Search Results (56)

The Wadi sheep (WAD) is a unique Chinese indigenous breed previously reported to show adaptation to humid and saline–alkali lowlands, disease resistance, high fecundity, and favorable meat quality. However, the recent widespread introduction of commercial sheep breeds has led to a sharp decline in the purebred WAD population, posing serious threats to the preservation of its unique genetic resources. Therefore, there is an urgent need to assess the current population structure and genetic diversity of WAD to support its conservation and sustainable utilization. In this study, we systematically analyzed genomic variation, population structure, and selection signatures using whole-genome resequencing data from 30 WAD sheep and 80 publicly available genomes representing five other breeds obtained from the NCBI database. Population genomic analyses revealed that WAD retains substantial genetic diversity and exhibits a distinct population structure, shaped by its unique breeding history. Selection signature analyses using F_ST, π ratio, and XP-EHH identified 457 candidate genes under positive selection, which are associated with key biological processes including environmental adaptation, immune defense, muscle traits, growth, and reproduction. These findings identify genomic regions potentially related to reported WAD traits and provide a theoretical basis for its conservation, molecular breeding, and sustainable utilization in lowland environments. Full article

Turpan Black (TBL) and Altay (ALT) sheep are indigenous breeds adapted to extreme heat and severe cold in their respective native environments. However, the mechanisms underlying their divergent meat quality remain unclear. Using longissimus dorsi muscle from 15 TBL and 15 ALT sheep, we integrated phenotypic evaluation with non-targeted metabolomics and proteomics to elucidate the impact of environmental adaptation on ovine meat quality. Compared to the cold-adapted ALT sheep, the heat-tolerant TBL sheep exhibited lower post-mortem pH, reduced cooking loss, smaller muscle fiber cross-sectional area, and elevated selenium and magnesium levels. Multi-omics identified 99 differentially expressed proteins and 364 differentially expressed metabolites. Core divergence was enriched in lipid and amino acid metabolism and stress response networks, particularly the Apelin signaling, glycerophospholipid metabolism, and ferroptosis pathways. Lipid remodeling driven by glycerophospholipid metabolism emerged as a critical bridge linking adaptation to meat quality. Notably, glycero-3-phosphocholine, regulated by GPCPD1 and related enzymes, maintained cell membrane homeostasis and osmotic pressure, thereby enhancing water-holding capacity and tenderness. These findings reveal the multi-omics basis of climate-driven divergence in ovine meat quality, offering theoretical support for breeding stress-resilient, high-quality indigenous sheep breeds in extreme environments. Full article

Duolang sheep, an indigenous breed of southern Xinjiang, are significant for their agricultural systems due to their adaptation to arid and semi-arid environments. This review integrates recent advancements in Duolang’s reproductive biology, genomic studies, and management strategies to address the breed’s reproductive efficiency under challenging ecological conditions. Reproductive traits such as puberty onset, estrous cycle characteristics, and seasonal breeding are influenced by complex genetic and several environmental factors. Numerous remarkable genomic findings highlight key loci related to fecundity, including the Booroola FecB mutation, as well as genes involved in steroidogenesis, folliculogenesis, and HPG axis regulation. Despite the genetic potential for increased prolificacy, Duolang sheep often exhibit low litter sizes, largely constrained by detrimental environmental factors and management practices. This review emphasizes the significance of integrating genetics, nutrition, and reproductive management to optimize productivity. Strategies such as nutritional flushing, hormone-based estrous synchronization, and selective breeding for increased litter size are discussed, with a focus on minimizing the risks associated with early puberty and lamb survival. Furthermore, the review explores the potential of genomic selection, marker-assisted breeding, and advanced reproductive technologies to enhance the breed’s performance. Finally, the review outlines future research directions, necessitating the development of genomic resources, precise breeding programs, and field trials on reproductive interventions to accelerate genetic gains in Duolang sheep. This integrated approach promises to improve reproductive outcomes, with implications for sustainable sheep production in Xinjiang and similar environments across the globe. Full article

