Pangenomics has become an important framework for representing genetic diversity beyond a single linear reference genome. In agricultural species, it improves access to structural variants (SVs), copy number variations (CNVs), presence/absence variations (PAVs), and non-reference regulatory or coding sequences that may contribute to domestication, adaptation, and breeding traits. This review summarizes recent progress in long-read sequencing, telomere-to-telomere (T2T) assembly, and graph-based genome analysis, with emphasis on both livestock and crop systems. We first define the conceptual boundary between pangenome representations and reference-based variant catalogs. We then compare three major technical routes: variant integration, reference-guided iterative graph construction, and reference-free graph construction. Their performance is evaluated in terms of accuracy, scalability, coordinate consistency, reference bias, computational demand, annotation transfer, and suitability for downstream breeding questions. We further discuss how pangenome resources support hidden variant discovery, QTL and GWAS interpretation, environmental adaptation analysis, and multi-omics-based candidate prioritization. Importantly, we highlight unresolved limitations, including graph complexity, pipeline-dependent SV calls, incomplete functional annotation, weak cross-study comparability, and the difficulty of distinguishing causal variants from linked or neutral variation. This review therefore treats pangenome studies as connected but non-equivalent evidence: resource-building studies establish representational breadth, method papers define technical feasibility, and trait-focused studies provide varying levels of biological support. Apparent inconsistencies among studies are interpreted as signals of differences in sampling, genome complexity, validation depth, and graph construction strategy rather than as simple disagreements.

The semi-domesticated gayal (Bos frontalis) is an endangered browsing ruminant inhabiting the rugged Eastern Himalayan foothills, and maintains an energy-intensive lifestyle on nutrient-poor, fiber-rich feed. However, the dietary, microbial, and host physiological features underlying this adaptation remain poorly understood. Here, we analyzed fecal metagenomes from ten bovine populations (n = 334) to characterize dietary composition. Then we profiled the four-chambered (FC) stomach microbiome in adult gayal (Bos frontalis), yak (Bos grunniens), and taurine cattle (Bos taurus). Host transcriptomes were profiled across the FC stomach in adult individuals from gayal, yak and cattle. Dietary analysis revealed a woody plant-dominated, bamboo-rich dietary pattern in gayal. Gastric metagenomes in gayal showed high population-level microbial diversity, pronounced individual-associated community structure, and functional potentials related to aromatic compound transformation, nitrogen metabolism, and metabolic flexibility. Transcriptomes revealed compartment-specific specialization in the gayal stomach, including rumen immune signatures and reticulum contractile/electrophysiological features. Exploratory compartment-level integration further suggested possible consistency between host transcriptomic features and microbial functional potential. Together, these multi-omics findings suggest a host-microbiome system potentially associated with the utilization of chemically complex, low-quality forage, providing a framework for understanding digestive features of browsing ruminants and for conserving host-associated gastrointestinal microbiomes.

With the rapid development of omics technologies, metabolomics and lipidomics have become important tools for elucidating the molecular basis of reproductive performance in livestock. These approaches, which focus on small metabolites and lipid species, provide valuable insights into dynamic interactions between genes, proteins, and the environment, offering a high level of sensitivity. This review summarizes key methodological advances in metabolomics and lipidomics and their applications to gametogenesis, oocyte maturation, embryo development, and pregnancy maintenance. It highlights how metabolic and lipid pathways, particularly those involving energy metabolism, redox regulation, lipid remodeling, and cell-cell signaling, affect reproductive cell quality. This review further integrates biomarkers identified from semen, follicular fluid, oocytes, embryos, and uterine tissues, highlighting their potential roles in fertility assessment. Together, these insights enhance our understanding of metabolic regulation in reproduction and support the effective application of metabolomics and lipidomics in improving livestock fertility.

