Genetic variations of Toll-like receptor 4 gene in exon 2 of South African Dorper sheep.

Objective: The study was conducted to identify the sequence variation of Toll-like receptor 4 (TLR4) in exon 2 of South African Dorper sheep. Materials and Methods: Blood samples were collected from fifty (n = 50) South African Dorper sheep aged between 3 and 4 years. The Deoxyribonucleic acid (DNA) was extracted, amplified, and sequenced for the TLR4 gene. DNA sequencing was used to identify the sequence variations of the TLR4 gene in South African Dorper sheep. Results: The results showed that one synonymous single nucleotide polymorphism (SNP) of the TLR4 gene in exon 2 position T2249C was identified. Two genotypes (TT and TC) were discovered from the identified SNP. The dominant genotype was TT (0.60) over TC (0.40), with the dominant allele T (0.80) over C (0.20). The results also indicated that the used population was in the Hady-Weinberg Equilibrium. Polymorphism genetic analysis findings suggest that the identified sequence variation of TLR4 in exon 2 of South African Dorper sheep was moderate polymorphism. Conclusion: TLR4 gene at exon 2 of South African Dorper sheep had the SNP (T>C) at position 2249 bp with two genotypes (TT and TC).

Combined transcriptome and metabolome analysis reveals breed-specific regulatory mechanisms in Dorper and Tan sheep.

BACKGROUND: Dorper and Tan sheep are renowned for their rapid growth and exceptional meat quality, respectively. Previous research has provided evidence of the impact of gut microbiota on breed characteristics. The precise correlation between the gastrointestinal tract and peripheral organs in each breed is still unclear. Investigating the metabolic network of the intestinal organ has the potential to improve animal growth performance and enhance economic benefits through the regulation of intestinal metabolites. RESULTS: In this study, we identified the growth advantage of Dorper sheep and the high fat content of Tan sheep. A transcriptome study of the brain, liver, skeletal muscle, and intestinal tissues of both breeds revealed 3,750 differentially expressed genes (DEGs). The genes PPARGC1A, LPL, and PHGDH were found to be highly expressed in Doper, resulting in the up-regulation of pathways related to lipid oxidation, glycerophospholipid metabolism, and amino acid anabolism. Tan sheep highly express the BSEP, LDLR, and ACHE genes, which up-regulate the pathways involved in bile transport and cholesterol homeostasis. Hindgut content analysis identified 200 differentially accumulated metabolites (DAMs). Purines, pyrimidines, bile acids, and fatty acid substances were more abundant in Dorper sheep. Based on combined gene and metabolite analyses, we have identified glycine, serine, and threonine metabolism, tryptophan metabolism, bile secretion, cholesterol metabolism, and neuroactive ligand-receptor interaction as key factors contributing to the differences among the breeds. CONCLUSIONS: This study indicates that different breeds of sheep exhibit unique breed characteristics through various physiological regulatory methods. Dorper sheep upregulate metabolic signals related to glycine, serine, and threonine, resulting in an increase in purine and pyrimidine substances. This, in turn, promotes the synthesis of amino acids and facilitates body development, resulting in a faster rate of weight gain. Tan sheep accelerate bile transport, reduce bile accumulation in the intestine, and upregulate cholesterol homeostasis signals in skeletal muscles. This promotes the accumulation of peripheral and intramuscular fat, resulting in improved meat quality. This work adopts a joint analysis method of multi-tissue transcriptome and gut metabolome, providing a successful case for analyzing the mechanisms underlying the formation of various traits.

Reproductive performance and productivity of local and Dorper x local crossbred ewes under community-based management system, Ethiopia.

This study evaluated the reproductive and productivity of local and Dorper crossbred ewes in a community-based management system. We analyzed data collected from 2013 to 2021, taking into account different factors such as dam-breed, location, type of birth, season, and year of lambing. Lambing was observed all year-round, but the majority (35%) occurred in September, October, and December. This suggests that pasture availability, which is influenced by climatic-factors, may play a role in the seasonality of lambing. Litter-size at birth and weaning did not show any significant difference. Age at first lambing varied between breeds (P < 0.001), while lambing-interval and annual reproductive rates were unaffected by dam-breed (P > 0.05). The annual number of lambing per year significantly varied based on location and lambing seasons (P < 0.001), with a higher frequency during the major rainy-season compared to the dry-season (1.58vs1.42), highlighting the influence of feed availability. Productivity indices of ewes were calculated. Location and season of lambing had a significant impact on annual ewe productivity, while the ewe genotype showed no significant influence on productivity indices, except for the weight of lambs produced per kilogram of metabolic weight (0.84vs0.72 lambs per kg ewe and year; P < 0.01: 2.02vs1.77 kg lamb per kg0.75 ewe and year), where local ewes outperformed Dorper crossbred ewes. The difference in annual-productivity indices between local and Dorper crossbred ewes was more evident when considering the postpartum weight, as the ewes exhibited higher postpartum weights. However, both ewe genotypes produced comparable lamb weights per year (20.91vs20.16 kg lamb weaned per ewe and year for local and Dorper crossbred ewes, respectively). In summary, under low-input conditions, Dorper crossbred ewes demonstrated comparable reproductive performances and productivity traits to local ewes. Nevertheless, breed and environmental factors identified in this study should be taken into account to enhance sheep productivity in both local and Dorper crossbred ewes.

