Genetic and phenotypic diversity in Zulu sheep populations: Implications for exploitation and conservation

Dietary supplementing South African indigenous rams with flaxseed oil and ascorbic acid improves cryopreserved semen quality and in vitro fertility

The purpose of this study was to evaluate how ascorbic acid with dietary flaxseed oil affects the quality and fertility of cryopreserved ram sperm in South African indigenous rams. Treatment diets were supplemented 60 days before semen collection to afford proper spermatogenesis, adaptation to the feed formulated and fed throughout the study. Semen was collected with the use of artificial vagina following dietary supplementation with five treatment diets (neg. cont. - negative control, pos. cont. - positive control, FLO - 5% Flaxseed oil, ASA - 4% Ascorbic acid, and FLO + ASA). Semen was then extended using tris-based extender and cryopreserved using the programmable freezer (CBS Freezer 2100 series, Laboratory consumables & chemical suppliers, America). Ovaries were collected from a neighbouring slaughter house and conveyed to the lab in 0.9% saline at 37 °C. Data (sperm parameters and in vitro fertility) was then exposed to the GLM (General Linear Model) in Minitab 17. Pearson's correlation coefficient was utilized to investigate the relationship between cryopreserved sperm quality and in vitro fertility. The student Least Significant Difference Test was used to separate the treatment means, and differences were accepted when the p-value was less than 0.05. The FLO + ASA group had higher (p < 0.05) progressive (36.33 ± 1.87), total (88.24 ± 2.24), rapid motility (27.52 ± 1.74), intact plasma membrane (75.67 ± 2.08), total fertilization (65.98 ± 7.39), and total cleavage (66.19 ± 6.50) when compared to other treatment groups. Total fertilization rate had a medium significant (p < 0.001) medium correlation with the progressive motility (r2 = 0.435), total motility (r2 = 0.447) and rapid motility (r2 = 0.409). In conclusion, dietary flaxseed and ascorbic acid (FLO + ASA) improves cryopreserved semen quality, in vitro fertilization rate, and the total cleavage rate. Noteworthy, the progressive, total and rapid motility play a crucial in the in vitro fertilization rate.

A systematic review on the prospects of X- and Y-sexed semen in ruminant livestock: implications for conservation, a South African perspective

South Africa is home to numerous indigenous and locally developed sheep (Nguni Pedi, Zulu, and Namaqua Afrikaner, Afrino, Africander, Bezuidenhout Africander, Damara, Dorper, Döhne Merino, Meat Master, South African Merino, South African Mutton Merino, Van Rooy, and Dorper), goat (SA veld, Tankwa, Imbuzi, Bantu, Boer, and Savanna) and cattle (Afrigus, Afrikaner, Bolowana, Bonsmara, Bovelder, Drakensberger, South African Angus, South African Dairy Swiss, South African Friesland, South African Red, and Veld Master) animals. These breeds require less veterinary service, feed, management efforts, provide income to rural and or poor owners. However, most of them are under extinction risks and some with unknown status hence, require immediate conservation intervention. To allow faster genetic progress on the endangered animals, it is important to generate productive animals while reducing wastages and this can be achieved through sex-sorted semen. Therefore, this systematic review is aimed to evaluate the prospects of X and Y-sexed semen in ruminant livestock and some solutions that can be used to address poor sex-sorted semen and its fertility. This review was incorporated through gathering and assessing relevant articles and through the data from the DAD-IS database. The keywords that were used to search articles online were pre-gender selection, indigenous ecotypes, fertility, flow cytometry, artificial insemination, conservation, and improving sexed semen. Following a careful review of all articles, PRISMA guidelines were used to find the articles that are suitable to address the aim of this review. Sex-sorted semen is a recently introduced technology gaining more attention from researchers particularly, in the conservation programs. Preselection of semen based on the sex chromosomes (X- and or Y-bearing chromosomes) is of paramount importance to obtain desired sex of the offspring and avoid animal wastage as much as possible. However, diverse factors can affect quality of semen of different animal species especially after sex-sorting. Flow cytometry is a common method used to select male and female sperm cells and discard dead and abnormal sperm cells during the process. Thus, sperm sexing is a good advanced reproductive technology (ART) however, it is associated with the production of oxidative stress (OS) and DNA fragmentation (SDF). These findings, therefore, necessitates more innovation studies to come up with a sexing technology that will protect sperm cell injuries during sorting in frozen-thawed.

Whole-Genome SNP Characterisation Provides Insight for Sustainable Use of Local South African Livestock Populations

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.

Application of linear body measurements for predicting live weight in Ouled Djellal breed

The objective of this study was to predict the body weight of 66 females and 15 males Ouled Djellal breed aged over 2 years using fourteen simple linear body measurements and CREVAT formula. The total body length (TBDL), body length (BDL), scapular-ischial length (SIL), withers height (WH), heart girth (HG), chest depth (CD), paunch girth (PG), shoulder width (SW), hip-width (HW), trochanter width (TW), ischia width (IW), pelvis length (PL), cannon length (CL) and cannon perimeter (CP) were measured in centimeters, and body weight (BW) was determined in kilogram using a weighing scale. Results of the correlation coefficient showed that heart girth and the withers height were highly correlated with body weight (r = 0.93 and r =0.91 respectively), with variations by sex. Results of the stepwise regression showed that heart girth (HG), withers height (WH), scapular-ischiallength (SIL) and thecannon perimeter (CP) are the best prediction parameters of body weight in animals studied. From the CREVAT formula, the body weight was estimated by the HG (in meters): BW = 57.9 HG3. According to the different statistical methods used and the formula of CREVAT, we can conclude that body weight in Ouled Djellal breed can be estimated using simple linear body measurement of heart girth.

