Prevalence and tick loads in Nguni cattle reared in different environmental conditions across four provinces of South Africa.

Background and Aim: In tropical and subtropical countries, ixodid ticks are among livestock's most economically important ectoparasites. Although Nguni cattle from South Africa have adapted to harsh environments, it is unknown whether they will be resistant to ticks, and the diseases carried by ticks under various climatic conditions. Therefore, this study aimed to compare tick load and estimate the prevalence of different tick species among Nguni cattle under different environmental conditions. Materials and Methods: Tick counts were conducted monthly under natural challenges over 2 years on 586 Nguni cattle located at ARC-Roodeplaat and Loskop farms (warmer climate), Mukhuthali Nguni Community and the University of Fort Hare farms (cooler climate). The generalized linear model procedure of the Statistical Analysis System was used to analyze the data. It fitted the location (farm), sex, year, month or season, and animal age as covariates. Results: The tick species (relative prevalence) observed were as follows: Amblyomma hebraeum (42%), Rhipicephalus evertsi (22%), Rhipicephalus (Boophilus) spp. (16%), Rhipicephalus appendiculatus (11%), Hyalomma marginatum (5%), and Rhipicephalus simus (4%). Tick infestation was significantly affected by location, season, year, month of the tick counting and age of the animal. Loskop farm had the highest tick count (m = 30.69) and showed the largest variation in tick count. Compared to the other seasons, higher tick counts were seen during the hot-dry (September-November) and hot-wet (December-February) seasons. A. hebraeum was the dominant tick species across all four farms, followed by R. evertsi. The perianal region (under the tail head), the perineum and the belly body locations were the most preferred tick attachment sites. Conclusion: These results provide useful information for developing appropriate control strategies for ticks and tick-borne diseases in these provinces of South Africa. Further work must investigate the feasibility of genetic improvement for tick resistance.

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.

Current situations of animal data recording, dairy improvement infrastructure, human capacity and strategic issues affecting dairy production in sub-Saharan Africa.

An online survey on the state of existing dairy data, dairy improvement infrastructure and human capacity in sub-Saharan Africa (SSA) was undertaken with the aim of assessing whether the state of existing animal recording, dairy improvement methods and key issues facing dairy production together with means of addressing the issues differ among countries and regions of SSA. Respondents comprised experts and practitioners in livestock production and genetic resources from research institutes, animal breeding companies, universities, non-governmental organisations and government agricultural ministries. The main dairy farming system in which the respondents were involved was mixed crop-livestock system (30.2%), and this was mainly practised in the private land tenure system (46.3%). Data were analysed using linear model and paired Student t test in R software package. Respondents identified key issues affecting dairy production as poor genetic assessment of imported exotic breeds and crosses in Africa (62.3%), fluctuations in milk prices within both the formal and informal markets (50.9%), no comprehensive sire ranking systems (39.6%), housing and health management regimes which adversely affect milk yield (32.1%), poor market networks for dairy products (25.5%), poor feeding (13.3%), inadequate genetic technologies (9.4%) and poor animal performance recording systems (9.4%). Respondents emphasised the need for updated breeding policies, sire ranking systems, adequate farm management systems, capacity building, across-country collaborations and joint genetic assessments of dairy breeds found in sub-Saharan Africa. The current situation of dairy production though similar for the different countries, differed in order of emphasis and magnitude across the countries and regions in sub-Saharan Africa.

Comparative performance of dairy cows in low-input smallholder and high-input production systems in South Africa.

The aim of this study was to benchmark the performance of dairy cows in the low-input smallholder system against their counterparts in the high-input system, in South Africa. Data comprised of cow performance records from the national dairy recording scheme. Performance measures included production (305-day yields of milk, fat, and protein), lactation length, somatic cell count (SCC), and reproductive traits, represented by age at first calving (AFC) and calving interval (CI). Least squares means of each trait were compared between the two systems, and lactation curves for production traits and SCC were plotted for each production system. Mean yields of milk, fat, and protein were significantly (P < 0.05) lower in the smallholder (4097 ± 165, 174 ± 5.1, and 141 ± 4.5 respectively) compared to the high-input system (6921 ± 141, 298 ± 4.7, and 245 ± 4.1 respectively). Mean lactation length was significantly (P < 0.05) shorter for the smallholder (308 ± 15.1) than the high-input system (346 ± 12.8). Log-transformed somatic cell count (SCS) was, however, significantly (P < 0.05) higher in the smallholder (2.41 ± 0.01) relative to the high-input system (2.27 ± 0.01). Cows in high-input herds showed typical lactation curves, in contrast to the flat and low peaking curves obtained for the smallholder system. Cows on smallholder herds had their first calving significantly (P < 0.05) older (30 ± 0.5) than those in the high-input system (27 ± 0.5). There was, however, no significant difference (P < 0.05) in CI between the two systems. These results highlight large room for improvement of dairy cow performance in the smallholder system and could assist in decision-making aimed at improving the productivity of the South African dairy industry.

