South Africa (SA) holds a unique position on the African continent with a rich diversity in terms of available livestock resources, vegetation, climatic regions and cultures. The livestock sector has ...been characterized by a dual system of a highly developed commercial sector using modern technology vs. a developing sector including emerging and smallholder farmers. Emerging farmers typically aim to join the commercial sector, but lag behind with regard to the use of modern genetic technologies, while smallholder farmers use traditional practices aimed at subsistence. Several factors influence potential application of genomics by the livestock industries, which include available research funding, socio-economic constraints and extension services. State funded Beef and Dairy genomic programs have been established with the aim of building reference populations for genomic selection with most of the potential beneficiaries in the well-developed commercial sector. The structure of the beef, dairy and small stock industries is fragmented and the outcomes of selection strategies are not perceived as an advantage by the processing industry or the consumer. The indigenous and local composites represent approximately 40% of the total beef and sheep populations and present valuable genetic resources. Genomic research has mostly provided insight on genetic biodiversity of these resources, with limited attention to novel phenotypes associated with adaptation or disease tolerance. Genetic improvement of livestock through genomic technology needs to address the role of adapted breeds in challenging environments, increasing reproductive and growth efficiency. National animal recording schemes contributed significantly to progress in the developed sector with regard to genetic evaluations and estimated breeding values (EBV) as a selection tool over the past three decades. The challenge remains on moving the focus to novel traits for increasing efficiency and addressing welfare and environmental issues. Genetic research programs are required that will be directed to bridge the gap between the elite breeders and the developing livestock sector. The aim of this review was to provide a perspective on the dichotomy in the South African livestock sector arguing that a realistic approach to the use of genomics in beef, dairy and small stock is required to ensure sustainable long term genetic progress.
The Angora goat populations in Argentina (AR), France (FR) and South Africa (SA) have been kept geographically and genetically distinct. Due to country-specific selection and breeding strategies, ...there is a need to characterize the populations on a genetic level. In this study we analysed genetic variability of Angora goats from three distinct geographical regions using the standardized 50k Goat SNP Chip. A total of 104 goats (AR: 30; FR: 26; SA: 48) were genotyped. Heterozygosity values as well as inbreeding coefficients across all autosomes per population were calculated. Diversity, as measured by expected heterozygosity (HE) ranged from 0.371 in the SA population to 0.397 in the AR population. The SA goats were the only population with a positive average inbreeding coefficient value of 0.009. After merging the three datasets, standard QC and LD-pruning, 15 105 SNPs remained for further analyses. Principal component and clustering analyses were used to visualize individual relationships within and between populations. All SA Angora goats were separated from the others and formed a well-defined, unique cluster, while outliers were identified in the FR and AR breeds. Apparent admixture between the AR and FR populations was observed, while both these populations showed signs of having some common ancestry with the SA goats. LD averaged over adjacent loci within the three populations per chromosome were calculated. The highest LD values estimated across populations were observed in the shorter intervals across populations. The Ne for the Angora breed was estimated to be 149 animals ten generations ago indicating a declining trend. Results confirmed that geographic isolation and different selection strategies caused genetic distinctiveness between the populations.
Information on phenotypic and morphometric variation is important in the characterisation of indigenous cattle breeds. The objective of this study was to assess the morphological variation of the ...indigenous Angone, Landim, and Tete cattle breeds of Mozambique, kept under traditional management systems. These breeds are farmed mainly for meat and draught power, although they can produce some milk, especially the Landim. Data were collected through a survey of twenty-three villages in Maputo, Gaza, Inhambane (southern Mozambique), and Tete (central Mozambique) provinces. A total of 614 heads of adult animals including 140 Angone, 292 Landim, and 182 Tete were sampled. The collected qualitative and quantitative data were examined using SPSS version 16. The dominant coat pattern was even (no spotting) (59.5 %), with black being the most common coat colour (51.5 %), followed by light brown (26.5 %). The three breeds showed morphological differentiation based on size, body weight, and horn shape. Landim males and females were significantly (p<0.05) heavier than their Tete and Angone counterparts. Across breeds, the majority of cattle (95.2 %) had horns, and 66.9 % of these horns were curved. Individual assignment using discriminant function analysis revealed that 73.0 % of Landim, 77.4 % of Angone, and 59.9 % of Tete cattle were correctly assigned to their respective populations. Results from this study indicate a considerable phenotypic variation of Mozambican indigenous cattle and will assist in future improvement and conservation programs.