Contribution of gut microbiomes and their metabolomes to the performance of Dorper and Tan sheep.

Background: Livestock is an excellent source of high nutritional value protein for humans; breeding livestock is focused on improving meat productivity and quality. Dorper sheep is a distinguished breed with an excellent growth performance, while Tan sheep is a Chinese local breed famous for its delicious meat. Several studies have demonstrated that the composition of gut microbiome and metabolome modulate host phenotype. Methods: In the present study, we performed 16S amplicon sequencing and metabolomic analyses of the rumen and hindgut microbiome of 8-month-old Dorper and Tan sheep, raised under identical feeding and management conditions, to explore the potential effects of gut microbiome and its metabolites on growth performance and meat quality. Results: Our study identified Lactobacillus, a marker genus in the rumen, to be significantly associated with the levels of fumaric acid, nicotinic acid, and 2-deoxyadenosine (P-value < 0.05). Statistical analysis showed that nicotinic acid was significantly negatively correlated with body weight (P-value < 0.01), while 2-deoxyadenosine was significantly positively correlated with fatty acids content (P-value < 0.05). There was a biologically significant negative correlation between Phascolarctobacterium and deoxycytidine levels in the hindgut. Deoxycytidine was significantly positively correlated with body weight, protein, and amino acid content. Differences in rumen fermentation patterns that are distinctive among breeds were identified. Tan sheep mainly used Lactobacillus and fumaric acid-mediated pyruvic acid for energy supply, while Dorper sheep utilize glycogenic amino acids. The difference of iron metabolism in the hindgut of Dorper sheep affects lipid production, while Phascolarctobacterium in Tan sheep is related to roughage tolerance. The accumulation of nucleosides promotes the growth performance of Dorper sheep. Conclusion: These findings provide insights into how the microbiome-metabolome-dependent mechanisms contribute to growth rate and fat contents in different breeds. This fundamental research is vital to identifying the dominant traits of breeds, improving growth rate and meat quality, and establishing principles for precision feeding.

Metabonomic identification of serum biomarkers related to heat stress tolerance of sheep.

Heat stress is considered as a limiting factor for sheep production; it is necessary to screen for sheep breeds with heat tolerance. This study was to compare the serum metabolomes of Hu sheep and Dorper sheep and identify potential biomarkers related to heat stress. The results revealed that the respiratory rate, heart rate, and rectal temperature of Dorper sheep were significantly higher than those of Hu sheep. Compared to Dorper sheep, the serum activities of total antioxidant capacity and glutathione peroxidase in Hu sheep were significantly higher, while the concentration of malondialdehyde was lower. Metabolomics analysis identified 107 differential serum metabolites. The pathways enriched from the altered serum metabolites between the two breeds were mainly involved in protein metabolism, carbohydrate metabolism, and lipid metabolism. The levels of antioxidant- and energy-related metabolites were higher in the serum of Hu sheep than that of Dorper sheep; however, the levels of lipid catabolism- and inflammation-related were higher in the serum of Dorper sheep. The results indicate that Hu sheep had better heat stress resistance capability than Dorper sheep. Moreover, high levels of metabolites in the serum of Hu sheep are potential biomarkers for heat stress tolerance, including l-methionine, s-adenosylmethionine, and nicotinuric acid.

Relationship between rumen microbial differences and traits among Hu sheep, Tan sheep, and Dorper sheep.

