Species richness and adaptation of the invasive cattle tick, Rhipicephalus microplus (Acari: Ixodidae) on camps grazed by sheep in the Eastern Cape Province, South Africa.

The seasonal dynamics and distribution of ticks play a pivotal role in the epidemiology of tick-borne diseases. The objective of this study was to establish the seasonal abundance and species richness of questing ixodid ticks on Amathole Montane Grassland camps grazed by sheep. Ticks questing for hosts were collected monthly for a period of three years by dragging flannel strips attached to a wooden spar over the vegetation. At each occasion, six replicate drag-samples were made in camps grazed by sheep. Of the questing ticks (n = 14 891) collected from the vegetation, the most abundant larvae were those of Rhipicephalus microplus (95.04%) followed by Rhipicephalus appendiculatus (2.32%), Rhipicephalus evertsi (1.56%), Rhipicephalus decoloratus (1.03%), Rhipicephalus simus (0.03) and Amblyomma hebraeum (0.02%). Comparing the two Rhipicephalus (Boophilus) spp., R. microplus (98.9%) outcompete the indigenous tick, R. decoloratus (1.1%). The R. microplus larvae were significantly higher (P < 0.05) in 2015 (2.11±0.108), 2016 (2.02 ± 0.076) and 2017 (1.94±0.075) during spring than any other season. There were no significant differences (P ˃ 0.05) from R. appendiculatus questing ticks collected in autumn (0.27±0.007; 0.30±0.052) and spring (0.33±0.007; 0.20±0.052) for 2015 and 2016, respectively. The study showed that the cattle tick, R. microplus adapted very well on host species, in this case sheep, and encroached to areas that were too cold for its adaptation.

A within- and across-country assessment of the genomic diversity and autozygosity of South African and eSwatini Nguni cattle.

In southern Africa, the Nguni cattle breed is classified as an indigenous and transboundary animal genetic resource (AnGR) 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 exist both across countries (ES: eSwatini; SA: South Africa) and within countries (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 genome-wide profiles of runs of homozygosity (ROH) and heterozygosity (ROHet) as well as inbreeding levels and population structure. The highest percentage (39.8%) of the 2168 ROH segments was 4-8 Mbp in length, whereas 65% of the 935 ROHet segments fell within the 0.5-1 Mbp length category. Inbreeding coefficients indicated positive but low inbreeding (FROH>1Mbp range: 0.025 for SA-S to 0.029 for SA-R). Principal component (PCA) and population structure analyses illustrated genome-level distinctness of (1) the Nguni from global indicine (Boran) and taurine (Hereford) breeds (K = 3), (2) the SA Nguni populations from the ES Nguni population (K = 4), and (3) different Nguni ecotypes within countries (K = 8). Furthermore, greater admixture was observed for the SA-R population compared to purebred SA-S population (shared ancestry = 0.631 ± 0.353 compared to 0.741 ± 0.123), and fewer genomics-defined ES ecotypes were observed than phenotypically (pre)defined. Overall, the results illustrated that genetic uniqueness within the sampled Nguni cattle resulted from both geographic isolation and exposure to different breeding strategies (and, selection pressures). A further loss of genetic variability should be monitored to prevent the endangerment of unique and beneficial ecotypes.

Genetic parameter estimates for milkability traits and their relationship with somatic cell score in South African Holstein cattle.

Milkability is an important functional trait, which is directly related to milking costs and udder health. There are no milkability traits incorporated in the South African dairy cattle breeding objectives and genetic parameter estimates for these traits are not available in this population. The main objective of the study was, therefore, to estimate the genetic parameters for milkability traits and its correlation with somatic cell scores in South African Holstein cattle. Data consisted of production and milkability records of 2719 Holstein cows, from ten herds, collected from 2016 to 2018. Genetic parameters were estimated by a multi-trait animal model using the restricted maximum likelihood (REML) procedure. Means for milking time (MT), average milk flow (AMF), maximum milk flow (MMF), and somatic cell score (SCS) were 5.20 min, 1.91 kg/min, 2.99 kg/min, and 2.06, respectively. The heritability estimates were low to moderate from 0.19 ± 0.07, 0.24 ± 0.06, 0.36 ± 0.11, and 0.41 ± 0.12, respectively, for SCS, AMF, MT, and MMF. The genetic correlations were significant (P < 0.05) among the three milkability traits ranged from - 0.31 ± 0.05 between AMF and MT to 0.85 ± 0.02 between AMF and MMF. Positive genetic correlations were observed between AMF and MMF, while the correlations for MT with the remaining milkability traits were negative. Genetic correlations of SCS with AMF, MMF, and MT were - 0.13 ± 0.04, 0.13 ± 0.04, and - 0.25 ± 0.12, respectively. The mean estimated breeding value (EBV) was estimated using cattle birth dates, and there was an increase in AMF of 0.0001 kg/min EBV per year on cattle born during the period 2002 to 2014. Maximum milk flow also showed an increasing genetic trend of 0.0003 kg/min per year over the same period. On the other hand, the genetic trend for MT was undesirable, as it increased by 0.0003 kg/min per year. The moderate to high heritability estimates for milkability traits showed that selection for improvement was possible in South African Holstein cattle. High genetic correlation between AMF and MMF implied that these two may be regarded as the same trait. Milking time can contribute towards improving the accuracy of estimating EBVs for SCS in a multi-trait analysis, and vice versa, due to the moderate correlation between the two traits. The marginal genetic trend in milkability traits may be an interrelated response to selection of other traits already under selection in the population such as SCS. Results of the current study provided a basis for including milkability traits of South African Holstein cattle in the breeding objectives.

Genetic parameters for tick counts across months for different tick species and anatomical locations in South African Nguni cattle.

The objective of the study was to characterise genetic parameters across months for different tick species and anatomical locations in South African Nguni cattle. Tick counts were conducted monthly, over a 2-year period, on 586 Nguni cattle under natural infestation, from four herds located in different provinces of South Africa. The counts were recorded for six species of ticks (Amblyomma hebraeum, Rhipicephalus evertsi evertsi, Rhipicephalus decoleratus and microplus (Boofilids), Rhipicephalus appendiculatus, Rhipicephalus simus and Hyalomma marginatum) attached on eight anatomical locations on the animals and were summed by species and anatomical location. Heritability estimates, phenotypic and genetic correlations were estimated on a monthly basis using mixed linear models, fitting univariate and bivariate sire models. Fixed effects considered were location, sex, year and age as a covariate. Tick counts were higher in the hot months, and A. hebraeum was the most dominant tick species. Heritability estimates for tick count varied by month and trait and ranged from 0 to 0.89. Genetic correlations were mostly positive, and low to high, with some negative correlations with high standard error. Phenotypic correlations were low to moderate. In general, high genetic correlations were observed between whole body count and the anatomical location counts, suggesting that it may not be necessary to conduct whole body counts. Counts from the belly and perineum appeared to be the most suitable surrogate traits for whole body count. These findings provide useful information for developing strategies for the practical implementation of genetic selection, as a supplement to the traditional tick control measures.

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

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.