The reference genome serves as a fundamental resource for sheep genetic research and molecular breeding, and iterative improvements in assembly quality have directly driven advances in these fields. A systematic literature review was conducted by retrieving relevant studies from major scientific databases using predefined keywords related to sheep reference genomes and genome assembly technologies, followed by structured screening and comparative analysis of eligible publications. This review systematically summarizes the developmental trajectory of the sheep reference genome from early fragmented assemblies to telomere-to-telomere (T2T) genome assembly approaches. Different genome versions are comparatively analyzed from multiple perspectives, including assembly strategies, quality metrics, and functional annotation. Importantly, we propose a genome-resolution-driven analytical framework that explicitly links successive improvements in reference genome completeness with paradigm shifts in sheep genetic analysis, ranging from marker-based studies to structural variation- and multi-omics-enabled trait dissection. Particular emphasis is placed on the potential applications and biological research value of T2T genomes in assembly methodologies and multi-omics integrative analyses. Furthermore, the practical significance of different reference genome versions in genetic dissection, trait mapping, and breeding applications is reviewed, and future directions for sheep genome research are discussed. This review provides both a systematic synthesis and a forward-looking conceptual roadmap for advancing sheep molecular genetics and precision breeding in the T2T genomics era.

Background: The Chungtien schizothoracin (Ptychobarbus chungtienensis) is a threatened freshwater fish endemic to the Qinghai–Tibet Plateau and adjacent high-altitude regions of northwestern Yunnan, China. Although a complete mitochondrial genome of P. chungtienensis has been previously reported, direct comparison with a mitogenome generated using high-accuracy long-read sequencing can provide additional information on mitochondrial genome structure and sequence variation. This study aimed to assemble and annotate a complete mitogenome of P. chungtienensis using PacBio HiFi sequencing and to compare its mitogenomic characteristics with previously published Ptychobarbus mitogenomes. Methods: High-molecular-weight genomic DNA from a single specimen was sequenced using PacBio HiFi long-read technology. The mitochondrial genome was assembled using MitoHiFi, annotated using MitoFinder followed by manual curation, and compared with previously published Ptychobarbus mitogenomes. Phylogenetic relationships were evaluated using maximum-likelihood analysis with expanded taxon sampling, and selection pressure on the 13 mitochondrial protein-coding genes was assessed using dN/dS-based branch and branch-site models. Results: The assembled mitogenome is 16,583 bp in length and contains the typical 37 mitochondrial genes, including 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes, together with a control region and the origin of light-strand replication (OL). The overall A + T content was 54.97%. Direct comparison with the previously reported 16,970 bp mitogenome showed that the 387 bp length difference was concentrated in non-coding regions, particularly the control region and the tRNA-Thr–tRNA-Pro intergenic region. Phylogenetic analysis based on 22 complete mitogenomes placed the newly assembled P. chungtienensis sequence in a strongly supported mitochondrial clade with Schizothorax macropogon (bootstrap = 100%), whereas the previously reported P. chungtienensis sequence clustered with P. kaznakovi (bootstrap = 100%), indicating that the two P. chungtienensis records represent distinct mitochondrial lineages. The dN/dS values of all 13 mitochondrial protein-coding genes were below 1, and neither branch nor branch–site analyses detected significant evidence of lineage-specific positive selection. Conclusions: This long-read-based mitogenome provides a high-quality genomic resource for P. chungtienensis and reveals substantial mitochondrial sequence and lineage variation among available records. These results provide a basis for comparative mitogenomic and conservation genetic studies while also indicating that species-level phylogenetic relationships and high-altitude adaptation should not be inferred from mitochondrial data alone.

ABSTRACT Horses are major domestic animals and cultural symbols that have accompanied humans for millennia. They underpin transport, agriculture, warfare and sport, and also provide a model for studying domestication, complex traits and adaptive evolution. Recent work in equine genomics has now generated a much richer picture of how these roles are grounded in the genome. This review brings together advances in several connected areas: the construction and refinement of reference assemblies; genomic reconstructions of origin, domestication and dispersal; global and regional patterns of genetic diversity; and the molecular basis of key traits such as athletic performance, coat colour, body size, environmental adaptation and inherited myopathies. The transition from EquCab1.0/2.0 to EquCab3.0 and a complete Y‐chromosome sequence illustrates how long‐read and Hi‐C/T2T data improve genome completeness and the representation of complex regions. On this foundation, high‐coverage resequencing of ancient and modern horses has clarified the geographical core of domestication in the Volga–Don region, the Bronze Age replacement of earlier domestic lineages and the long‐term impact of human management on behaviour, conformation and mobility. Comparative analyses of mitochondrial DNA, Y‐chromosomal haplotypes and autosomal runs of homozygosity further reveal a combination of diverse maternal lineages, highly constrained paternal lineages and breed‐specific inbreeding histories. Against this background, studies of representative traits show how association signals, functional experiments and clinical evidence can be linked to practical tools for breeding and health management, for example through MSTN‐guided performance profiling, EPAS1‐based altitude adaptation and molecular tests for GYS1, SCN4A, PPIB and MYH1. We conclude by considering how telomere‐to‐telomere assemblies, pangenome resources, improved structural‐variant detection and closer integration between population genomics and functional studies may support conservation, health surveillance and molecular breeding in diverse horse populations.