Rumen microbes play an important role in the growth and development of ruminants. Differences in variety will affect the rumen community structure. The three excellent sheep breeds were selected for this study (Hu sheep, Tan sheep, and Dorper sheep) have different uses and origins. The sheep were raised on the same diet to 180 d of age in a consistent environment. 16S rDNA V3 to V4 region sequencing was used to assess the rumen microbes of 180 individuals (60 per breed). There were differences in microbial diversity among different sheep breeds (P < 0.05). Principal coordinate analysis showed that the three varieties were separated, but also partially overlapped. Linear discriminant analysis effect size identified a total of 19 biomarkers in three breeds. Of these biomarkers, five in Hu sheep were significantly negatively correlated with average feed conversion rate (P < 0.05). Six biomarkers were identified in the rumen of Dorper sheep, among which Ruminococcus was significantly positively correlated with body weight at 80 d (P < 0.05). In Tan sheep, Rikenellaceae_RC9_gut_group was significantly positively correlated with meat fat, and significantly positively correlated with volatile fatty acids (VFAs), such as butyric acid and isobutyric acid (P < 0.05). The Rikenellaceae_RC9_gut_group may regulate Tan mutton fat deposition by affecting the concentration of VFAs. Functional prediction revealed enrichment differences of functional pathways among different sheep breeds were small. All were enriched in functions, such as fermentation and chemoheterotrophy. The results show that there are differences in the rumen microorganisms of the different sheep breeds, and that the microorganisms influence the host.

The rumen is the most important digestive organ of ruminants, and the rumen microflora plays an important role in the process of digestion. This study compared the differences in rumen microbes of different breeds of sheep, identified key biomarkers of each breed, and analyzed their correlation with important economic traits of sheep. The results showed that the biomarkers of various breeds were significantly correlated with key traits. Therefore, we believe that there is a link between sheep rumen microbes and the differential traits of different breeds of sheep. This provides a new idea for sheep trait improvement.

Genetic Basis of Dorper Sheep (Ovis aries) Revealed by Long-Read De Novo Genome Assembly.

Dorper sheep (Ovis aries) (DPS), developed in the 1930s by crossing Dorset Horn and Blackhead Persian sheep in South Africa, is a world-famous composite breed for mutton production. The genetic basis underlying this breed is yet to be elucidated. Here, we report the sequencing and assembly of a highly contiguous Dorper sheep genome via integration of Oxford Nanopore Technology (ONT) sequencing and Hi-C (chromatin conformation capture) approaches. The assembled genome was around 2.64 Gb with a contig N50 of 73.33 Mb and 140 contigs in total. More than 99.5% of the assembled sequences could be anchored to 27 chromosomes and they were annotated with 20,450 protein-coding genes. Allele-specific expression (ASE) genes of Dorper sheep were revealed through ASE analysis and they were involved in the immune system, lipid metabolism, and environmental adaptation. A total of 5,701 and 456 allelic sites were observed in the SNP and indels loci identified from relevant whole-genome resequencing data. These allelic SNP and INDEL sites were annotated in 1,002 and 294 genes, respectively. Moreover, we calculated the number of variant sites and related genes derived from the maternal and paternal ancestors, revealing the genetic basis of outstanding phenotypic performance of Dorper sheep. In conclusion, this study reports the first reference genome of Dorper sheep and reveals its genetic basis through ASE. This study also provides a pipeline for mining genetic information of composite breeds, which has an implication for future hybrid-breeding practices.

Meat Quality, Fatty Acid Content and NMR Metabolic Profile of Dorper Sheep Supplemented with Bypass Fats.

The supplementation of rumen bypass fat (RBF) has remained one of the preferred approaches used to decrease undesirable saturated fatty acids (FA) and increase beneficial unsaturated FA in the meat. This study was planned to evaluate the influences of rumen bypass fats on meat quality, fatty acid and metabolic profiles in male Dorper sheep (n = 36) with 24.66 ± 0.76 kg (mean ± standard error) initial body weight. Treatment comprised a basal diet (30:70 rice straw to concentrate) with no added RBF as a control (CON), basal diet with prilled fat (PF), basal diet with prilled fat plus lecithin (PFL) and basal diet with calcium soap of palm fatty acids (CaS). The findings revealed that cooking loss, drip loss and shear force in longissimus dorsi (LD) muscle were not affected by RBF supplementation, while meat pH was significantly higher in the CaS on aging day 1. However, the diet supplemented with prilled fat and lecithin modified the meat's fatty acid profile significantly by increasing unsaturated fatty acids and decreasing saturated fats. The relative quantification of the major differentiating metabolites found in LD muscle of sheep showed that total cholesterol, esterified cholesterol, choline, glycerophosphocholine and glycerophospholipids were significantly lower in CaS and PFL diets, while glycerol and sphingomyelin were significantly higher in CaS and PFL diets. Most of the metabolites in the liver did not show any significant difference. Based on our results, the supplementation of protected fats did not have a negative influence on meat quality and the meat from Dorper sheep fed prilled fat with lecithin contained more healthy fatty acids compared to other diets.

