Genetic diversity and population structure of Tibetan sheep breeds determined by whole genome resequencing

Prevalence and Molecular Characterization of Parasitic Lice in Tibetan Yaks, Pigs and Sheep

The infestation of ectoparasites poses a severe problem in animal breeding, severely affecting animal health and causing substantial economic losses. However, limited information is available regarding lice infestations in plateau livestock. To address this, we collected and examined lice samples from Tibetan yaks, pigs and sheep, amplifying the rrnS and cox1 genes for evolutionary analysis. The results revealed that the prevalence of lice was 51.3% (95% CI: 44.0-58.6%) in yaks, Tibetan sheep and Tibetan pigs, with regional prevalence ranging from 7.7% to 67.5%. Morphometric analysis showed that female lice were bigger than male lice. In Tibetan pigs, females exhibited a prominent longer body length (p < 0.05), belly length (p < 0.01) and body length to body width ratio (p < 0.05). In yaks, females had longer body length (p < 0.01) and body width (p < 0.05). For Tibetan sheep, female lice had larger body length (p < 0.001), body width (p < 0.001), head length (p < 0.05) and belly length (p < 0.05). Additionally, molecular identification revealed that lice infesting wild and domestic yaks were Linognathus vituli with 96.59-98.78% (wild yaks) and 96.33-98.71% (yaks) similarity to the OL677823.1 isolate. Lice infesting Tibetan sheep were identified as Linognathus africanus, showing 99.02-99.76% similarity to the OP948898.1 isolate. Lice from Tibetan pigs were identified as Haematopinus apri, with 96.38-98.31% similarity to the ON000922.1 isolate. Moreover, cox1 gene analysis of lice from Tibetan pigs showed 96.97-97.72% similarity to the KC814616.1 isolate. It is concluded that these findings could provide valuable insights into the prevention and control of lice-related diseases in plateau animals, enhancing animal health and mitigating economic losses.

Effect of different Lys/Met ratios in a low-protein diet on the meat quality of Tibetan sheep: A transcriptomics- and metabolomics-based analysis

This study integrated the the effects of dietary Lys/Met ratio in a low protein diet on the meat quality in Tibetan sheep. A total of 90 weaned Tibetan sheep, 2 months old with initial weight of 15.37 ± 0.92 kg were randomly divided into 3 treatments, which were supplemented with Lys/Met ratio at 3 (LP-H), 2 (LP-M), and 1 (LP-L) in the basal diet (10 % crude protein), respectively. After slaughter (150 days of age), the growth performances and meat quality of longissimus dorsi muscle were evaluated. The LP-L group showed significantly higher final body weight compared to the LP-M group (P < 0.05). Serum albumin and total protein levels were significantly higher in the LP-L group than in the LP-H group (P < 0.05). Furthermore, meat from the LP-L group had significantly higher protein, calcium, and vitamin E content compared to the LP-M group (P < 0.05). Transcriptomic analysis revealed 3,479 differentially expressed genes enriched in pathways related to muscle growth, energy metabolism, and signaling transduction. Metabolomic analysis identified 771 differential metabolites, significantly enriched in ABC transporters, beta-alanine metabolism, and taste transduction pathways. Integrated analysis highlighted the upregulation of the ABCD4 gene and L-valine metabolite in the LP-L group, contributing to improved phenotypic traits. These findings provide molecular insights into the regulatory mechanisms underlying the effects of dietary Lys/Met ratios on Tibetan sheep meat quality and offer a basis for developing nutritional strategies to enhance premium meat production.

Impact of Lysine to Methionine Ratios on Antioxidant Capacity and Immune Function in the Rumen of Tibetan Sheep: An RNA-Seq Analysis

With global protein prices on the rise, lowering protein levels in animal feed, together with balancing diet composition and reducing nitrogen emissions, can both reduce the environmental impact of agriculture and save on feed costs. However, the formulation of an ideal amino acid (AA) composition is crucial for better protein utilization by livestock. This study aimed to investigate the effects of different lysine to methionine ratios on the antioxidant capacity and immune function of the rumen in Tibetan sheep. Ninety male Tibetan sheep, weaned at 2 months of age, were randomly divided into three groups (1:1, 2:1 and 3:1 lysine ratios) and subjected to a 100-day feeding trial. RNA sequencing (RNA-seq) was utilized to analyse the impact of different AA ratios on gene expression in rumen tissue, whereas the levels of antioxidant enzymes (total antioxidant capacity [T-AOC], superoxide dismutase [SOD], glutathione peroxidase [GSH-Px] and catalase [CAT]) and immunoglobulins (immunoglobulin A [IgA], immunoglobulin G [IgG] and immunoglobulin M [IgM]) were evaluated. The results indicated that the 1:1 group significantly upregulated the expression of PTGS2, PLA2G12A and PLA2G4 genes, enhancing antioxidant enzyme activity, reducing free radical production and modulating systemic immune responses. COL16A1 and KCNK5 were highly expressed in the protein digestion and absorption pathway, maintaining the structural integrity and function of the rumen epithelium. BMP4 and TGFBR2 were significantly enriched in the cytokine-cytokine receptor interaction pathway and positively correlated with CAT and T-AOC. ITGA8 was upregulated in the 1:1 group, participating in the regulation of various cellular signalling pathways. ATP2B1 was enriched in the cyclic guanosine monophosphate (cGMP)- protein kinase G (PKG) signalling and mineral absorption pathways, primarily influencing oxidative stress and immune responses by regulating intracellular calcium ion concentration. This study demonstrates that a 1:1 lysine to methionine ratio is most beneficial for enhancing the antioxidant capacity and immune function of the rumen in Tibetan sheep.

