Ticks and tick-borne diseases are among the main causes of economic loss in the South African cattle industry through high morbidity and mortality rates. Concerns of the general public regarding chemical residues may tarnish their perceptions of food safety and environmental health when the husbandry of cattle includes frequent use of acaricides to manage ticks. The primary objective of this study was to identify single nucleotide polymorphism (SNP) markers associated with host resistance to ticks in South African Nguni cattle. Tick count data were collected monthly from 586 Nguni cattle reared in four herds under natural grazing conditions over a period of two years. The counts were recorded for six species of ticks attached in eight anatomical locations on the animals and were summed by species and anatomical location. This gave rise to 63 measured phenotypes or traits, with results for 12 of these traits being reported here. Tick count (x) data were transformed using log10(x+1) and the resulting values were examined for normality. DNA was extracted from hair and blood samples and was genotyped using the Illumina BovineSNP50 assay. After quality control (call rate >90%, minor allele frequency >0.02), 40,436 SNPs were retained for analysis. Genetic parameters were estimated and association analysis for tick resistance was carried out using two approaches: a genome-wide association (GWA) analysis using the GenABEL package and a regional heritability mapping (RHM) analysis. The Bonferroni genome-wide (P<0.05) corrected significance threshold was 1.24×10(-6), with 2.47×10(-5) as the suggestive significance threshold (P<0.10) (i.e., one false positive per genome scan) in the GWA analysis. Likelihood ratio test (LRT) thresholds for genome-wide and suggestive significance were 13.5 and 9.15 for the RHM analysis. Six ixodid tick species were identified, with Amblyomma hebraeum (the vector for Heartwater disease) being the dominant species. Heritability estimates (h(2)) from the fitted animal and sire models ranged from 0.02±0.00 to 0.17±0.04 for the transformed tick count data. Several genomic regions harbouring quantitative trait loci (QTL) were identified for different tick count traits by both the GWA and RHM approaches. Three genome-wide significant regions on chromosomes 7, 10 and 19 were identified for total tick count on the head, total body A. hebraeum tick count and total A. hebraeum on the perineum region, respectively. Additional regions significant at the suggestive level were identified on chromosomes 1, 3, 6, 7, 8, 10, 11, 12, 14, 15, 17, 19 and 26 for several of the traits. The GWA approach identified more genomic regions than did the RHM approach. The chromosomal regions identified here as harbouring QTL underlying variation in tick burden form the basis for further analyses to identify specific candidate genes and polymorphisms related to cattle tick resistance and provide the potential for marker-assisted selection in Nguni cattle.

Genome-wide association study for tick resistance in South African Nguni cattle

Single nucleotide polymorphism arrays have created new possibilities for performing genome-wide studies to detect genomic regions harboring sequence variants that affect complex traits. However, the majority of validated SNPs for which allele frequencies have been estimated are limited primarily to European breeds. The objective of this study was to perform SNP discovery in three South African indigenous breeds (Afrikaner, Drakensberger, and Nguni) using whole genome sequencing. DNA was extracted from blood and hair samples, quantified and prepared at 50 ng/μl concentration for sequencing at the Agricultural Research Council Biotechnology Platform using an Illumina HiSeq 2500. The fastq files were used to call the variants using the Genome Analysis Tool Kit. A total of 1,678,360 were identified as novel using Run 6 of 1000 Bull Genomes Project. Annotation of the identified variants classified them into functional categories. Within the coding regions, about 30% of the SNPs were non-synonymous substitutions that encode for alternate amino acids. The study of distribution of SNP across the genome identified regions showing notable differences in the densities of SNPs among the breeds and highlighted many regions of functional significance. Gene ontology terms identified genes such as MLANA, SYT10, and CDC42EP5 that have been associated with coat color in mouse, and ADAMS3, DNAJC3, and PAG5 genes have been associated with fertility in cattle. Further analysis of the variants detected 688 candidate selective sweeps (ZHp Z-scores ≤ -4) across all three breeds, of which 223 regions were assigned as being putative selective sweeps (ZHp scores ≤-5). We also identified 96 regions with extremely low ZHp Z-scores (≤-6) in Afrikaner and Nguni. Genes such as KIT and MITF that have been associated with skin pigmentation in cattle and CACNA1C, which has been associated with biopolar disorder in human, were identified in these regions. This study provides the first analysis of sequence data to discover SNPs in indigenous South African cattle breeds. The information will play an important role in our efforts to understand the genetic history of our cattle and in designing appropriate breed improvement programmes.

