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 relationship between weaning weight and milk yield in Nguni cattle.

A study was conducted to estimate the genetic relationship between weaning weight and milk yield in Nguni cattle. Milk yield data (n=125) were collected from 116 Nguni cows from Mara Research Station located in Limpopo Province and Loskop South Farm located in Mpumalanga Province using the weigh-suckle-weigh technique. Weaning weight data (n=19 065) were obtained from stud Nguni cattle from 146 herds distributed throughout South Africa. Estimates of (co)variance components for milk yield and weaning weight were calculated using PEST and VCE softwares. The average weaning weight, age of the calf at weaning and 24-h milk yield was 158.94 kg, 210 days and 5.25 kg/day, respectively. Heritability estimates for milk yield, direct and maternal weaning weight were 0.22±0.238, 0.47±0.039 and 0.25±0.029, respectively. Estimates of genetic correlations for milk yield and maternal weaning weight, milk yield and direct weaning weight, direct and maternal weaning weight were 0.97±0.063, -0.71±0.416 and -0.56±0.247, respectively. The results indicate that maternal weaning weight is genetically highly predictive of milk yield in Nguni cattle. Maternal breeding values for weaning weight could therefore be used as a selection criterion to improve milk yield in Nguni cattle.

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.

Genetic analysis of body weights of individually fed beef bulls in South Africa using random regression models.

The aim of this study was to estimate genetic parameters for body weights of individually fed beef bulls measured at centralized testing stations in South Africa using random regression models. Weekly body weights of Bonsmara bulls (N = 2919) tested between 1999 and 2003 were available for the analyses. The model included a fixed regression of the body weights on fourth-order orthogonal Legendre polynomials of the actual days on test (7, 14, 21, 28, 35, 42, 49, 56, 63, 70, 77, and 84) for starting age and contemporary group effects. Random regressions on fourth-order orthogonal Legendre polynomials of the actual days on test were included for additive genetic effects and additional uncorrelated random effects of the weaning-herd-year and the permanent environment of the animal. Residual effects were assumed to be independently distributed with heterogeneous variance for each test day. Variance ratios for additive genetic, permanent environment and weaning-herd-year for weekly body weights at different test days ranged from 0.26 to 0.29, 0.37 to 0.44 and 0.26 to 0.34, respectively. The weaning-herd-year was found to have a significant effect on the variation of body weights of bulls despite a 28-day adjustment period. Genetic correlations amongst body weights at different test days were high, ranging from 0.89 to 1.00. Heritability estimates were comparable to literature using multivariate models. Therefore, random regression model could be applied in the genetic evaluation of body weight of individually fed beef bulls in South Africa.

Diversity and origin of South African chickens.

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.

Genetic diversity and conservation of South African indigenous chicken populations.

In this study, we compare the level and distribution of genetic variation between South African conserved and village chicken populations using microsatellite markers. In addition, diversity in South African chickens was compared to that of a reference data set consisting of other African and purebred commercial lines. Three chicken populations Venda, Ovambo and Eastern Cape and four conserved flocks of the Venda, Ovambo, Naked Neck and Potchefstroom Koekoek from the Poultry Breeding Resource Unit of the Agricultural Research Council were genotyped at 29 autosomal microsatellite loci. All markers were polymorphic. Village chicken populations were more diverse than conservation flocks. structure software was used to cluster individuals to a predefined number of 2 ≤ K ≤ 6 clusters. The most probable clustering was found at K = 5 (95% identical runs). At this level of differentiation, the four conservation flocks separated as four independent clusters, while the three village chicken populations together formed another cluster. Thus, cluster analysis indicated a clear subdivision of each of the conservation flocks that were different from the three village chicken populations. The contribution of each South African chicken populations to the total diversity of the chickens studied was determined by calculating the optimal core set contributions based on Marker estimated kinship. Safe set analysis was carried out using bootstrapped kinship values calculated to relate the added genetic diversity of seven South African chicken populations to a set of reference populations consisting of other African and purebred commercial broiler and layer chickens. In both core set and the safe set analyses, village chicken populations scored slightly higher to the reference set compared to conservation flocks. Overall, the present study demonstrated that the conservation flocks of South African chickens displayed considerable genetic variability that is different from that of the assumed founder populations (village chickens).

