Genetic diversity and population structure among six cattle breeds in South Africa using a whole genome SNP panel

Information about genetic diversity and population structure among cattle breeds is essential for genetic improvement, understanding of environmental adaptation as well as utilization and conservation of cattle breeds. This study investigated genetic diversity and the population structure among six cattle breeds in South African (SA) including Afrikaner (n=44), Nguni (n=54), Drakensberger (n=47), Bonsmara (n=44), Angus (n=31) and Holstein (n=29). Genetic diversity within cattle breeds was analyzed using three measures of genetic diversity namely allelic richness (AR), expected heterozygosity (He) and inbreeding coefficient (f). Genetic distances between breed pairs were evaluated using Nei’s genetic distance. Population structure was assessed using model-based clustering (ADMIXTURE). Results of this study revealed that the allelic richness ranged from 1.88 (Afrikaner) to 1.73 (Nguni). Afrikaner cattle had the lowest level of genetic diversity (He=0.24) and the Drakensberger cattle (He=0.30) had the highest level of genetic variation among indigenous and locally-developed cattle breeds. The level of inbreeding was lower across the studied cattle breeds. As expected the average genetic distance was the greatest between indigenous cattle breeds and Bos taurus cattle breeds but the lowest among indigenous and locally-developed breeds. Model-based clustering revealed some level of admixture among indigenous and locally-developed breeds and supported the clustering of the breeds according to their history of origin. The results of this study provided useful insight regarding genetic structure of South African cattle breeds

Genomics Tools for the Characterization of Genetic Adaptation of Low Input Extensively Raised Chickens

Evolutionary change emanating from differential contribution of genotypes to the next generation can determine success in survival and reproduction in chickens. For extensively raised chickens reared under low-input production systems in smallholder farming areas, conditions of resources deprivation and exposure to diverse and threatening natural selection pressures are common in many countries worldwide. Numerous studies have demonstrated that village chickens and other extensively raised chicken populations represent a valuable source of biodiversity adapted to the local production conditions and selection pressures. Manipulation of their acquired adaptive genetic diversity depends on unravelling the selection footprints in the genomes of these chickens that could point towards candidate genes for traits that enable the animals to survive under the harsh production environments. This chapter summarizes the evidence for chickens’ adaptation to extreme environments and describes an inventory of modern tools that could be used in characterizing the production systems of chicken genetic resources. The role of natural selection in shaping the biodiversity of chicken genetic resources is discussed. The continued advancement of biotechnological tools to assess chicken populations has been beneficial to research in genetic adaptation. Genomics tools, as evidenced by assays of whole genome and transcriptome sequences, and single nucleotide polymorphism (SNP) genotypes of chickens, now allow analyses of functional genomic regions that are linked to adaptation. The use of these methods to characterize and investigate signatures of selection in the chicken genomes is highlighted. This chapter looks at how information on the selection hotspots in the chicken genomes can be manipulated to improve genetic adaptation in indigenous chicken populations with the desire to transfer the benefits to other chicken breeds raised under similar production systems

Reconstructing the origin and dispersal patterns of village chickens across East Africa: insights from autosomal markers

Unravelling the genetic history of any livestock species is central to understanding the origin, development and expansion of agricultural societies and economies. Domestic village chickens are widespread in Africa. Their close association with, and reliance on, humans for long-range dispersal makes the species an important biological marker in tracking cultural and trading contacts between human societies and civilizations across time. Archaezoological and linguistic evidence suggest a complex history of arrival and dispersion of the species on the continent, with mitochondrial DNA (mtDNA) D-loop analysis revealing the presence of five distinct haplogroups in East African village chickens. It supports the importance of the region in understanding the history of the species and indirectly of human interactions. Here, through a detailed analysis of 30 autosomal microsatellite markers genotyped in 657 village chickens from four East African countries (Kenya, Uganda, Ethiopia and Sudan), we identify three distinct autosomal gene pools (I, II and III). Gene pool I is predominantly found in Ethiopia and Sudan, while II and III occur in both Kenya and Uganda. A gradient of admixture for gene pools II and III between the Kenyan coast and Uganda's hinterland (P = 0.001) is observed, while gene pool I is clearly separated from the other two. We propose that these three gene pools represent genetic signatures of separate events in the history of the continent that relate to the arrival and dispersal of village chickens and humans across the region. Our results provide new insights on the history of chicken husbandry which has been shaped by terrestrial and maritime contacts between ancient and modern civilizations in Asia and East Africa

