalence of antibodies to E. ruminantium was 64.87% (445/686) with the highest seroprevalence reported for Limpopo (95.50%) and lowest for Northern Cape (20.29%). Highest seroprevalence for antibodies to E. ruminantium was observed in goats from endemic regions (76.09%), and from smallholder production systems (89.54%). High seroprevalence was also observed in non-descript indigenous goats (85.04%), adult goat (69.62%), in does (67.46%) and goats infested with ticks (85.79%). The logistic model showed a gradient of increasing risk for commercial meat type Savanna (OR=3.681; CI=1.335-10.149) and non-descript indigenous (OR=3.466; CI=1.57-7.645) compared to Boer goats and for goats from the smallholder production system (OR=2.582; CI=1.182-5.639) and those with ticks (OR=3.587; CI=2.105-6.112). Results from this study showed that E. ruminantium infections were prevalent but were widely and unevenly distributed throughout South Africa. Findings from the study facilitate identification and mapping of risk areas for heartwater and its endeminicity in South Africa and should be taken into consideration for future disease control strategies and local goat improvement programs.

Background Bacillus endophyticus is a soil plant-endophytic bacterium, while B. anthracis is the causative agent of anthrax. The virulence factors of B. anthracis are the plasmid encoded tripartite toxins (pXO1) and poly-γ-glutamic acid (PGA) capsule (pXO2). B. endophyticus isolated alongside B. anthracis from animals that died of anthrax in Northern Cape Province (NCP), South Africa, harbored polyglutamate genes. The study compared the characteristics of B. anthracis and B. endophyticus with other Bacillus species with a focus on the presence of the PGA capsule or/and unbound PGA. The morphology and whole genome sequence analysis of B. endophyticus strains and B. anthracis were compared. Results In conventional microbiology, B. endophyticus showed gram-positive round-shaped rods in single/short chains, which were endospore-forming, non-motile, non-haemolytic with white and dry colonies, and γ-phage resistant. B. anthracis was differentiated from B. endophyticus based on the latter’s box-shaped rods in pairs/long chains, white-grey and slimy colonies, encapsulated and γ-phage susceptible. The study identified a PGA polyglutamate synthase operon that consisted of pgsBCA, γ-glutamyltranspeptidase (ggt) and pgsE in B. endophyticus genomes. Conclusions PGA regions of B. anthracis contain capBCADE genes located in the pXO2 required for capsulation formation, while B. endophyticus contain the pgsBCAE genes in the chromosome. Whole genome and microbiology analysis identified B. endophyticus, as a non-capsuled endospore-forming bacterium that consists of PGA required for biosynthesis. B. endophyticus strains do not synthesize surface associated PGA, therefore capsule visualization of B. anthracis is a key diagnostic characteristic. The study highlights the significance of using whole genome shotgun sequencing to identify virulence and other important genes that might be present amongst unknown samples from natural outbreaks. None of the B. anthracis related plasmids or virulence genes were found in the B. endophyticus genomes. Electronic supplementary material The online version of this article (10.1186/s12866-018-1205-9) contains supplementary material, which is available to authorized users.

Copy number variations (CNVs) comprise deletions, duplications, and insertions found within the genome larger than 50 bp in size. CNVs are thought to be primary role-players in breed formation and adaptation. South Africa boasts a diverse ecology with harsh environmental conditions and a broad spectrum of parasites and diseases that pose challenges to livestock production. This has led to the development of composite cattle breeds which combine the hardiness of Sanga breeds and the production potential of the Taurine breeds. The prevalence of CNVs within these respective breeds of cattle and the prevalence of CNV regions (CNVRs) in their diversity, adaptation and production is however not understood. This study therefore aimed to ascertain the prevalence, diversity, and correlations of CNVRs within cattle breeds used in South Africa. Illumina Bovine SNP50 data and PennCNV were utilized to identify CNVRs within the genome of 287 animals from seven cattle breeds representing Sanga, Taurine, Composite, and cross breeds. Three hundred and fifty six CNVRs of between 36 kb to 4.1 Mb in size were identified. The null hypothesis that one CNVR loci is independent of another was tested using the GENEPOP software. One hunded and two and seven of the CNVRs in the Taurine and Sanga/Composite cattle breeds demonstrated a significant (p ≤ 0.05) association. PANTHER overrepresentation analyses of correlated CNVRs demonstrated significant enrichment of a number of biological processes, molecular functions, cellular components, and protein classes. CNVR genetic variation between and within breed group was measured using phiPT which allows intra-individual variation to be suppressed and hence proved suitable for measuring binary CNVR presence/absence data. Estimate PhiPT within and between breed variance was 2.722 and 0.518 respectively. Pairwise population PhiPT values corresponded with breed type, with Taurine Holstein and Angus breeds demonstrating no between breed CNVR variation. Phylogenetic trees were drawn. CNVRs primarily clustered animals of the same breed type together. This study successfully identified, characterized, and analyzed 356 CNVRs within seven cattle breeds. CNVR correlations were evident, with many more correlations being present among the exotic Taurine breeds. CNVR genetic diversity of Sanga, Taurine and Composite breeds was ascertained with breed types exposed to similar selection pressures demonstrating analogous incidences of CNVRs.