Qilian sheep are an important indigenous Tibetan sheep breed adapted to cold and hypoxic environments. To explore hepatic nutrient metabolism in Qilian sheep, this study compared liver transcriptomic profiles between Qilian sheep and Oula sheep raised under similar natural grazing and management conditions. Six 10-month-old ewes from each breed were selected, and three high-quality liver RNA samples from each group were used for transcriptome sequencing. A total of 1640 differentially expressed genes were identified using the thresholds of |log2FoldChange| > 1 and false discovery rate < 0.05, including 922 upregulated and 718 downregulated genes in Qilian sheep compared with Oula sheep. KEGG enrichment analysis showed that these genes were mainly associated with lipid metabolism, amino acid metabolism, the PPAR signaling pathway, fatty acid biosynthesis, and fatty acid β-oxidation. qRT-PCR validation confirmed the differential expression of 11 candidate genes, including RGN, LPGAT1, BHMT2, SDS, GK, PC, MIOX, HMGCS2, PNPLA3, ACAA2, and HADHA. These results suggest that Qilian sheep and Oula sheep differ in hepatic gene expression patterns related to lipid utilization, amino acid metabolism, and energy regulation, providing candidate genes and pathways for understanding breed-associated hepatic metabolic characteristics. Full article

Indigenous sheep breeds represent valuable reservoirs of genetic diversity shaped by long-term adaptation to local environments and management systems. Greek autochthonous sheep breeds remain underrepresented in genomic and functional studies. The objective of this study was to characterize and compare coding sequence variation in three indigenous Greek sheep breeds—Lesvos (LES), Serres (SER), and Thrace (THR)—and to identify shared and breed-associated functional patterns. The study was designed using a two-stage approach, comprising a discovery (exploratory) phase and a validation phase. In the discovery phase, whole genome sequencing data (one animal per breed; total n = 3; mean sequencing depth ~36.9×) were analyzed to identify protein-altering exonic variants, focusing on missense single-nucleotide polymorphisms (SNPs) and exonic insertions/deletions (indels). Variants were examined at breed-specific and comparative levels, followed by functional enrichment analyses using Gene Ontology (GO) and KEGG pathways. Normalized variant density metrics identified genes with elevated polymorphism levels. In the validation phase, a subset of prioritized missense SNPs was genotyped in an independent cohort of 54 animals (18 per breed) using MassARRAY genotyping. Genes harboring prioritized missense SNPs showed a conserved enrichment profile across breeds, dominated by genome maintenance, DNA repair, cytoskeletal organization, and core regulatory functions. Distinct breed-associated patterns were also observed. LES showed enrichment in metabolic, biosynthetic, and sensory-related processes, SER in regulatory and signaling functions, and THR in cytoskeletal, extracellular matrix, and organelle-associated pathways. Polymorphism density analyses highlighted highly variable genes across breeds, including olfactory receptor (OR) gene families, keratin-associated protein genes (KRTAPs), and loci involved in immune and regulatory functions (e.g., PRKDC, CDH15). The validation phase confirmed the expected allele frequency patterns for most prioritized SNPs, supporting the robustness of the approach. This study identifies functionally relevant coding variation across Greek indigenous sheep breeds, revealing conserved genomic patterns and breed-associated signatures linked to metabolic, structural, and regulatory processes. Full article

The unique ecological gradients of Xinjiang have fostered a rich reservoir of genetic resources in local sheep populations. However, the population genetic structure, adaptive mechanisms to extreme environments, and the genetic basis underlying key economic traits of these breeds remain poorly understood. To address this gap, we performed whole-genome resequencing of 140 individuals from seven indigenous sheep populations—Altay, Bayinbuluke, Kazakh, Kirgiz, Bashibai, Turpan Black, and Yemule White—identifying 18,700,507 high-quality SNPs. Genetic diversity analyses revealed that all populations exhibited comparable levels of genetic diversity, with modest variation across breeds, with Turpan Black sheep exhibiting the highest observed heterozygosity (Ho = 0.3110) and proportion of polymorphic sites, whereas Kirgiz sheep showed comparatively lower values. Population structure analyses consistently indicated that geographic isolation is the primary driver of genetic differentiation, with Kirgiz sheep from the Pamir Plateau in southern Xinjiang displaying the greatest genetic distance relative to northern Xinjiang populations. By integrating multiple selection signature detection methods—including F_ST, π ratio, and XP-CLR—we found that genes under selection in Kirgiz sheep were significantly enriched in biological pathways related to stem cell pluripotency regulation (e.g., BMPR1B), DNA repair (e.g., DDB2), and neural development, thereby elucidating their unique genetic adaptations to high-altitude environments. In contrast, Turpan Black sheep appear to cope with heat stress through mechanisms involving basal transcriptional regulation (e.g., GTF2I), maintenance of protein homeostasis (e.g., DNAJB14), and melanin biosynthesis (e.g., MC1R). Furthermore, comparative analysis of body size identified a suite of candidate genes associated with growth and development (e.g., CUX1, KIT), which are primarily involved in transcriptional regulation, protein kinase activity, and the ubiquitin-mediated proteolytic system, thereby revealing a multi-layered genetic regulatory network governing body conformation. Collectively, this study provides a comprehensive genomic framework for understanding the genetic structure, adaptive evolution, and molecular basis of economically important traits in indigenous sheep breeds from Xinjiang, offering valuable candidate targets for future functional validation and precision breeding programs. Full article

