Routine hoof-trimming data provides insight into the occurrence of claw lesions in Holstein herds in the central region of South Africa.

Claw lesions in dairy cows contribute significantly to lameness, causing distress and discomfort for affected cows and raising welfare concerns. Despite increased awareness, lameness incidence continues to rise. Defining and recording claw traits are particularly problematic. In South Africa (SA), claw data is limited to paper-based records kept by private hoof trimmers. This research analysed claw-trimming data from five dairy farms over 6 years to examine the occurrence and recording of claw lesions in SA Holstein cattle. Lesion identification followed the Claw Lesion Identification in Dairy Cattle brochure. Among the recorded lesions, digital dermatitis (DD) had the highest prevalence (64.02%), followed by sole ulcers (SU; 8.59%), white line disease (WLD; 6.27%), and sole haemorrhage (SH; 4.28%), and most lesions occurred in the rear feet. Chi-square tests and correspondence analysis (CA) were employed to explore the relationships between lesions, feet, and housing. Results indicated that the prevalence of SU and SH showed high similarity for foot and lesion association, and that these were more highly associated with the rear feet. Additionally, the prevalence of DD and interdigital phlegmon were strongly associated, and closely associated with SU, and all these lesions were associated with both dirt lot and free-stall housing systems. CA further confirmed a close association between WLD and SH, and the prevalence of these lesions in the combination housing system. Results of this study highlight the complexity of lesion data and that specific associations between lesions could lead to simplifying the recording thereof. Consolidating the most informative claw lesions into categories will aid in the practical prevention, management, and treatment of lameness on-farm.

Exploring the effect of auditory stimuli on activity levels, milk yield and faecal glucocorticoid metabolite concentrations in Holstein cows.

Health and welfare are inextricably linked within efficient and sustainable dairy production, and several potential risk factors may affect the well-being of dairy cows, including chronic stress. Although auditory stimuli could be used as a tool to decrease the potential stress that cows might experience, it is seldom applied to livestock production systems due to the perception that enrichment is an unnecessary expense. This study aimed to explore the effect of auditory stimuli as a form of enrichment in a Holstein herd by monitoring fecal glucocorticoid metabolite (fGCM) concentrations (a non-invasive, stress-associated biomarker). Cow activity level and milk yield were also measured. Nine cows in their second and third lactation were divided into 3 groups, using a Latin Square experimental design, exposing each cow group to each of the 3 treatments, namely constant exposure (CE), limited exposure (LE), and no exposure (NE) to classical music. FGCMs were quantified using a group-specific enzyme immunoassay detecting 11,17-dioxoandrostanes. Compared to LE and NE animals, cows exposed to constant music had significantly lower fGCM concentrations (P = 0.012), as well as higher milk yields (P < 0.0001) and lowered activity levels during the morning (P = 0.005) and the evening activity period (P = 0.048). These findings indicate that auditory stimuli in the form of classical music may have a positive effect on the welfare of cows as well as milk yield, which hold economic benefits for the producer and potentially reduces the number of cows needed for profitable production.

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.

Moving towards sustainable breeding objectives and cow welfare in dairy production: a South African perspective.

Genetic advancements have resulted in improved dairy production over many decades, due to the focus of breeding objectives on production as the driving force for genetic progress and overall farm profitability. Major advancements were made in the easy-to-measure traits with moderate to high heritability, which resulted in unintended consequences on herd fertility, health, and welfare of cows. In addition, climate change and animal welfare concerns demanded balanced breeding objectives and selection approaches for sustainable production-including health and longevity. The inclusion of genomic information into genetic evaluations has been proved to benefit traits associated with welfare and sustainable production. Cow welfare traits remain complex and suitable phenotypes are not always easy to measure or readily available for genetic evaluations. The challenge for improvement of cow welfare often lies within implementation of sensitive and measurable parameters. The aim of this review was to explore the reconsideration of breeding objectives in the dairy industry towards sustainable dairy production and cow welfare with reference to selection of dairy animals in South Africa.

Population structure of indigenous southern African goats based on the Illumina Goat50K SNP panel.

In this study, the genetic structure of indigenous Tswana and Swazi goats using the Illumina Goat50K SNP array was investigated. Two South African commercial goat breeds were included to investigate admixture with the indigenous populations in southern Africa. A total of 144 DNA samples including Boer goats (n = 24), Kalahari Red (n = 24), Swazi (n = 48), and Tswana goats (n = 48) were genotyped. Statistical analysis was performed using PLINK version 1.07. Genetic diversity, measured as expected heterozygosity, was estimated at 0.390, 0.398, 0.413, and 0.387 for Boer, Kalahari Red, Tswana, and Swazi goats, respectively. The individual inbreeding coefficient varied from 0.019 ± 0.05 to 0.011 ± 0.06 for the Tswana and Swazi goats, respectively. The Principal component analysis clustered the populations according to geographical origin and breed type. Linkage disequilibrium (LD) for shorter intervals (0-10 kb) ranged from 0.44 to 0.56 and commercial breeds had higher values. Effective population sizes decreased with generations and at the 13th generation ranged between 87 for Boer to 266 for Tswana goats. The Tswana population exhibited the highest level of genetic variation and effective population size, which holds potential for improved production in marginal regions. A national strategy is required to maintain genetic diversity in communal goat production systems through well-structured breeding and conservation programs.

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.

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.

A survey analysis of indigenous goat production in communal farming systems of Botswana.