Ascaridia galli is one of the most common nematode affecting chickens. This study characterized A. galli parasites collected from South African village chickens of Limpopo (n=18) and KwaZulu-Natal (n=22) provinces using the 510bp sequences of cytochrome C oxidase subunit 1 gene of the mitochondrial DNA. Fourteen and 12 polymorphic sites were observed for Limpopo and KwaZulu-Natal sequences, respectively. Six haplotypes were observed in total. Haplotype diversity was high and ranged from 0.749 for Limpopo province to 0.758 for KwaZulu-Natal province isolates. There was no genetic differentiation between A. galli from Limpopo and KwaZulu-Natal provinces. The six South African haplotypes were unique compared to those published in the GeneBank sampled from Hy-line chickens raised under organic farming in Denmark. The utility of cytochrome C oxidase subunit 1 gene as a potential genetic marker for studying A. galli in village chicken populations is presented.

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.

Smallholder farmers in Africa and other developing countries raise village chickens under low input production systems characterised by minimal management and veterinary interventions. However, vil...

In Africa, extensively raised livestock populations in most smallholder farming communities are exposed to harsh and heterogeneous climatic conditions and disease pathogens that they adapt to in order to survive. Majority of these livestock species, including goats, are of non-descript and uncharacterized breeds and their response to natural selection presented by heterogeneous environments is still unresolved. This study investigated genetic diversity and its association with environmental and geographic conditions in 194 South African indigenous goats from different geographic locations genotyped on the Illumina goat SNP50K panel. Population structure analysis revealed a homogeneous genetic cluster of the Tankwa goats, restricted to the Northern Cape province. Overall, the Boer, Kalahari Red, and Savanna showed a wide geographic spread of shared genetic components, whereas the village ecotypes revealed a longitudinal distribution. The relative importance of environmental factors on genetic variation of goat populations was assessed using redundancy analysis (RDA). Climatic and geographic variables explained 22% of the total variation while climatic variables alone accounted for 17% of the diversity. Geographic variables solitarily explained 1% of the total variation. The first axis (Model I) of the RDA analysis revealed 329 outlier SNPs. Landscape genomic approaches of spatial analysis method (SAM) identified a total of 843 (1.75%) SNPs, while latent factor mixed models (LFMM) identified 714 (1.48%) SNPs significantly associated with environmental variables. Significant markers were within genes involved in biological functions potentially important for environmental adaptation. Overall, the study suggested environmental factors to have some effect in shaping the genetic variation of South African indigenous goat populations. Loci observed to be significant and under selection may be responsible for the adaption of the goat populations to local production systems.

Enterotoxigenic Escherichia coli (ETEC) and shiga toxin E. coli (STEC) are important causes of colibacillosis in piglets. Recently, enteroaggregative E. coli heat-stable enterotoxin 1 (EAST-1) has been implicated in pig diarrhoea. This study investigated the prevalence of enterotoxin [heat-labile toxins (LT), heat-stable toxin a (STa), heat-stable toxin b (STb)], shiga toxins (Stx1, Stx2, Stx2e), enteroaggregative heat-stable E. coli (EAST-1), associated fimbriae (F4, F5, F6, F41, F18ab, F18ac) and non-fimbrial adhesins [adhesin involved in diffuse adherence 1 (AIDA-1), attaching and effacing factor, porcine attaching- and effacing-associated factor] in South African pigs. A total of 263 E. coli strains were isolated from Landrace (n = 24), Large White (n = 126), Duroc (n = 28) and indigenous (n = 85) breeds of piglets aged between 9 and 136 days. PCR was used in the analysis. Virulent genes were detected in 40.3 % of the isolates, of which 18.6, 0.4 and 17.5 % were classified as ETEC, STEC and enteroaggregative E. coli (EAEC), respectively. Individual genes were found in the following proportions: STb (19.01 %), LT (0.4 %), STa (3.4 %), St2xe (1.1 %) and EAST-1 (20.2 %) toxins. None of the tested fimbriae were detected in ETEC and STEC isolates. About one third of the ETEC and STEC isolates was tested negative for both fimbrial and non-fimbrial adhesins. Twenty-five pathotypes from ETEC-, EAEC- and STEC-positive strains were identified. Pathotypes EAST-1 (30.2 %), STb (13.2 %) and STb/AIDA-1 (10.4 %) were most prevalent. The study provided insight on possible causes of colibacillosis in South African pigs.