/pdf/genome-wide-snp-discovery-in-indigenous-cattle-breeds-of-h7ecedwbcd.pdf

Genome-Wide SNP Discovery in Indigenous Cattle Breeds of South Africa.

Objective This work was conducted to examine the association between body weight (BW) and biometric traits viz. head width (HW), head length (HL), ear length (EL), body length (BL), rump height (RH), withers height (WH), sternum height (SH), rump width (RW), and heart girth (HG) and to determine the direct and indirect effects of biometric traits on BW. Materials and methods Sixty female and twenty male Nguni cattle between the ages of one to four years were used. Pearson correlation and path analysis were used for data analysis. Results Correlation results recognized that BW had a positive highly significant correlation with RW (r = 0.70**), RH (r = 0.90**), HG (r = 0.90**), SH (r = 0.90**), and WH (r = 0.93**) in male, whereas SH (r = 0.34**), WH (r = 0.55**), RH (r = 0.70**), and HG (r = 0.76**) had a positive highly significant correlation with BW of female Nguni cattle. Path analysis showed that RW (13.35) had the highest direct effect, whereas SH had an indirect effect on BW of male Nguni cattle. In female Nguni cattle, RH (4.87) had the highest direct effect, whereas HL had an indirect effect on BW. Conclusion Association findings suggest that improvement of RW, RH, HG, SH, HG, and WH might result in the increase in BW of Nguni cattle. Path analysis results suggest that RW and RH might be used as a selection criterion during breeding to increase BW of Nguni cattle. The results of the current study might be used by cattle farmers to estimate BW using biometric traits.

Correlation and path analysis of body weight and biometric traits of Nguni cattle breed.

Cattle populations arrived in Southern Africa almost 2000 years ago, brought by farming communities migrating southwards. For centuries, cattle have been an integral component of livestock production to meet the animal protein needs of a growing population and they are also important in many cultural and religious events, as repositories of wealth and signifiers of social status. Selection within these cattle populations led to the development of breeds such as the Nguni, Afrikaner and Drakensberger that are well adapted to the local production environment. Genetic information has been generated for most of these populations, providing new insights into their ancestry and indicating moderate levels of diversity and relatively low inbreeding. Indigenous cattle breeds are present in both the well-developed commercial sector as well as the developing South African livestock sector. These breeds have been included in several research studies, mostly focusing on their production and adaptive potential. Genetic improvement of the local cattle populations and breeds, which are often more resilient to local environmental conditions, has the potential to improve the productivity of the small-scale production developing sector and contribute to the alleviation of poverty.

https://www.mdpi.com/2071-1050/13/8/4388/pdf

Capitalizing on the Potential of South African Indigenous Beef Cattle Breeds: A Review

High-throughput genomic markers provide an opportunity to assess important indicators of genetic diversity for populations managed in livestock breeding programs. While well-structured breeding programs are common in developed countries, in developing country situations, especially in West Africa, on-farm performance and pedigree recordings are rare, and thus, genomic markers provide insights to the levels of genetic diversity, inbreeding and introgression by other breeds. In this study, we analysed key population parameters such as population structure, admixture and levels of inbreeding in three neighbouring populations of African taurine and taurine × Zebu crosses managed by community-based breeding programs in the South-West of Burkina Faso. The three populations were pure Baoule (called Lobi locally) in sedentary production systems, Baoule x Zebu crossbreds in sedentary systems and Zebu × Baoule crossbreds in transhumant production systems, respectively. The total sample analysed included 631 animals and 38,207 single nucleotide polymorphisms after quality control. Results of principal component and admixture analyses confirmed the genetic background of two distinct ancestral populations (taurine and zebuine) and levels of admixture in all three breeding populations, including the presumably pure Baoule group of animals. Inbreeding levels were moderate, compared to European dairy and beef cattle populations and higher than those of Brazilian Nellore cattle. Very few animals with inbreeding levels indicating parent-offspring or full sib mating were observed, and inbreeding levels indicating half sib mating were also rare. For the management of breeding populations, farmers were advised to exchange best young bulls. The crossbreeding levels of presumably pure Baoule animals are of concern to the breeding program due to the high level of endangerment of pure African taurine cattle populations across West Africa. Future rounds of bull selection in the community-based breeding program will make use of genomic information about admixture levels.