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.

Estimation of genetic parameters for functional longevity in the South African Holstein cattle using a piecewise Weibull proportional hazards model.

Non-genetic factors influencing functional longevity and the heritability of the trait were estimated in South African Holsteins using a piecewise Weibull proportional hazards model. Data consisted of records of 161,222 of daughters of 2,051 sires calving between 1995 and 2013. The reference model included fixed time-independent age at first calving and time-dependent interactions involving lactation number, region, season and age of calving, within-herd class of milk production, fat and protein content, class of annual variation in herd size and the random herd-year effect. Random sire and maternal grandsire effects were added to the model to estimate genetic parameters. The within-lactation Weibull baseline hazards were assumed to change at 0, 270, 380 days and at drying date. Within-herd milk production class had the largest contribution to the relative risk of culling. Relative culling risk increased with lower protein and fat per cent production classes and late age at first calving. Cows in large shrinking herds also had high relative risk of culling. The estimate of the sire genetic variance was 0.0472 ± 0.0017 giving a theoretical heritability estimate of 0.11 in the complete absence of censoring. Genetic trends indicated an overall decrease in functional longevity of 0.014 standard deviation from 1995 to 2007. There are opportunities for including the trait in the breeding objective for South African Holstein cattle.

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.

An analysis of the genetic relationship between udder health and udder conformation traits in South African Jersey cows.

A multi-trait animal model was used to estimate genetic parameters among lactation somatic cell score (SCS) and udder-type traits in South African Jersey cattle, through restricted maximum likelihood (REML) procedures. Data comprised records on 18 321 Jersey cows in 470 herds, collected through the National Milk Recording Scheme from 1996 to 2002. Average SCS in the first three lactations (SCS1, SCS2 and SCS3) were considered as different traits and the udder-type traits were fore udder attachment (FUA), rear udder height (RUH), rear udder width (RUW), udder cleft (UC), udder depth (UD), fore teat placement (FTP), rear teat placement (RTP) and fore teat length (FTL). Heritability estimates for the respective lactation SCS were 0.07 ± 0.01, 0.11 ± 0.01 and 0.11 ± 0.02. Udder-type traits had heritability estimates ranging from 0.14 ± 0.01 for UD to 0.30 ± 0.02 for FTL. Genetic correlations between SCS and udder-type traits ranged from -0.003 ± 0.07 between FUA and SCS3 to -0.50 ± 0.07 between UD and SCS3. Slow genetic progress is expected when selection is applied independently on SCS and udder-type traits, due to the generally low heritabilities. Tightly attached shallow udders with narrowly placed rear teats are associated with low SCS in the Jersey population.

Estimation of genetic parameters and variance components for growth traits of Nguni cattle in Limpopo Province, South Africa.

Estimates of (co)variance and genetic parameters of birth, weaning (205 days) and yearling (365 days) weight were obtained using single-trait animal models. The data were analysed by restricted maximum likelihood, fitting an animal model that included direct and maternal genetic and permanent environmental effects. The data included records collected between 1976 and 2001. The pedigree information extended as far back as early 1960s. The heritabilities for direct effects of birth, weaning and yearling weights were 0.36, 0.29 and 0.25, respectively. Heritability estimates for maternal effects were 0.13, 0.16 and 0.15 for birth, weaning and yearling weights, respectively. The correlations between direct and maternal additive genetic effects were negative for all traits analysed. The results indicate that both direct and maternal effects should be included in a selection programme for all the traits analysed.

Relationships between longevity and linear type traits in Holstein cattle population of Southern Africa.

Relationships between longevity and linear type traits were estimated using data on 34,201 cows with lifetime information and linear type scores. The longevity trait considered was the number of lactations initiated and the linear type traits were rump height, body depth, angularity, rear udder height, fore udder attachment, udder depth, fore teat placement and fore teat length. Fixed effects included in the models were herd year, season of calving and herd-date of classification-classifier and days in milk. Age at first calving and age at classification were included as linear and quadratic covariates. Heritability estimates were low for longevity and moderate for most type traits except rump height and fore teat length. All the phenotypic correlations between longevity and the linear type traits were slightly positive (0.01 to 0.09) except the relationships with rump height and fore teat length which were -0.01 and -0.02, respectively. Genetic correlations between longevity and udder traits as well as angularity were moderate to high and positive (0.22 to 0.48). The only notable negative genetic correlations were longevity with body depth and fore teat length (-0.15 and -0.07, respectively). The genetic correlations suggest that selection for udder traits and angularity should improve longevity in the Holstein cattle population.