A total of 153 communal farmers in four agro-ecological regions of Botswana were interviewed using a structured questionnaire. The aims of the survey were to characterise existing communal goat production systems, evaluate the importance of goats to farmers and identify breeding practices and constraints encountered in goat production in Botswana. Data was collected on socio-economic parameters, general and breeding management practices and major constraints limiting goat production in Botswana. All respondents were small-scale communal farmers with 63% respondents practising mixed crop-livestock farming and 37% keeping livestock as their primary activity. The majority (33%) of respondents were older than 60 years. Over 80% of the farmers kept goats for cash required for tuition, school uniforms and household commodities as well as re-stocking of animals. Most farmers (62%) kept indigenous crossed genotypes. Generally, uncontrolled mating was practised with the majority of farmers (41%) using on-farm reared bucks for more than two years of breeding and communal bucks (36%) as an alternative. The major constraints limiting goat productivity in communal areas included uncontrolled breeding, predators, theft and diseases. Issues raised by farmers should be considered in designing and implementing effective breeding programs for goats to improve their overall productivity and contribution to poverty alleviation in these communities.

Polyceraty (multi-horns) in Damara sheep maps to ovine chromosome 2.

Polyceraty (presence of multiple horns) is rare in modern day ungulates. Although not found in wild sheep, polyceraty does occur in a small number of domestic sheep breeds covering a wide geographical region. Damara are fat-tailed hair sheep, from the south-western region of Africa, which display polyceraty, with horn number ranging from zero to four. We conducted a genome-wide association study for horn number with 43 Damara genotyped with 606 006 SNP markers. The analysis revealed a region with multiple significant SNPs on ovine chromosome 2, in a location different from the mutation for polled in sheep on chromosome 10. The causal mutation for polyceraty was not identified; however, the region associated with polyceraty spans nine HOXD genes, which are critical in embryonic development of appendages. Mutations in HOXD genes are implicated in polydactly phenotypes in mice and humans. There was no evidence for epistatic interactions contributing to polyceraty. This is the first report on the genetic mechanisms underlying polyceraty in the under-studied Damara.

Population genetic structure of Ascaridia galli of extensively raised chickens of South Africa.

Ascaridia galli is one of the most common nematode affecting chickens. This study characterized A. galli parasites collected from South African village chickens of Limpopo (n=18) and KwaZulu-Natal (n=22) provinces using the 510bp sequences of cytochrome C oxidase subunit 1 gene of the mitochondrial DNA. Fourteen and 12 polymorphic sites were observed for Limpopo and KwaZulu-Natal sequences, respectively. Six haplotypes were observed in total. Haplotype diversity was high and ranged from 0.749 for Limpopo province to 0.758 for KwaZulu-Natal province isolates. There was no genetic differentiation between A. galli from Limpopo and KwaZulu-Natal provinces. The six South African haplotypes were unique compared to those published in the GeneBank sampled from Hy-line chickens raised under organic farming in Denmark. The utility of cytochrome C oxidase subunit 1 gene as a potential genetic marker for studying A. galli in village chicken populations is presented.

Evaluation of biochemical parameters and genetic markers for association with meat tenderness in South African feedlot cattle.

A large proportion of South African feedlot cattle are crossbreds of Brahman (BrX, Bos indicus), and Simmental (SiX, Bos taurus). A sample of 20 grain fed bulls from each of these crossbreeds was used to compare meat quality with that of the small frame indigenous Nguni (NgX, Sanga) by evaluating a variety of biochemical and genetic parameters previously shown to be associated with meat tenderness. Shear force values were generally high (5.6kg average at 14days post mortem), with SiX animals higher than BrX or NgX (P=0.051) despite higher calpastatin:calpain ratio in BrX (P<0.05). Calpain activity and cold shortening were both correlated with tenderness for all classes. The sample size was too small to accurately estimate genotypic effects of previously published markers in the CAST and CAPN1 genes, but the allele frequencies suggest that only modest progress would be possible in these South African crossbreds using these markers.

Phenotypic variation of native chicken populations in northwest Ethiopia.

Seven indigenous chicken populations were identified and characterized from four administrative zones in northwest Ethiopia. A total of three hundred chickens were characterized under field conditions for qualitative and quantitative traits following standard chicken descriptors. Large phenotypic variability among chicken populations was observed for plumage color. About 25.49, 22.3, and 16.4 % of the chickens have white, grayish and red plumage colors, respectively. The rest showed a considerable heterogeneity like black, multicolor, black with white tips, red brownish and white with red striped plumage colors. The following characteristics were also displayed: plain head shape (51.18%), yellow shank color (64.42%) and pea comb (50.72%). About 97.52% of the chickens did not have feathers on their legs. Variations were also observed on quantitative characters such as shank length, egg size and body weight and other reproductive traits characterized on intensive management system.

Village-based indigenous chicken production system in north-west Ethiopia.

Surveys using both purposive and random sampling methods was carried out in four zones of north-west Ethiopia to describe the village-based poultry production systems and constraints in order to design future improvement and conservation strategies. The majority of the respondents were female (74.16%). This indicated that most of the time the women, whether in male-headed or female-headed households, are responsible for chicken rearing while the men are responsible for crop cultivation and other off-farm activities. About 99% of the respondents gave supplementary feeds to their chickens. Almost all farmers provided night shelter for their chickens, in part of the kitchen (1.36%), in the main house (39.07%), in hand-woven baskets (7.29%), in bamboo cages (1.51%) or in a separate shed purpose-made for chickens (50.77%). The major causes of death of chickens during the study were seasonal outbreaks of Newcastle disease (locally known as fengele) and predation. It is important to collect and conserve local poultry breeds before they are fully replaced by the so-called improved breeds. As most of the poultry production is managed by women, focusing on training and education of women will enable not only the improvement of poultry production but also family planning and the overall living standards of the family and the community.