Whole-genome resequencing (WGRS) is a critical branch of whole-genome sequencing (WGS), primarily targeting species with existing reference genomes. By aligning sequencing data to the reference genome, WGRS enables precise detection of genetic variations in individuals or populations. As a core technology in genomic research, WGS holds profound significance in ruminant studies. It not only reveals the intricate structure of ruminant genomes but also provides essential data for deciphering gene function, variation patterns, and evolutionary processes, thereby advancing the exploration of ruminant genetic mechanisms. However, WGS still faces several challenges, such as incomplete and inaccurate genome assembly, as well as the incomplete annotation of numerous unknown genes or gene functions. Although WGS can identify a vast number of genomic variations, the specific relationships between these variations and phenotypes often remain unclear, which limits its potential in functional studies and breeding applications. By performing WGRS on multiple samples, these assembly challenges can be effectively addressed, particularly in regions with high repeat content or complex structural variations. WGRS can accurately identify subtle variations among different individuals or populations and further elucidate their associations with specific traits, thereby overcoming the limitations of WGS and providing more precise genetic information for functional research and breeding applications. This review systematically summarizes the latest applications of WGRS in the analysis of ruminant genetic structures, genetic diversity, economic traits, and adaptive traits, while also discussing the challenges faced by this technology. It aims to provide a scientific foundation for the improvement and conservation of ruminant genetic resources.

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.

Hemoglobin metabolism disorder can result in systemic iron overload, leading to pigmentation in multiple organs. Although these disorders are often of genetic origin, the specific genes and mechanisms remain incompletely understood. Lanping black bone sheep (LP–BBS), a unique population from the high altitudes along the Hengduan Mountains in Yunnan province, exhibits hyperpigmentation in multiple tissues. Investigating the genetic and environmental factors underlying this phenotype provides a natural model to better understand hemoglobin metabolism disorder. LP-BBS were found to exhibit increased red blood cell counts, elevated hemoglobin levels, and systemic iron overload, evidenced by hyperpigmentation in various tissues. Histological and molecular analyses revealed that hyperpigmentation is driven by ferriheme overload, an inheritable quantitative trait influenced by both genetic variation and environmental factors. Genome-wide association studies identified FRRS1L as a candidate gene, with significant mutations in its 3′-untranslated region (3′-UTR) reducing FRRS1L expression. Functional assays demonstrated that insufficient FRRS1L expression promotes ferriheme accumulation in reticuloendothelial cells and macrophages, as confirmed in vitro using FRRS1L knockdown models. Ferriheme overload was associated with oxidative stress and systemic inflammation, causing pathological damage to critical organs such as the kidney, liver, and uterus. This study identifies FRRS1L as a key contributor to ferriheme overload through aberrant hemoglobin metabolism in LP–BBS. These findings offer new insights into the genetic basis and pathological mechanisms of iron overload disorders, providing a potential target for therapeutic intervention. Moreover, LP–BBS serves as a valuable natural model for studying hematogenous pigment disorders and their interplay with environmental factors.

The differentiation and lipid metabolism of preadipocytes are crucial processes in IMF deposition. Studies have demonstrated that SIRT4 plays essential roles in energy metabolism and redox homeostasis, with its expression being coordinately regulated by multiple transcription factors associated with energy and lipid metabolism. In this study, the findings of multiple omics analysis reveal that SIRT4 significantly up-regulates the expression of genes involved in adipogenesis and enhances the differentiation and lipid deposition of bovine preadipocytes. Furthermore, SIRT4 profoundly influences the expression pattern of metabolites by increasing the abundance of substances involved in lipid synthesis while decreasing those that promote lipid oxidative decomposition. Additionally, SIRT4 broadly up-regulates the expression levels of various lipid classes, including glycerolipids, glycerophospholipids, sphingolipids, and sterol lipids. These findings not only provide a theoretical basis for molecular breeding and genetic improvement in beef cattle, but also offer potential therapeutic approaches for energy homeostasis disorders and obesity.