In the present work, the population diversity and structure of three populations of native Mozambican cattle were studied, to develop knowledge that is required for sound conservation and genetic ...improvement programs of these genetic resources. A total of 228 animals (Landim, Angone, and Tete) were genotyped using the International Dairy and Beef version three (IDBV3) SNP BeadChip array. Population parameters varied within a limited scope, with the average minor allele frequency (MAF) ranging from 0.228 ± 0.154 in the Angone to 0.245 ± 0.145 in the Tete population, while estimates of expected heterozygosities varied from 0.304 ± 0.166 in the Angone to 0.329 ± 0.148 in the Tete population. Low positive (0.065 ± 0.109) inbreeding rates were detected in the three cattle groups. Population structure and admixture analyses indicated low genetic differentiation and various degrees of admixture among the populations. The effective population size has decreased over time and at 12 generations ago ranged between 349 (Tete) and 929 (Landim). The average linkage disequilibrium (LD) of the studied populations ranged from 0.400 ± 0.213 (Tete) to 0.434 ± 0.232 (Landim). The findings of this study will be valuable for formulating management and conservation strategies for indigenous Mozambican cattle populations.
The erosion of genetic diversity limits long-term genetic gain and impedes the sustainability of livestock production. In the South African (SA) dairy industry, the major commercial dairy breeds have ...been applying estimated breeding values (EBVs) and/or have been participating in Multiple Across Country Evaluations (MACE). The transition to genomic estimated breeding values (GEBVs) in selection strategies requires monitoring of the genetic diversity and inbreeding of current genotyped animals, especially considering the comparatively small population sizes of global dairy breeds in SA. This study aimed to perform a homozygosity-based evaluation of the SA Ayrshire (AYR), Holstein (HST), and Jersey (JER) dairy cattle breeds. Three sources of information, namely 1) single nucleotide polymorphism (SNP) genotypes (3,199 animals genotyped for 35,572 SNPs) 2) pedigree records (7,885 AYR; 28,391 HST; 18,755 JER), and 3) identified runs of homozygosity (ROH) segments were used to quantify inbreeding related parameters. The lowest pedigree completeness was for the HST population reducing from a value of 0.990 to 0.186 for generation depths of one to six. Across all breeds, 46.7% of the detected ROH were between 4 megabase pairs (Mb) and 8 Mb in length. Two conserved homozygous haplotypes were identified in more than 70% of the JER population on
autosome (BTA) 7. The JER breed displayed the highest level of inbreeding across all inbreeding coefficients. The mean (± standard deviation) pedigree-based inbreeding coefficient (F
) ranged from 0.051 (±0.020) for AYR to 0.062 (±0.027) for JER, whereas SNP-based inbreeding coefficients (F
) ranged from 0.020 (HST) to 0.190 (JER) and ROH-based inbreeding coefficients, considering all ROH segment coverage (F
), ranged from 0.053 (AYR) to 0.085 (JER). Within-breed Spearman correlations between pedigree-based and genome-based estimates ranged from weak (AYR: 0.132 between FPED and F
calculated for ROH <4Mb in size) to moderate (HST: 0.584 between F
and F
). Correlations strengthened between F
and F
as the ROH length category was considered lengthened, suggesting a dependency on breed-specific pedigree depth. The genomic homozygosity-based parameters studied proved useful in investigating the current inbreeding status of reference populations genotyped to implement genomic selection in the three most prominent South African dairy cattle breeds.
Local cattle and sheep populations are important for animal production and food security in South Africa. These genetic resources are well adapted to the diverse climatic conditions and hold ...potential to be utilized in production systems subjected to climate change. The local beef breeds are well integrated into commercial livestock production systems with access to performance recording and genetic evaluations, while local sheep breeds are mainly utilised in smallholder and communal systems. The GeneSeek
®
Genomic Profiler™ Bovine 150 K SNP genotyping array was used to evaluate the diversity and inbreeding status of four indigenous (Boran, Drakensberger, Nguni, Tuli), two composite (Bonsmara and Beefmaster) and two exotic (SA Hereford and Charolais) beef breeds. The Illumina
®
Ovine 50 K SNP BeadChip was used to investigate five indigenous (Black Head Persian, Damara, Fat tail, Namaqua Afrikaner, Pedi) and three commercial (Dorper, Dohne Merino and SA Merino) populations. Although ascertainment bias was indicated by the low MAF (the autosome-wide proportion of SNPs with MAF< 0.05 ranged from 6.18 to 9.97% for cattle, and 7.59–13.81% for sheep), moderate genomic diversity was observed (mean H
o
ranged from 0.296 to 0.403 for cattle, and 0.327 to 0.367 for sheep). Slightly higher levels of ROH-based inbreeding were calculated for cattle (F
ROH
range: 0.018–0.104), than for sheep populations (F
ROH
range: 0.002–0.031). The abundance of short ROH fragments (mean proportion of <4 Mb fragments: 0.405 for cattle, and 0.794 for sheep) indicated ancient inbreeding in both species. The eight cattle populations were categorized into indicine, taurine or Sanga subspecies based on principal component, model-based clustering and phylogenetic analyses, with high levels of admixture observed within the Drakensberger, Nguni and Tuli breeds. Within the sheep populations, a clear distinction could be seen between the dual-purpose breeds, the meat breed and the indigenous breeds. Despite directional selection practiced in the cattle breeds, genomic diversity was moderate with low inbreeding. The non-commercialized, indigenous sheep populations are more vulnerable with small effective populations. These results emphasise the value of genomic information for effective management to exploit the potential contribution of local genetic cattle and sheep resources in a changing environment.
