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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

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).

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.

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.

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.

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.

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.

* Agricultural Research Council, Animal Production Institute, Private Bag X2, Irene, 0062, South Africa; † Department of Animal Science, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa; ‡ Discipline of Animal and Poultry Science, University of KwaZulu-Natal, Private Bag X01, Scottsville, 3209, Pietermaritzburg, South Africa; and § Institute of Farm Animal Genetics, Friedrich Loeffler Institut, Holtystr. 10, 31535 Neustadt-Mariensee, Germany