Genetic structure of South African Nguni (Zulu) sheep populations reveals admixture with exotic breeds

The population of Zulu sheep is reported to have declined by 7.4% between 2007 and 2011 due to crossbreeding. There is insufficient information on the genetic diversity of the Zulu sheep populations in the different area of KwaZulu Natal where they are reared. The study investigated genetic variation and genetic structure within and among eight Zulu sheep populations using 26 microsatellite markers. In addition, Damara, Dorper and South African Merino breeds were included to assess the genetic relationship between these breeds and the Zulu sheep. The results showed that there is considerable genetic diversity among the Zulu sheep populations (expected heterozygosity ranging from 0.57 to 0.69) and the level of inbreeding was not remarkable. The structure analysis results revealed that Makhathini Research Station and UNIZULU research station share common genetic structure, while three populations (Nongoma, Ulundi and Nquthu) had some admixture with the exotic Dorper breed. Thus, there is a need for sustainable breeding and conservation programmes to control the gene flow, in order to stop possible genetic dilution of the Zulu sheep.

Differences in tick infestation of Tunisian sheep breeds

Different infestation patterns by ixodid ticks were studied in three sheep breeds in Tunisia: Barbarine, Queue Fine de l'Ouest and their cross-bred animals. During one year, 700 sheep were monitored and examined for tick infestation. A total of 722 ticks were collected from sheep ears. The most frequent tick species was by far Rhipicephalus sanguineus sensu lato (99%) and there were few specimens of Rhipicephalus bursa (1%) (p < 0.001). Overall infestation prevalence was estimated at 10.4%. The lowest infestation prevalence was in Barbarine sheep (7.3%), followed by Queue Fine de l'Ouest (16.7%) and the highest prevalence was in cross-bred sheep (19.1%) (p < 0.001). Mean overall infestation intensity was 1.6 ticks/sheep: lowest in Barbarine (1.4), followed by Queue Fine de l'Ouest (1.7) and cross-bred sheep (1.8). Similarly, abundance was lowest in Barbarine sheep (0.1), and was 0.3 in Queue Fine de l'Ouest and cross-bred animals. The results demonstrated a reduced infestation, possibly due to reduced attractiveness and/or increased resistance to tick infestation, of the Barbarine breed compared with the other two breeds. Further behavioural, genetic and molecular studies are needed to explain the mechanisms for the lower infestation indicators.

Genetic and phenotypic variation among four Nguni sheep breeds using random amplified polymorphic DNA (RAPD) and morphological features

This study was conducted to investigate phenotypic and genetic differentiation among the four Nguni sheep breeds. Sheep with two permanent incisors and above were sampled from areas, namely KwaZulu-Natal (Zulu sheep), Limpopo (Pedi sheep), Mozambique (Landim sheep) and Swaziland (Swazi sheep). The Dorper was used as an out-group. Eight morphometric variables were measured from each animal, and blood samples were collected (n = 50 per population) for genetic characterization. The mean body weights for sheep were 30.41 ± 0.41, 35.34 ± 0.43, 35.23 ± 0.43, 37.63 ± 0.42 and 52.84 ± 0.30 for Swazi, Zulu, Landim, Pedi and Dorper, respectively. Morphometric cluster analysis showed the Landim, Swazi and Zulu breeds in one cluster. The Pedi sheep were closer to the Dorper than to the other Nguni sheep. Random amplified polymorphic DNA (RAPD) technique was used to assess genetic variation. Eight primers were selected for analysis based on band pattern quality, reproducibility and the presence of distinctive bands. The Swazi sheep formed a cluster with Zulu sheep, and the Pedi formed a cluster with the Dorper. These results confirm indications by other researchers that Pedi sheep are genetically distant from Zulu and Swazi sheep breeds. This could indicate the possibility of cross breeding Zulu and Swazi sheep as a possible conservation strategy to control inbreeding. The mtDNA should be analyzed to trace the relationships between Pedi and the three Nguni sheep breeds through maternal lines.