Effects of Supplementation of Rumen Protected Fats on Rumen Ecology and Digestibility of Nutrients in Sheep.

Rumen protected fats (RPF) are known to improve animal performance without affecting rumen metabolism in sheep. However, comparative effects of prilled fat, prilled fat with lecithin and calcium soap have not been fully studied. Hence this experiment was planned using 36 male Dorper sheep in a completely randomized design in four treatment groups. The diets included: Basal diet (70:30 concentrate to rice straw) with no added RPF as a control (CON), basal diet plus prilled fat (PF), basal diet plus prilled fat with lecithin (PFL) and basal diet plus calcium soap (CaS). The trial lasted 90 days following two weeks adaptation period. The body weights, average daily gain and gain to feed ratio were not affected by treatments. The intake and digestibilities of dry matter, organic matter, crude protein and neutral detergent fibre were not affected, while those for ether extract and crude fibre differed (p < 0.05). RPF had no effect on concentrations of ammonia nitrogen, total volatile fatty acids and total bacterial population. The concentrations of rumen total saturated fatty acids, unsaturated fatty acids, total n - 3, total n - 6, unsaturated fatty acids:saturated fatty acids and polyunsaturated fatty acids:saturated fatty acids differed (p < 0.05) among the treatments with RPF supplementation. Hence supplementation of different types of protected fats did not influence animal performance in Dorper sheep.

Effects of corn supplementation on the antioxidant activity, selected minerals, and gene expression of selenoprotein and metallothionein in serum, liver, and kidney of sheep-fed palm kernel cake: urea-treated rice straw diets.

This study aimed to determine influence of corn inclusion on glutathion peroxidase (GPx) activity, selected minerals concentration, and gene expression in sheep-fed palm kernel cake (PKC) and urea-treated rice straw. Twenty-seven of Dorper sheep were divided into three groups and fed a basal diet of (20% rice straw and 80% concentrate) with addition of ground corn at either 0% (T1), 5% (T2), or 10% (T3), respectively. After 120 days feeding trial, all animals were slaughtered and tissue samples of kidney, liver, and muscles were taken for enzyme and mineral analyses. The results showed that Cu concentration in the liver was lower treatment T3 compared to the control and T2. The serum activity of GPx was higher in T2 than in T3 at day 120 of experiment. Serum malondialdehyde (MDA) concentrations decreased at day 80 in sheep on T3, whereas MDA of liver increased linearly with increasing corn supplementation. The qRT-PCR analyses revealed significant up-regulation of ATP7A and MIa genes in T3, while hepatic Cu/Zn SOD, GPx1, and GPx4 mRNA showed a higher expression in lamb hepatocytes in T3 compared to those on T1. Present study results suggest that feeding PKC as basal diet can increase antioxidant activity, but cause liver dysfunction in sheep. Inclusion corn was found to regulate transcriptional levels of the GPx family and metallothionein genes. These genes may play a role in the antioxidant protection response and reduce incidence of toxicity associated with Cu.

Three slow skeletal muscle troponin genes in small-tailed Han sheep (Ovis aries): molecular cloning, characterization and expression analysis.

To explore the basic characteristics and expressing profile of the three slow skeletal muscle troponin genes TNNC1 (Troponin C type 1), TNNI1 (troponin I type 1) and TNNT1 (troponin T type 1). Three purebred Dorper sheep and another three purebred small-tailed Han sheep were selected. The sequence of the genes from the small-tailed Han sheep was cloned using rapid amplification of cDNA ends and reverse transcription-polymerase chain reaction; The characteristics of the predicted amino acids sequences were analyzed using bioinformatics analysis software; Gene expression analyses were performed using quantitative reverse transcription PCR. The full-length cDNA sequences of the genes were 707, 898, and 1001 bp, respectively, and were submitted to GenBank under accession numbers KR153938, KT218688 and KT218690. The three predicted proteins were predicted to be hydrophilic, non-secretory proteins and contain several phosphorylation sites. Multiple alignments and phylogenetic tree analyses showed that the predicted proteins were relatively conserved in mammals. The expression results of the three genes in eight tissues of Dorper and small-tailed Han sheep revealed that the three genes had a similar mRNA expression pattern, whereas distinct differences were observed among the eight tissues of the two sheep species. We cloned the full-length cDNA of the three genes, analyzed the amino acid sequences, and determined the expression levels of the genes. These results might play important roles in facilitating the future research of the three genes.