Genetic diversity of United States Rambouillet, Katahdin and Dorper sheep

BACKGROUND

Managing genetic diversity is critically important for maintaining species fitness. Excessive homozygosity caused by the loss of genetic diversity can have detrimental effects on the reproduction and production performance of a breed. Analysis of genetic diversity can facilitate the identification of signatures of selection which may contribute to the specific characteristics regarding the health, production and physical appearance of a breed or population. In this study, breeds with well-characterized traits such as fine wool production (Rambouillet, N = 745), parasite resistance (Katahdin, N = 581) and environmental hardiness (Dorper, N = 265) were evaluated for inbreeding, effective population size (Ne), runs of homozygosity (ROH) and Wright's fixation index (FST) outlier approach to identify differential signatures of selection at 36,113 autosomal single nucleotide polymorphisms (SNPs).

RESULTS

Katahdin sheep had the largest current Ne at the most recent generation estimated with both the GONe and NeEstimator software. The most highly conserved ROH Island was identified in Rambouillet with a signature of selection on chromosome 6 containing 202 SNPs called in an ROH in 50 to 94% of the individuals. This region contained the DCAF16, LCORL and NCAPG genes that have been previously reported to be under selection and have biological roles related to milk production and growth traits. The outlier regions identified through the FST comparisons of Katahdin with Rambouillet and Dorper contained genes with known roles in milk production and mastitis resistance or susceptibility, and the FST comparisons of Rambouillet with Katahdin and Dorper identified genes related to wool growth, suggesting these traits have been under natural or artificial selection pressure in these populations. Genes involved in the cytokine-cytokine receptor interaction pathways were identified in all FST breed comparisons, which indicates the presence of allelic diversity between these breeds in genomic regions controlling cytokine signaling mechanisms.

CONCLUSIONS

In this paper, we describe signatures of selection within diverse and economically important U.S. sheep breeds. The genes contained within these signatures are proposed for further study to understand their relevance to biological traits and improve understanding of breed diversity.

Multiomics Analyses Provide New Insight into Genetic Variation of Reproductive Adaptability in Tibetan Sheep

Domestication and artificial selection during production-oriented breeding have greatly shaped the level of genomic variability in sheep. However, the genetic variation associated with increased reproduction remains elusive. Here, two groups of samples from consecutively monotocous and polytocous sheep were collected for genome-wide association, transcriptomic, proteomic, and metabolomic analyses to explore the genetic variation in fecundity in Tibetan sheep. Genome-wide association study revealed strong associations between BMPR1B (p.Q249R) and litter size, as well as between PAPPA and lambing interval; these findings were validated in 1,130 individuals. Furthermore, we constructed the first single-cell atlas of Tibetan sheep ovary tissues and identified a specific mural granulosa cell subtype with PAPPA-specific expression and differential expression of BMPR1B between the two groups. Bulk RNA-seq indicated that BMPR1B and PAPPA expressions were similar between the two groups of sheep. 3D protein structure prediction and coimmunoprecipitation analysis indicated that mutation and mutually exclusive exons of BMPR1B are the main mechanisms for prolific Tibetan sheep. We propose that PAPPA is a key gene for stimulating ovarian follicular growth and development, and steroidogenesis. Our work reveals the genetic variation in reproductive performance in Tibetan sheep, providing insights and valuable genetic resources for the discovery of genes and regulatory mechanisms that improve reproductive success.

Complete mitochondrial genomes reveal the phylogenetic relationships of Duoma with eight representative sheep breeds and two ovis species

The Ovis aries Duoma breed is one of the most important alpine grassland-type sheep breeds in China. In this current study, we first reported the complete mitochondrial genome of Duoma sheep. Mitochondrial genome is 16,618 bp in length and exhibits the same typical structure as the other published sheep breeds. The genome contains 37 genes (22 tRNA, two rRNA, and 13 protein-coding genes (PCGs)) and a control region (D-loop region). Phylogenetic analysis shows that the Duoma sheep breed is closer to Ganjia sheep. Our findings will help the further evolution and conservation studies of Duoma sheep.