Sheep (Ovis aries), domesticated from wild Asian mouflon ~10,000 years ago, are an important livestock species adapted to various ecological environments. Recent advancements in high-throughput sequencing and global environmental databases have facilitated the exploration of genetic–environmental associations, uncovering the genetic and epigenetic mechanisms behind sheep’s adaptation to multiple environments. Studies show that HIF-1α and EPAS1 enhance high-altitude adaptation via hypoxic stress regulation; UCP1 contributes to cold adaptation through non-shivering thermogenesis; SLC4A4 and GPX3 increase drought resistance by regulating renal water reabsorption; and SOCS2 likely plays a role in metabolic and stress response regulation. Additionally, sheep adapt to temperature, drought, and environmental stress through DNA methylation, transcriptional regulation (e.g., SOD1, GPX4), heat shock proteins (e.g., HSP70), and metabolic pathways (e.g., UCP1). These findings offer valuable insights for improving sheep breeding and genetic enhancement. This review summarizes the mechanisms of adaptation to high altitude, cold, heat, drought, and comprehensive climate stress.

With the rapid advancement of high-throughput sequencing technologies, whole genome sequencing (WGS) has emerged as a crucial tool for studying genetic variation and population structure. Utilizing population genomics tools to analyze resequencing data allows for the effective integration of selection signals with population history, precise estimation of effective population size, historical population trends, and structural insights, along with the identification of specific genetic loci and variations. This paper reviews current whole genome sequencing technologies, detailing primary research methods, relevant software, and their advantages and limitations within population genomics. The goal is to examine the application and progress of resequencing technologies in this field and to consider future developments, including deep learning models and machine learning algorithms, which promise to enhance analytical methodologies and drive further advancements in population genomics.

Multi-omics studies have multiplied associations, but many still lack causal resolution and a clear path to application. We present a practical roadmap built on four sequential steps: first, identify signals from genome-wide association studies; second, confirm these signals through regulatory colocalization and transcriptome-wide association analyses; third, integrate the evidence using network analyses and causal inference; and, fourth, test shortlisted candidates through functional and phenotypic validation. The roadmap is supported by three safeguards that make results reliable and reusable: containerized workflows that ensure end-to-end reproducibility, harmonization across batches with concise minimum-information records, and consistent identifier mapping with quality control across data layers. Across four classes of traits-growth and development, carcass and meat quality, reproduction, and environmental adaptation and resilience-we prioritize signals that remain robust across ancestries and environments, highlight modules with explicit regulatory support, and advance candidates that have already progressed to functional testing. Two application tracks follow from this process: integrating stable candidates into selection indices with context-dependent weighting, and recording and targeting mechanistic nodes for nutritional and management interventions. Taken together, this roadmap improves causal interpretability, strengthens cross-population robustness, and shortens the path from statistical association to genetic evaluation and industry uptake.

Goats (Capra hircus) are a widely distributed livestock known for their exceptional environmental adaptability. This review presents an integrated overview of recent advances in understanding the genetic and molecular mechanisms underlying goat adaptation to heat, cold, and high-altitude hypoxia. We first discuss the development of high-quality reference genomes, including recent telomere-to-telomere assemblies. We then examine major adaptive genes such as HSP70, ACTHR, EPAS1, SLC2A1, FGF12, and UCP1, and their roles in thermoregulation, oxygen metabolism, and stress resistance. Additionally, the review explores the synergistic role of immune signaling pathways in environmental adaptation, as well as the regulatory effects of epigenetic mechanisms such as DNA methylation, histone modification, and non-coding RNAs. Future efforts should focus on integrating multi-omics data to uncover the complex molecular networks involved in goat adaptation. This comprehensive synthesis offers valuable insights for precision breeding and long-term sustainability in the context of environmental challenges and climate change.