Tibetan sheep, a unique breed indigenous to the Qinghai–Tibet Plateau, exhibit remarkable adaptations to high-altitude hypoxia, and their muscle quality is a key economic determinant. However, the molecular mechanisms by which exercise regulates meat quality in this breed remain poorly understood. This study aimed to systematically investigate the effects of different exercise volumes on the biceps femoris muscle of Tibetan sheep, integrating histological analysis with high-throughput transcriptome sequencing. We compared a low-exercise group with a high-exercise group and found that long-term endurance exercise resulted in phenotypic changes suggestive of a shift toward oxidative muscle fiber characteristics. This adaptation was characterized by significantly reduced muscle fiber diameter and cross-sectional area, alongside a crucial increase in intramuscular fat content, collectively enhancing meat tenderness, flavor, and juiciness. Transcriptomic analysis revealed extensive gene expression reprogramming, identifying 208 mRNAs and 490 lncRNAs that were differentially expressed and primarily associated with muscle fiber transition and energy metabolism. Furthermore, we constructed a putative lncRNA-miRNA-mRNA competing endogenous RNA network based on expression correlations and bioinformatic predictions, highlighting potential key regulatory axes such as LOC105603384/miR-16-z/MYLK3, LOC121820630/miR-381-y/NOX4, and LOC132659150/oar-miR-329a-3p/NF1. These findings provide a new perspective on the molecular basis of exercise-induced muscle adaptation in high-altitude animals and offer a solid theoretical framework for improving meat quality through scientific livestock management. Full article

Duolang sheep, a meat–fat dual-purpose breed indigenous to Xinjiang, China, has been cultivated traditionally by the local Uyghur people for its prolificacy and precocious sexual maturity, while little research on the population structure and trait inheritance characteristics of Duolang sheep is available. This study employed whole-genome resequencing data from a cohort of 60 Duolang sheep to dissect their genetic population structure and genes related to reproductive traits. A total of 1565 Gb of high-quality data with an average depth of 14.06× was generated. After SNP calling and quality control, 31,300,060 SNPs were identified. Following linkage disequilibrium (LD)-based pruning, a total of 4,479,177 high-quality SNPs were retained for subsequent analyses. Based on these SNPs, the internal genetic structure of the Duolang sheep population was elucidated, with 14 kinship outliers detected through principal component analysis (PCA). Furthermore, LD decay analysis revealed that the r² declined below 0.1 at approximately 10 kb, indicating a relatively low level of selection pressure in the population. Within the population, Tajima’s D and iHS methods detected 517,218 and 82,534 candidate SNPs under selection, respectively, with 24,453 SNPs overlapping between the two methods. By splitting Duolang sheep into single-lamb (n = 29) and multiple-lamb (n = 12) subgroups according to litter size, 267,654 SNPs were identified by XP-CLR, while 184,179 SNPs suffering from selection were detected by F_ST and 62,150 by XP-EHH. Functional enrichment analysis of selected genes reveals the selection directions (domestication, growth, and reproduction) and related candidate genes in the Duolang sheep population, including ESRRA, ESRRB, OXT, FSHR, ESR2, GNRHR, and BMPR1B. This study provides the first comprehensive genomic landscape of Duolang sheep, elucidating genetic signatures of its adaptive traits. Full article

To mitigate antimicrobial resistance and drug residues, the use of growth-promoting antibiotics in livestock has been prohibited, prompting interest in safe natural alternatives. Lanping black-boned sheep, an indigenous high-altitude breed in Yunnan, exhibit unique physiological traits but relatively low feed efficiency. This study evaluated the effects of three natural additives—guanidinoacetic acid (GAA, 1 g/sheep/day), Ampelopsis grossedentata flavonoids (AGF, 1 g/sheep/day), and 5,6-dimethylbenzimidazole plus cobalt (5,6-DMB + Co; 100 mg 5,6-DMB + 0.5 mg Co/sheep/day)—on serum biochemistry and rumen microbiota in twenty-four Lanping black-boned sheep fed under grazing conditions for 90 days following a 10-day adaptation period. GAA and 5,6-DMB + Co increased serum globulin (p < 0.05), whereas AGF reduced urea concentrations (p < 0.05). Only GAA decreased ruminal pH (p < 0.05). All additives enhanced microbial richness (p < 0.05), with 5,6-DMB + Co inducing the most pronounced community restructuring. Taxonomically, AGF and 5,6-DMB + Co decreased Firmicutes and enriched Verrucomicrobiota, while AGF uniquely increased Cyanobacteria. GAA selectively reduced Quinella, AGF decreased Christensenellaceae_R-7_group and NK4A214_group, and 5,6-DMB + Co markedly enriched Rikenellaceae_RC9_gut_group (p < 0.05). Microbial shifts were closely associated with biochemical indices, including positive associations of Prevotella with AST and Rikenellaceae_RC9_gut_group with total protein (p < 0.05). Overall, GAA mainly affected protein-related indices, AGF lowered serum urea, and 5,6-DMB + Co increased within-sample diversity with accompanying community reweighting, providing a theoretical basis for developing sustainable feeding strategies to enhance both productivity and health in Lanping black-boned sheep. Full article