South Africa is one of the major goat-producing countries with over 6 million goats, 63% of which are farmed under smallholder communal farming systems where poor nutrition, disease infestation, and harsh climatic conditions are common. The Boer, Kalahari Red, and Savanna breeds were developed in South Africa and have turned out to be regionally and internationally relevant. Adaptation and tolerance to local conditions are crucial for survival of these goat genetic resources in suboptimal conditions. The full genetic potential of veld goat populations is not yet fully unraveled. Complete mtDNA sequencing and diversity analysis revealed multiple maternal lineages in South African goat populations that were shared amongst the breeds and populations with absence of population sub-structuring. Median joining network analysis using different mtDNA genes suggests that South African populations have multiple maternal lineages that are shared with other global populations. Caprine SNP50K panel data analysis highlighted elevated levels of genetic diversity in South African indigenous goats compared to industrial breeds as well as the utility of the genome-wide SNP marker panels in population genetic studies. Landscape genomic analysis suggests a strong role of environmental factors in shaping the genetic diversity of South African indigenous goats. Selected loci responsible for the adaption of goat populations to local production systems may be targeted in breed improvement programs particularly under marginalized communal production systems. Successful sequencing and analysis of the Tankwa and other South African goat genomes could screen for potentially numerous genomic variants such as copy number variants. Community-based breeding programs would be the appropriate tool for breed improvement allowing sharing of production capital, pooling of resources and services and enabling joint processes of decision-making. Genomics could complement breed improvement efforts by providing pedigree estimates and can be useful in monitoring and control of inbreeding and genetic gain.

Goats are an important source of livelihood especially in smallholder communities. Infections with gastrointestinal nematodes (GIN) remain the most prevalent parasitic diseases affecting small ruminants. The study was conducted to assess management, the level of knowledge and control of gastrointestinal nematodes. Surveys were conducted in Chipinge, Shurugwi, Binga, Tsholotsho and Matobo districts, representing the five natural/agro-ecological regions (NR) in Zimbabwe. Data was collected in 135 households using a pre-tested semi-structured questionnaire. Results indicated that goats were ranked the most important livestock species, with high flock sizes in NR IV and V. Partitioning of roles was such that the adult males were involved in decision-making while females and children were involved in day-to-day management of animals. Farmers showed low levels of input use, with natural pasture (98.4%) being the main feed source and indigenous breeds (73.2%) being kept. Farmers ranked food and financial benefits as the main reasons for keeping goats. Gastrointestinal nematodes ranked the highest as the most common disease, with majority of farmers (57%) not controlling or treating animals and 63% of farmers not having knowledge on the spread of GIN. Access to veterinary services, anthelmintic class used and breeds used by the farmers had the highest effects on parasitic infections in households. Farmer education is required for capacitation of farmer in terms of disease prevention and control so as to improve goat production.

The opportunities for sustainable utilisation and conservation of chicken genetic resources in Southern Africa need to be addressed. Indigenous chickens are an important animal genetic resource amongst resource-limited rural communities of Southern Africa. They play an important socio-economic role in traditional and religious ceremonies of rural households. They are important in customary rites, such as gift payments. Although the productivity of indigenous chickens in terms of growth and number of eggs per hen per year is low, its production is attained with minimal labour and rearing inputs. The low inputs and, consequently, low risk is one of the major advantages of indigenous chickens production. The conservation of these valuable chicken genetic resources is necessary in the light of the rapid loss of indigenous breeds and strains through commercial dilution and breed replacement. All varieties of domestic species and species with potential for domestication are considered to be important candidates for conservation. Indigenous chicken populations with economic potential, scientific use and cultural or aesthetic interest are of particular importance but all indigenous chickens which are unique and endangered should be incorporated into conservation efforts. This phenotypic information could be useful to standardise the different phenotypes within a region or country and design some criteria for characterisation and description of the indigenous chicken populations into breeds. Molecular markers are an indispensable tool to understand the genetic structures of populations. The assessed phenotypic coupled with genetic information could be a powerful tool towards the promotion of conservation and utilisation of indigenous chicken genetic resources.