Classification of four ovine breeds of southern peninsular zone of India: Morphometric study using classical discriminant function analysis

Six morphometric traits (height at withers, body length, chest girth, ear length, tail length and body weight) were analyzed to characterize from a breed point of view 1981 sheep from four ovine breeds (Bellary, Kenguri, Hassan and Mandya) of southern peninsular zone of India. Discriminant Function Analysis was used to distinguish between four breeds by morphometric traits. The population variability showed Kenguri ewes were the largest and heaviest followed by Bellary, Hassan and Mandya whereas Kenguri rams were followed by Bellary, Mandya and Hassan. Overall sexual dimorphism (m/f) was 1.13, with Kenguri males being 47% heavier than females. The coefficient of variation of all traits in four breeds ranged from 4.06% to 30.28%. The flocks and age effects showed a high heterogeneity among females of different flocks. Height at withers was most discriminating trait in separating the four sheep breeds. The Mahalanobis distance of the morphological traits between Kenguri and Mandya sheep was most while the least differentiation was observed between Kenguri and Bellary sheep. Nearest neighbour discriminant analysis showed that most Kenguri sheep were classified into their source population followed by Mandya. However, varied percentages of misclassification between different breeds were observed showing the level of genetic exchange that has taken place between the breeds overtime. UPGMA based dendrogram showed formation of two separate groups; Mandya and Hassan clustered together while Bellary and Kenguri formed other group.

Genetic diversity and population structure of the endangered Namaqua Afrikaner sheep

The Namaqua Afrikaner is an endangered sheep breed indigenous to South Africa, primarily used in smallholder farming systems. Genetic characterization is essential for the breed's conservation and utilization. In this study, a genetic characterization was performed on 144 Namaqua Afrikaner sheep kept at the Karakul Experimental Station (KES), Carnarvon Experimental Station (CES), and a private farm Welgeluk (WGK) using 22 microsatellite markers. The mean number of alleles observed was low (3.7 for KES, 3.9 for CES, and 4.2 for WGK). Expected heterozygosity values across loci ranged between 46 % for WGK, 48 % for KES, and 55 % for CES, indicating low to moderate genetic variation. The analysis of molecular variance revealed that 89.5 % of the genetic variation was due to differences within populations. The population structure confirmed the differentiation of three clusters with high relationships between the CES and WGK populations. In the population structure comparison with Pedi and South African Mutton Merino sheep, limited hybridization between the Namaqua Afrikaner sheep and both of these breeds was observed. The results of this study will serve as a reference for genetic management and conservation of Namaqua Afrikaner sheep.

Evaluation of confidence limit estimates of cluster analysis on molecular marker data

BACKGROUND

Diversity studies employ cluster analysis as a statistical tool, whereby relationships between individuals are shown in a dendrogram, mostly accompanied by bootstrap support for merging branches to indicate confidence limits. The objective of this study was to evaluate the reliability of the currently applied method of obtaining confidence limit estimates in cluster analysis and to propose an improved alternative bootstrap method.

RESULTS

It was illustrated via a simulation study that conventional bootstrap support for cluster analysis was affected by the sample size. The reliability of merging branches decreased with increasing number of individuals in the sample. Unlike the current bootstrap support for cluster analysis, the proposed method provides confidence intervals for the similarity coefficients between individuals. To facilitate the interpretation of similarity coefficients and confidence intervals, alternative graphical presentations are proposed for both 'similarity coefficients' and 'confidence interval range'.

CONCLUSION

The proposed bootstrap method is not affected by the number of individuals in the sample.

A review of some characteristics, socio-economic aspects and utilization of Zulu sheep: implications for conservation

Zulu sheep are Nguni sheep of Zululand and are adapted to the harsh conditions of KwaZulu-Natal. They are used by rural farmers for economic purposes. Their numbers are declining, indicating a potential extinction threat. Knowledge of their phenotypic and genotypic characteristics is essential for conservation planning. In this review, there is a focus on the utilization, socio-economic aspects, phenotypic and genotypic characteristics as well as a proposed breeding programme. A survey has shown that rural farmers in the areas of northern KwaZulu-Natal prefer to keep this breed for its adaptability, resistance to diseases and meat quality. Zulu sheep are small-framed multi-coloured animals. Mature males weigh up to 38 kg and females up to 32 kg. Based on four morphological traits and live weight, phenotypic diversity between three populations was estimated at 48%. A genetic diversity between these three populations was estimated at 22%. Live weight of Zulu sheep can be estimated using the heart girth and wither height measurements. Scrotum circumference of young rams (up to 22 months old) is reliable for estimating the live weight. Animals that were characterized in the studies were grazed extensively and no supplements were provided. There is therefore a potential of weight increase if these animals are reared in a semi-extensive environment. An open nucleus breeding scheme is thus recommended for a sustainable use and conservation of this breed. For more conclusive results, larger numbers of phenotypic and genetic characteristics, in larger numbers of Zulu sheep populations, should be investigated.

The Damara in the context of Southern Africa fat-tailed sheep breeds

Sheep production is one of the most important activities in animal production in tropical regions. Southern Africa (SA) fat-tailed sheep such as the Afrikaner, Namaqua Afrikaner, Nguni, Persian Black Head, Tswana, Pedi, Sabi, and particularly the Damara are important animal genetic resources very well adapted to their harsh home environments. In this review, autochthonous sheep genetic resources of SA are reviewed regarding history and productive performance. A special focus is made to the most internationalized of such breeds: the Damara. The following aspects are reviewed: history, standards, productive performance in SA, and importation to Australia. Finally, a reference is made to the influence of fat-tailed sheep formation of composite breeds such as the Dorper or the Meatmaster.