Genotype imputation as a cost-saving genomic strategy for South African Sanga cattle: A review

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, genomic

Some insights into the phenotypic and genetic diversity of indigenous pigs in southern Africa

Indigenous pigs in southern Africa are mainly owned by economically vulnerable groups in marginal areas where they are used as a source food, income and security. A study was carried out to achieve three objectives: to describe pig production systems, get a phenotypic description of the pigs and to characterize them genetically. A survey of 199 farmers in three districts in South Africa, (Vhembe, OR Tambo and Alfred Nzo) and one district in Zimbabwe (Chirumhnazu) was carried out. Additional farmers in Malawi (Dedza, Mchinji and Salima) and Zimbabwe (Mutoko) were sampled in order to meet the other two objectives. Most of the pigs (69.7%) were owned by women, with men owning 20.5% and children the remainder. Production of the pigs was constrained by several factors including disease, inadequate feeds, poor housing and lack of knowledge. The majority of the pigs were small and black with characteristics that are probably suited for thermoregulation in arid environments. The third objective was achieved through genotyping 111 pigs using 22 microsatellites. Preliminary results indicate very little differences across populations with an overall inbreeding coefficient of the subpopulation relative to the total population (FST) of 0.071. The results indicate that the indigenous pigs in southern Africa are relatively homogenous.Keywords: Conservation, Kolbroek, microsatellites, smallholder pig production, Windsnye

Genetic and phenotypic characterization of African goat populations to prioritize conservation and production efforts for small-holder farmers in sub-Saharan Africa

Food production systems in Africa depend heavily on the use of locally adapted animals. Goats are critical to small-holder farmers being easier to acquire, maintain, and act as scavengers in sparse pasture. Indigenous goats have undergone generations of adaptation and genetic isolation that have led to great phenotypic variation. These indigenous goats serve as a genetic reservoir for the identification of genes important to environmental adaptation, disease resistance, and improved productivity under local conditions. The immediate goal is to characterize African goat populations to prioritize conservation and production efforts and to develop genomic tools for use in selective breeding programs. We have established a standardized phenotypic scoring system to characterize goats including geographical information data, body measurements, photo characterization, and DNA. To date, 2,443 goats from 12 countries, representing 46 breeds have been sampled. Using the 50K goat beadchip, we report parameters of population structure of 620 African goats

Domestication of South African chicken genetic resources

Domestic animals are recognized as an important part of biodiversity and more conservation efforts to save rare breeds are made. Genetic relationship and the domestication of South African chickens is a point of interest, as the origin of the breeds is not exactly known. According to van Marle-Koster and Casey (2001), domestic chickens were introduced into Southern Africa by early traders during the 1600’s from India, Europe and sub-Saharan Africa. Some archaeological studies have indicated that chickens were introduced into Africa via the East Africa–Southeast Asia trade links (Macdonald 1992). Crawford (1990) reported that domesticated chickens were found in Mozambique by 1600. Using mtDNA sequence data, Akishinonomiya et al. (1996) reported that existing domestic chickens originated from Gallus gallus gallus in Thailand and adjacent regions, while recent studies by Liu et al. (2006), Oka et al. (2007) and Muchadeyi et al. (2008) suggested that domestication events occurred in Southeast Asia, South China and Indian subcontinent. The objective of this study is to determine the genetic relationship and the geographical origin of the South African conserved and field chicken populations using mtDNA sequence

Gene expression profiles of the small intestine of village chickens from an Ascaridia galli infested environment

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.Tthe Agricultural Research Council-BTP and the NRF under the Zambia/south Africa bilateral Research Program. Dr Malatji received an NRF-DST Professional Development Program research fellowship and University of Pretoria postgraduate support bursary.https://www.journals.elsevier.com/veterinary-parasitology-xpm2020Animal and Wildlife Science

Whole genome sequencing and identification of Bacillus endophyticus and B. anthracis isolated from anthrax outbreaks in South Africa

Abstract 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