In situ conservation of pig genetic resources requires understanding of the farming systems under which the pigs are kept. The objective of the study was to characterise smallholder pig production systems where indigenous pigs are kept in order to assess opportunities for in situ conservation of these pigs. Factors influencing pig herd sizes, ranking of pigs in smallholder production systems, breeds and breed preferences, pig ownership patterns, traits preferred by farmers and constraints to production were investigated in a survey involving 199 farmers from Chirimhanzu District of Zimbabwe, Vhembe, Alfred Nzo and O. R. Tambo Districts of South Africa.Income was the major factor influencing most pig production related parameters. Most pigs (69.67 %) were owned by women, with most of the women falling into the very low income group. Farmers kept pigs for several reasons that were common across geographical zones and income groups. The odds of a farmer ranking pigs first in the production system depended on the absence of other livestock (P0.05). Farmers in the higher income group tended to mention poor feed resources and access to information as constraints (P0.05) compared to the very low income group. There was preference heterogeneity in the breeds kept and the reasons for breed choice across the income groups and geographical zones. Fewer farmers in the very low income group (42.62 %) recognised the need to conserve local pigs compared to the low income group (80.49 %), the medium income group (50.00 %) and the high income group (100.00 %; χ (2) = 19.14; P0.001).It was concluded that farmers see value in local pigs and are willing to conserve them. In situ conservation programmes are possible and these should recognise the role of poor women in conserving and enhancing indigenous pig genetic resources.

The objectives of this study were to analyze the genetic diversity and structure of South African conserved and field chicken populations and to investigate the maternal lineages of these chicken populations. Four South African conserved chicken populations (n = 89), namely, Venda (VD_C), Ovambo, Naked Neck, and Potchefstroom Koekoek from the Animal Production Institute of the Agricultural Research Council, and 2 field populations, the Venda and Ovambo (OV_F), from which the Ovambo and the Venda conservation flocks were assumed to have been sampled, were genotyped for 460 bp of the mitochondrial DNA (mtDNA) D-loop sequence. Haplotypes of these chickens were aligned to 7 Japanese and 9 Chinese and Eurasian chicken mtDNA D-loop sequences taken from GenBank and reflecting populations from presumed centers of domestication. Sequence analysis revealed 48 polymorphic sites that defined 13 haplotypes in the South African chicken populations. All 6 South African conserved and field chicken populations observed were found to be polymorphic, with the number of haplotypes ranging from 3 for VD_C to 8 for OV_F. The lowest haplotype diversity, 0.54 ± 0.08, was observed in VD_C chickens, whereas the highest value, 0.88 ± 0.05, was observed in OV_F chickens. Genetic diversity between the 4 South African conserved and 2 field chicken populations constituted 12.34% of the total genetic variation, whereas within-population diversity constituted 87.66% of the total variation. The median network analysis of the mtDNA D-loop haplotypes observed in the South African conserved and field populations and the reference set resulted in 5 main clades. All 6 South African chickens were equally represented in the major clade, E, which is presumed to be of Indian subcontinent maternal origin and may have its roots in Southeast Asia. The results showed multiple maternal lineages of South African chickens. Conservation flocks and field chicken populations shared the major haplotypes A, D and E, which were presumed to be of Chinese, Southeast Asian, and Indian subcontinental origin.

Summary In this study, we compare the level and distribution of genetic variation between South African conserved and village chicken populations using microsatellite markers. In addition, diversity in South African chickens was compared to that of a reference data set consisting of other African and purebred commercial lines. Three chicken populations Venda, Ovambo and Eastern Cape and four conserved flocks of the Venda, Ovambo, Naked Neck and Potchefstroom Koekoek from the Poultry Breeding Resource Unit of the Agricultural Research Council were genotyped at 29 autosomal microsatellite loci. All markers were polymorphic. Village chicken populations were more diverse than conservation flocks. structure software was used to cluster individuals to a predefined number of 2 ≤ K ≤ 6 clusters. The most probable clustering was found at K = 5 (95% identical runs). At this level of differentiation, the four conservation flocks separated as four independent clusters, while the three village chicken populations together formed another cluster. Thus, cluster analysis indicated a clear subdivision of each of the conservation flocks that were different from the three village chicken populations. The contribution of each South African chicken populations to the total diversity of the chickens studied was determined by calculating the optimal core set contributions based on Marker estimated kinship. Safe set analysis was carried out using bootstrapped kinship values calculated to relate the added genetic diversity of seven South African chicken populations to a set of reference populations consisting of other African and purebred commercial broiler and layer chickens. In both core set and the safe set analyses, village chicken populations scored slightly higher to the reference set compared to conservation flocks. Overall, the present study demonstrated that the conservation flocks of South African chickens displayed considerable genetic variability that is different from that of the assumed founder populations (village chickens).