Wool traits such as fiber diameter, fiber length, and greasy fleece yield are economically significant characteristics in sheep breeding programs. Traditional genome-wide association studies (GWAS) have identified relevant genomic regions but often fail to capture the non-linear and polygenic architecture underlying these traits. In this study, we implemented a two-stage machine learning (ML)-based GWAS framework to dissect the genetic basis of wool traits in Central Anatolian Merino sheep. Phenotypic records were collected from 228 animals, genotyped with the Illumina OvineSNP50 BeadChip. In the first stage, feature selection was conducted using LASSO, Ridge Regression, and Elastic Net, generating a consensus SNP panel per trait. In the second stage, association modeling with Random Forest and Support Vector Regression (SVR) identified the most predictive models (R² up to 0.86). Candidate gene annotation highlighted biologically relevant loci: MTHFD2L and EPGN (folate metabolism and keratinocyte proliferation) for fiber diameter; COL5A2, COL3A1, ITFG1, and ELMO1 (extracellular matrix integrity and actin remodeling) for staple length; and FAP, DPP4, PLCH1, and NPTX1 (extracellular matrix remodeling, proteolysis, and sebaceous gland function) for greasy fleece yield. These findings demonstrate the utility of ML-enhanced GWAS pipelines in identifying biologically meaningful markers and propose novel targets for genomic selection strategies to improve wool quality and yield in indigenous sheep populations. Full article

Muscle traits are critical determinants of meat quality and productivity in sheep, influenced by both breed and anatomical region. Hanzhong sheep, an indigenous Chinese breed, are prized for tender, low-odor meat; yet, the molecular mechanisms underlying these traits remain poorly understood. In this study, we integrated meat quality assessment with metabolomic and transcriptomic profiling of the longissimus dorsi (HZ-B) and triceps brachii (HZ-T) muscles to elucidate biochemical and molecular bases of regional differences. The results, derived from metabolomic profiling, demonstrated that the muscle tissue of Hanzhong sheep contained abundant proteins (95 kinds) and fatty acids (150 kinds). The greater tenderness of HZ-B compared to HZ-T was associated with higher levels of dipeptides such as carnosine (FC = 1.07) and anserine (FC = 1.04), as well as upregulated expression of oxidative fiber-related genes MYH2 (FC = 2.92) and TPM1 (FC = 2.15). In contrast, HZ-T showed enrichment of flavor-associated metabolites, including acylcarnitines and glutamate, alongside higher expression of FBXO32 (FC = 0.35) and MYBPC1 (FC = 0.47), linked to structural integrity and muscle contraction. Integrated analysis revealed strong associations between metabolite abundance (carnosine/anserine) and key genes (FBXO32/GADL1), suggesting coordinated regulation of meat quality traits. These findings provide mechanistic insights into the metabolic and transcriptomic determinants of muscle quality in Hanzhong sheep, offering a foundation for genetic improvement and conservation strategies. Full article

Dorper sheep (DOR) are a commercially important mutton breed renowned for their high growth rate, favorable carcass composition, environmental adaptability, and natural wool shedding. In China, they are widely utilized as terminal sires to enhance growth and carcass yield in local breeds. To elucidate the genetic basis of these traits, we sequenced the genomes of 20 DOR and integrated the data with whole-genome sequences from 73 individuals representing four Chinese indigenous breeds. Analyses of genetic diversity, inbreeding coefficients, and population structure revealed reduced genomic diversity, elevated inbreeding levels, and clear genetic separation for DOR from other indigenous breeds. Selective sweep scans using F_ST, pi, and XP-EHH identified candidate genes involved in five major trait categories: growth performance and development (COL2A1, DAB2IP, EPYC, TSPAN18, WNT1, CTPS1, FBXW7, INSR, S100A6, SOCS2), energy metabolism (ACSS3, ADGRE3, CPT2, GCGR, PRKAA1), fat deposition and adipocyte differentiation (EHBP1, FOXP1, KLF12, PDGFD, RALGAPA2), immune response (CXCR6, IL17RB, NFKBIZ, TMEM154), and wool traits (CERS4, MITF). These results will provide novel insights into the genomic architecture of economically important traits in DOR and support their genetic improvement through informed crossbreeding with Chinese local breeds. Full article