•Number of southern African goats increased over the last two decades.•Many non-descript, indigenous goat populations with moderate genetic diversity.•Genetic improvement in harsh environments mainly ...due to natural selection.•Lack of animal recording is a major limiting factor in breeding programs.•Genomic technology could benefit genetic improvement within a formal strategy.
Goats migrated to southern Africa approximately 500–600 years ago, and have since fulfilled a crucial role in both ceremonial and food security aspects of African cultures. The increasing numbers of goats in this region indicate that their relative importance has not diminished over time, and that they still contribute significantly to the world population. Southern Africa hosts a large number of poorly described indigenous meat goat populations, which largely lack both phenotypic and genetic characterization, as well as three well-described locally developed commercial breeds namely the Boer goat, Kalahari Red and Savanna breeds. Characterization studies on these populations indicated sufficient levels of genetic diversity to sustain genetic improvement. Within the challenging environment and production system where these goats survive, most genetic improvement has however occurred on an adaptive level through natural selection. A lack of well-formulated breeding objectives, animal recording and infrastructure further limited genetic improvement reported in this species. The role that genomic tools can play to attain future genetic progress will depend on national and regional selection strategies, as well as training and capacity building in the field of animal breeding and genetics.
Goat rearing is one of the most common livestock farming activities in Mozambique and has the potential to play a powerful role in improving the livelihoods of resource-poor farmers. This study was ...conducted to investigate the status of goat husbandry practices in rural areas of southern Mozambique. Data were collected from a total of 45 smallholder goat keepers in three different villages through questionnaires complemented by interviews. Most households were dependent on crop production and livestock as their main source of income. Goats were reared under extensive systems where free grazing and tethering were the common feeding management practices with limited supplementation during the dry season. The flock sizes per household were predominantly small (13 ± 2.4) with uncontrolled breeding of goats. The goats were reared mainly as a source of meat for home consumption and a means of reserve cash income. All household members were involved in goat production but women and children had a minor role in terms of decision making. The main constrains limiting goat production were diseases, lack of veterinary services, limited size of grazing land and scarcity of feed resources. Intervention programs focused on improving the husbandry practices and veterinary assistance should be initiated to improve goat production and thereby improve the income and livelihood of the resource-poor farmers in Mozambique. This paper presents a summary of the results of a baseline study in the Namaacha and Moamba districts of Mozambique.
•LiGAPS-Beef model was used to simulate growth of pasture-based beef cattle in South Africa.•Simulated growth deviated 23%, or 0.078 kg per day from measured growth.•The model identified factors that ...define and limit growth of beef cattle over time.•Accurate estimates of metabolizable energy in feed are key when using Ligaps-Beef.•The model can be used to develop resilience strategies for South African beef farms.
Quantifying the performance of beef cattle in diverse agro-ecological regions with different climatic conditions could be used by stakeholders to develop region-specific resilience strategies and optimize livestock production systems. This study evaluated the ability of the mechanistic LiGAPS-Beef model as a tool to quantify beef production of selected cattle breed types in diverse agro-ecological regions in South Africa. The average daily gain (ADG) was simulated for Bos taurus, composite and Sanga breed types in three different agro-ecological regions i.e. Bloemfontein (semi-arid), Phalaborwa (semi-desert) and Buffalo Berlin (temperate oceanic). Simulated ADGs were compared to measured ADGs from eight experiments for calibration and validation. After calibration, the model simulated ADG of breed types with a mean absolute percentage error (MAPE) of 23%. Simulated and measured values were positively correlated (r = 0.88) and largely in agreement (index of agreement=0.92). Factors that define and limit growth, such as the genotype, heat stress, cold stress, and digestion capacity limitation, were identified. Consistent with literature, the model showed more heat stress on Bos taurus breed types than on composite and Sanga breed types in Phalaborwa, which was the warmest region included in the study. Sensitivity analysis by changing input parameters by ± 10% showed that the model was more sensitive to changes in metabolizable energy (ME) than crude protein (CP) implying that the accuracy of ME must be prioritised. Overall, the results showed that model performance was adequate and thus the LiGAPS-Beef model can be used to explore the effects of climate change and adaptive breeding strategies in future studies in South Africa.
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