POPREP: a generic report for population management.

Genetic variation provides a basis upon which populations can be genetically improved. Management of animal genetic resources in order to minimize loss of genetic diversity both within and across breeds has recently received attention at different levels, e.g., breed, national and international levels. A major need for sustainable improvement and conservation programs is accurate estimates of population parameters, such as rate of inbreeding and effective population size. A software system (POPREP) is presented that automatically generates a typeset report. Key parameters for population management, such as age structure, generation interval, variance in family size, rate of inbreeding, and effective population size form the core part of this report. The report includes a default text that describes definition, computation and meaning of the various parameters. The report is summarized in two pdf files, named Population Structure and Pedigree Analysis Reports. In addition, results (e.g., individual inbreeding coefficients, rate of inbreeding and effective population size) are stored in comma-separate-values files that are available for further processing. Pedigree data from eight livestock breeds from different species and countries were used to describe the potential of POPREP and to highlight areas for further research.

Effect of pre-weaning selection on estimates of genetic parameters and breeding values for post-weaning growth rate of beef bulls on test.

Data on South African Angus cattle consisting of 45 259 records on weaning weight (WWT), 4 360 records on average daily gain from on-farm test (ADG-D) and 1 118 from centralized test (ADG-C) were analyzed to evaluate the effect of pre-weaning selection on estimates of genetic parameters and subsequent estimated breeding values (EBV) for post-weaning average daily gain. (Co)variance components and genetic parameters for weaning weight (WWT), ADG-C and ADG-D were estimated by REML procedures fitting three different animal models. Model 1 was a univariate model of WWT, ADG-C or ADG-D and did not account for the effect of pre-weaning selection on post-weaning ADG. Model 2 was a two-trait model of WWT and either ADG-C or ADG-D. Model 3 was a multi-trait animal model including WWT, ADG-C and ADG-D. Estimates of heritability for ADG-C were 0.39 +/- 0.080, 0.42 +/- 0.060 and 0.44 +/- 0.010 from Model 1, 2 and 3 respectively. Corresponding estimates for ADG-D were 0.18 +/- 0.020, 0.19 +/- 0.020 and 0.21 +/- 0.020 respectively. Rank correlations based on EBVs for ADG-C for all bulls were 0.92, 0.83 and 0.94 for Model 1 vs. Model 2, Model 1 vs. Model 3, and Model 2 vs. Model 3, respectively and they indicated a possible re-ranking of bulls when including or excluding a correlated pre-weaning trait. Rank correlations for ADG-D also followed a similar trend. Inclusion of pre-weaning information in genetic analysis for post-weaning average daily gain is necessary to account for selection at weaning.

Genetic diversity in and conservation strategy considerations for Navajo Churro sheep.

The objectives of this study were to 1) evaluate the genetic diversity of Navajo-Churro sheep using pedigree information; 2) examine the distribution of the Navajo-Churro population; and 3) evaluate the effect of breeder dynamics on genetic conservation of the breed. Pedigree data and breeder information (city and state) were obtained from the Navajo-Churro Sheep Breed Association. Inbreeding coefficients were calculated for each individual animal using pedigree information. A geographic information system program was used to divide the United States into four regions and overlay breeder locations, flock size, and flock inbreeding level. The small correlation between level of inbreeding and flock size (r = -0.07, P = 0.07) indicated that inbreeding levels are not different across flock sizes. The mean flock inbreeding levels ranged from 0 to 11% across regions. The level of inbreeding did not differ among regions (P = 0.15), except for Region 4 (Kansas and Missouri; P = 0.001). The number of breeders registering sheep averaged 34 per year. Most of the breeders were transient, with only eight breeders maintaining ownership for more than 7 yr. Average inbreeding level for 2000 was found to be 1.2%, with a linear increase in inbreeding of 0.1%/yr over the period studied, suggesting a minimal loss of genetic diversity for the Navajo-Churro. However, given the relatively small effective population size (92) and the transient nature of the breeders, development of an ex situ cryo-preserved germplasm bank may be the best long-term strategy for maintaining this breed's genetic diversity.