Population structure, inbreeding and admixture in local cattle populations managed by community-based breeding programs in Burkina Faso.

The Nguni cattle breed has distinct populations that are adapted to the different ecological zones of Southern Africa. This study was carried out to assess genetic diversity and establish the relationships among South African (SA), Mozambican (Landim), and Swazi Nguni cattle populations, using 25 microsatellite markers. Genotypic data were generated from deoxyribonucleic acid (DNA) samples of 90 unrelated individuals of the three cattle populations, collected from government conservations and stud herds. DNA profiles of five local beef breeds were used as the reference populations. Most of the 25 microsatellite markers were highly polymorphic across the studied populations, with an overall polymorphic information content (PIC) mean of 0.676. Genetic diversity within populations was high with expected heterozygosity varying from 0.705 ± 0.024 (Landim) to 0.748 ± 0.021 (SA Nguni) and mean number of alleles being highest in the SA Nguni (7.52 ± 0.42). Average observed heterozygosity (0.597 ± 0.046) compared to the expected heterozygosity (0.719 ± 0.022) was lowest for the Swazi Nguni, which also had a high number of Hardy-Weinberg Equilibrium (HWE) deviated loci (13), confirming the relatively high level of inbreeding (0.158 ± 0.058) in that population. Analysis of molecular variance revealed only 9.61% of the total variation between the populations and 90.39% within populations. A short genetic distance (0.299) was observed between Landim and Swazi Nguni, with the SA Nguni (> 0.500) being the most genetically distant population. The distant relationship between SA Nguni and the other two Nguni cattle populations was further confirmed by a principal coordinates analysis. The three Nguni populations clustered independently from each other, despite some evidence of admixture. Therefore, it can be concluded that SA Nguni, Landim, and Swazi Nguni populations in Southern Africa exhibit high levels of genetic diversity and are genetically distant; with the two latter populations being less genetically apart. These results present useful information for the development of strategies for regional management of animal genetic resources, through conservation and sustainable utilisation.

Genetic diversity and relationships among three Southern African Nguni cattle populations.

Adaptation of animals to different environments is typically associated with structural and functional genomic variations. High throughput SNP genotyping and next-generation sequencing (NGS) have made it possible to study positive selection footprints and adaptation traits. Nguni is a small frame-size breed, mostly horned, and well known for being adapted to diverse South African environmental conditions. This study used previously identified selective sweeps to perform functional analysis of genes related to phenotypic characteristics in Nguni. Two hundred and sixty-four candidate selective sweeps were used for gene-set enrichment analysis in molecular functional categories (KEGG pathways) using the database for annotation, visualization, and integrated discovery (DAVID). In total, 107 genes were identified across all the chromosomes with 74 genes associated with eight phenotype queries, including fat content, milk production, walking ability, heat tolerance, meat production, reproduction, and bone and muscle development. Gene CRHR2 was associated with meat quality (juiciness and flavour). The IRAK3 gene was associated with decreased body size, feed intake and fatness in cattle, and CARD15 with disease resistance. Gene annotation using phenotype queries identified four genes (SPI, YWHAZ, RGS4, and RGS5) that were associated with myometrial relaxation in cattle. Genes such as NOD2 and IL21R were associated with inflammatory bowel diseases in cattle, whereas CPLS gene was associated with fat content. These genes are important to the phenotypic and adaptive characteristics present in South African Nguni cattle and hold potential for selection for traits of economic importance.