Local pigs in Southern Africa are an important component of resource-based subsistence farming systems and contribute substantially to the improvement of livelihoods of farmers. In addition to utilising by-products and feed resources that are otherwise of no use, they serve various socio-economic functions. The numbers, breeds and population genetic structures, attributes and risk status of these pigs are understudied. In the few studies to date, they have been shown to be tolerant to parasites that are endemic in their production environment. They also have a better chance to survive various disease outbreaks and have a higher capacity to utilise fibrous and poor quality feed resources compared to exotic breeds. Their production environment has also been described with women owning most of the pigs. The farmers tend to keep the herd sizes small in order to adequately meet the animals' nutrition needs. This leads to small populations that are vulnerable to inbreeding and disasters. In addition, there are no incentive systems in place to promote conservation of the pigs. There is an urgent need to address research and policy gaps, and to formulate strategies for the conservation of this resource.

An A/G Single Nucleotide Polymorphism (SNP) at position 1,892 of the Mx gene coding sequence has been linked to susceptibility/resistance to avian viral infection in vitro. Using PCR-RFLP and sequencing methods, 1,946 samples from 109 populations from Asia, Africa and Europe; grouped as indigenous village, commercial, fancy chicken as well as wild junglefowl were genotyped for the polymorphism. Allele and genotype frequencies were calculated. Only the G allele was present in Ceylon junglefowl Gallus lafayetti. Using the wild red junglefowl G. gallus population as reference, we assessed if the A/G alleles and genotypes frequencies have been affected by the breeding history and the geographic dispersion of domestic chicken. Within group variation was high but overall there were no significant variation in distribution of alleles and genotypes frequencies between the red junglefowl and indigenous village chickens (p>0.1946), with the exception of the East Asian group (p

Free ranging chickens reared by smallholder farmers represent genetic diversity suited for particular environments and shaped by the socio-economic and cultural values of the farming systems. This study sought to investigate the existence of chicken strains and evaluate the breeding goals and strategies used by village chicken farmers in Zimbabwe. A semi-structured questionnaire was administered to 97, 56, 70, 104 and 37 households randomly selected from five agro-ecological-zones I-V, respectively. Fifteen chicken strains mostly defined by morphological traits were reported in the five eco-zones. Production criteria such as body size, and fertility were highly ranked (ranging from 1.3 – 2.6) by farmers across all the eco-zones, while cultural traits were the least preferred production traits. As a common breeding practice, farmers chose the type of hens and cocks to retain for breeding purposes and these randomly mixed and mated with others from community flocks. Chicken body size was ranked the major determinant in choosing breeding animals followed by mothering ability, and fertility. More households culled chickens associated with poor reproductive performance, poor growth rates and those intolerant to disease pathogens. The focus on many negatively correlated production traits and the absence of farmer records compromises breeding strategies in these production systems.

The genetic structure and diversity of 15 Chinese indigenous chicken breeds was investigated using 29 microsatellite markers. The total number of birds examined was 542, on average 36 birds per breed. A total of 277 alleles (mean number 9.55 alleles per locus, ranging from 2 to 25) was observed. All populations showed high levels of heterozygosity with the lowest estimate of 0.440 for the Gushi chickens, and the highest one of 0.644 observed for Wannan Three-yellow chickens. The global heterozygote deficit across all populations (FIT) amounted to 0.180 (p

Summary This study assessed the genetic diversity in the growth hormone 1 gene (GH1) within and between South African goat breeds. Polymerase chain reaction-targeted gene amplification together with Illumina MiSeq next-generation sequencing (NGS) was used to generate the full length (2.54 kb) of the growth hormone 1 gene and screen for SNPs in the South African Boer (SAB) (n = 17), Tankwa (n = 15) and South African village (n = 35) goat populations. A range of 27–58 SNPs per population were observed. Mutations resulting in amino acid changes were observed at exons 2 and 5. Higher within-breed diversity of 97.37% was observed within the population category consisting of SA village ecotypes and the Tankwa goats. Highest pairwise FST values ranging from 0.148 to 0.356 were observed between the SAB and both the South African village and Tankwa feral goat populations. Phylogenetic analysis indicated nine genetic clusters, which reflected close relationships between the South African populations and the other international breeds with the exception of the Italian Sarda breeds. Results imply greater potential for within-population selection programs, particularly with SA village goats.