Climate change poses an increasing challenge to livestock production, making the identification of thermally resilient breeds crucial. This study investigated the expression patterns of eight thermal stress-related genes (HSP90AA1, HSPA8, HSPA1A, IL-6, IL-10, TNF-α, NOS-3, and SOD-2) in two strains of indigenous Pramenka sheep (Hercegovačka and Dubska) under different climatic conditions. Blood samples were collected from 96 sheep across four locations during summer and winter seasons. Gene expression was analyzed using RT-PCR and evaluated against comprehensive environmental data, including the temperature–humidity index (THI). Principal component analysis revealed distinct gene expression patterns between strains and seasons. The Hercegovačka strain showed consistently higher expression of HSP90AA1 compared to the Dubska strain in both seasons (summer: 5.81 vs. 2.47; winter: 4.38 vs. 1.19, p < 0.05), with all individuals exhibiting upregulation during summer and 95.8% showing upregulation during winter. Both strains demonstrated reduced expression of pro-inflammatory cytokines (IL-6, TNF-α) and increased expression of anti-inflammatory IL-10, suggesting maintained immunocompetence under thermal stress. The expression patterns of oxidative stress-related genes (SOD-2, NOS-3) indicated effective management of oxidative stress in both strains. These results suggest superior thermal adaptation in the Hercegovačka strain, particularly through HSP-mediated cellular protection mechanisms, while both strains show favorable immune and oxidative stress responses. These findings provide valuable insights for climate-resilient sheep breeding programs and the conservation of adaptive genetic resources. Full article

Tan sheep, a valuable indigenous breed in China, are vulnerable to coccidiosis caused by Eimeria ovinoidalis. In this case-control study, four 8-month-old Tan sheep raised under identical conditions were enrolled, including two with confirmed E. ovinoidalis infection (the Eo group) and two healthy controls (the HC group). Integrated metagenomic and untargeted metabolomic analyses were performed to assess gut microbiota and metabolic alterations. Results showed reduced alpha diversity and a distinct microbial composition in the Eo group. LEfSe identified 38 differentially abundant bacterial species, with Prevotella sp. and Fusobacterium necrophorum enriched in the Eo group and Faecalibacterium sp. and Lachnospira sp. enriched in the HC group. KEGG and VFDB analyses revealed significant differences in microbial functional pathways and virulence factor profiles. A total of 543 metabolites were differentially expressed, involving pathways related to inflammation, stress response, and amino acid metabolism. Microbiome–metabolome correlation analysis showed that Eo-associated bacteria were positively linked to pro-inflammatory metabolites, while HC-associated taxa correlated with markers of metabolic homeostasis. These findings provide new insights into the pathogenesis of ovine coccidiosis and may inform targeted interventions. Full article

Background: Complete environmental adaptation requires both survival and reproductive success. The hypoxic Qinghai-Tibet Plateau (>3000 m) challenges reproduction in indigenous species. Tibetan sheep, a key plateau-adapted breed, possess remarkable hypoxic tolerance, yet the genetic basis of their reproductive success remains poorly understood. Methods: We integrated transcriptomic and genomic data from Tibetan sheep and two lowland breeds (Small-tailed Han sheep and Hu sheep) to identify Tibetan sheep reproduction-associated genes (TSRGs). Results: We identified 165 TSRGs: four genes were differentially expressed (DEGs) versus Small-tailed Han sheep, 77 DEGs versus Hu sheep were found, and 73 genes were annotated in reproductive pathways. Functional analyses revealed enrichment for spermatogenesis, embryonic development, and transcriptional regulation. Notably, three top-ranked selection signals (VEPH1, HBB, and MEIKIN) showed differential expression. Murine Gene Informatics (MGI) confirmed that knockout orthologs exhibit significant phenotypes including male infertility, abnormal meiosis (male/female), oligozoospermia, and reduced neonatal weight. Conclusions: Tibetan sheep utilize an evolved suite of genes underpinning gametogenesis and embryogenesis under chronic hypoxia, ensuring high reproductive fitness—a vital component of their adaptation to plateaus. These genes provide valuable genetic markers for the selection, breeding, and conservation of Tibetan sheep as a critical genetic resource. Full article