https://www.ajol.info/index.php/sajas/article/download/224915/212189

Gene-set enrichment analysis of selective sweeps reveals phenotypic traits in Nguni cattle

The indigenous sheep breeds of South Africa are of importance than any other livestock within the country and they are subdivided into different breed’s types which differ based on their geographical origins of origin. These types are threatened with extinction due to terminal crossbreeding effect. An understanding of the genetic diversity of types is essential prior to conservation and implementation for proper breeding programmes. 96 South African Ovine samples, comprising of 25 Pedi, 25 Namaqua, 25 Swazi and 21 Damara were genotyped using the Ovine50KSNP BeadChip assay. Genome Studio (Illumina) software was used to make the genotypes from the raw genotypic data. Genotypic data were subjected to quality control (QC) measures using PLINK software. After QC of 54 241SNPs, 48 429 SNPs remained for analysis (MAF >0.05). The outcomes of this study delivered valuable understanding regarding genetic variation within and among four indigenous sheep breeds.

/pdf/genomic-diversity-and-population-structure-of-four-south-z0tcrbtmaj.pdf

Genomic diversity and population structure of four South African indigenous Sheep

The indigenous sheep breeds of South Africa, such as the Nguni, are well adapted to different ecological regions throughout the country. This has resulted into different ecotypes. However, it is not clear if the differences among Nguni sheep are genetically distinct. The present study aimed to use the latest technology to assess the genetic relationship between Nguni sheep ecotypes and the relationship to other selected South African breeds using SNP markers. In the current study, 144 South African sheep samples (75 Nguni sheep and 69 mixed-breed sheep as a reference) were genotyped using the OvineSNP50 Bead Chip assay from Illumina. The Nguni consisted of 25 Pedi, 25 Swazi, and 25 Zulu sheep, with the reference group comprising 25 Namaqua, 23 Dorper, and 21 Damara sheep. After quality control of 54,241 SNPs, 48,429 SNPs remained for analysis (MAF > 0.05). There were genetic differences in the Nguni sheep population; notably, the Zulu and Swazi populations clustered together, but with a clear distinction from the Pedi ecotype. Genetic admixtures were detected in the Damara and Dorper sheep. This is most likely a consequence of recent intermixing between indigenous and commercial breeds. The levels of genetic diversity within individual types were generally lower compared to commercial breeds. This study revealed an understanding regarding genetic variation within and among indigenous sheep breeds, which can be used as baseline information for establishing conservation and breeding programmes.

/pdf/the-genetic-assessment-of-south-african-nguni-sheep-breeds-2zg26xnp.pdf

The Genetic Assessment of South African Nguni Sheep Breeds Using the Ovine 50K Chip

Next generation sequencing have made it possible to study positive selection footprints and adaptation traits in livestock. South African (SA) Nguni cattle are well known for their adaption to harsh environments and can produce well. A total of 264 selective sweeps regions identified in Nguni were used to perform functional analysis of genes associated with phenotypic and adaptive characteristics. About 107 genes were identified across chromosomes with 58 genes associated with eight selected phenotypes queries. The CRHR2 gene was associated with meat quality, IRAK3 with decreased body size, feed intake and fatness, and CARD15 gene was associated with disease resistance. Four genes (SPI, YWHAZ, RGS4 and RGS5) were associated with myometrial relaxation in cattle. The NOD2 and IL21R genes were associated with inflammatory bowel diseases whereas CPLS gene was associated with fat content in cattle. These genes were significant to the phenotypic and adaptive features present in SA Nguni cattle and will assist in breeding. 

Khanyisani S Nxumalo

Papers

Genetic diversity and relationships among three Southern African Nguni cattle populations.

Gene-set enrichment analysis of selective sweeps reveals phenotypic traits in Nguni cattle

Genomic diversity and population structure of four South African indigenous Sheep

The Genetic Assessment of South African Nguni Sheep Breeds Using the Ovine 50K Chip

518. Functional analysis of selective sweeps to identify phenotypic traits in South African Nguni cattle