Goat milk is a vital component of China's dairy industry, renowned for its richness in lipids essential to human health. Polyunsaturated fatty acids (PUFAs), such as docosahexaenoic acid (C22:6n-3, DHA), are particularly valuable for their integration into phospholipids and triacylglycerols. While mammary cells can uptake and channel PUFAs into lipids for milk fat secretion, the broader functional effects of DHA within these cells remain unclear. This study demonstrated that DHA supplementation markedly altered levels of lipid subclasses in goat mammary epithelial cells (GMECs), as revealed by lipidomic analysis. DHA treatment significantly increased the levels of free DHA, alongside DHA-enriched triacylglycerols, phosphatidylcholine, phosphatidylethanolamine, and phosphatidylserine, thereby driving lipid remodeling in GMECs. Additionally, DHA modulated transcription of key fatty acid metabolism genes, such as SREBP1, FASD2, and FASN. Mechanistically, DHA supplementation activated the AMPK signaling pathway inhibiting fatty acid metabolism, and upregulated the expression of fatty acid transport gene-CD36 in GMECs. Knockdown or mutation of the fatty acid binding domain of CD36 diminished DHA-induced AMPK activation and transcriptional regulation of fatty acid metabolism genes in GMECs. In summary, DHA supplementation induces lipid remodeling in GMECs via the CD36-AMPK signaling axis, highlighting its potential to facilitate the development of DHA-enriched functional goat milk.

Lanping black-boned (LPBB) sheep are a unique and rare ruminant species, characterized by black pigmentation in the skin and internal organs. Thus far, LPBB are the only known animal with heritable melanin characteristics besides the black-boned chicken, and the only mammal known to contain a large amount of melanin in the body. LPBB have therefore attracted substantial research attention, due to their potential contribution to medicine. However, long periods of grazing freely and crossbreeding with Lanping normal sheep (LPN) have diluted LPBB breeding resources, posing a challenge to the protection of species. To ensure the effective conservation and management of LPBB genetic resources, the construction of a large-scale database of genotypic information is therefore very important. To achieve this, we established the first LPBB-specific SNP database, named Black-boned Sheep Genome SNP Database (BbGSD, http://202.203.179.115:3838/oarsnpdb) using sheep genotype data (100 LPBB and 50 LPN) across 46 894 242 SNP sites. In this database, we implemented four main function modules: (i) the "LD heatmap" module, which uses a heatmap to enable the interactive visualization of pairwise linkage disequilibrium (LD) measurements between SNPs; (ii) the "SNP distribution" module, which allows users to interactively visualize tabular genotype data as heat maps; (iii) the "Phylogenetics" module which enables phylogenetic analysis to explore the evolutionary history or genetic relationships of the LPBB sheep; and the "Diversity" module, which can be used to calculate and display the nucleotide diversity among sheep populations in user-specified genomic regions. BbGSD is essential for accelerating studies on the functional genomics and screening of molecular markers of molecular-assisted breeding in black-boned sheep. Database URL: http://202.203.179.115:3838/oarsnpdb.

This study aimed to investigate the effects of adding different proportions of Panax notoginseng residue (PNR) to the diet on the rumen microbial community structure, blood biochemical indices, and growth performance of Wenshan cattle. Fifteen Wenshan cattle with an average weight of 392.30 ± 22.57 kg were randomly divided into three groups, a control group, a 3% PNR group, and a 6% PNR group, with five cattle in each group, for a 100-day feeding trial. The results show that adding PNR to the diet modulates the abundance and diversity of rumen microorganisms in Wenshan cattle, primarily affecting the relative abundances of key bacterial phyla such as Firmicutes, Proteobacteria, and Bacteroidetes. At the genus level, the relative abundances of Fibrobacter and Butyrivibrio exhibited trends of either decreasing and then increasing or increasing then decreasing with the amount of PNR added, indicating a complex regulatory effect of PNR on the rumen microbial community. The addition of PNR decreased blood glucose and blood lipid levels in Wenshan cattle. Moreover, PNR addition also increased the average daily weight gain of Wenshan cattle, demonstrating its positive effect on enhancing growth performance. In summary, PNR, as a feed resource, has potential application value in the feeding of Wenshan cattle. It not only regulates the rumen microbial community structure and improves metabolic health but also effectively enhances animal growth performance.

The EPAS1 gene plays a central role in hypoxia adaptation in high-altitude animals. Using over 400 blood samples from goats across elevations in Yunnan (500-3500 m), this study examined hematological traits, genetic polymorphisms, and protein structure. Red blood cell (RBC) and hemoglobin (HGB) levels increased significantly with altitude (p < 0.05), reflecting improved oxygen transport. A non-synonymous SNP (g.86650 A>T, p.Gln556Leu) exhibited adaptive selection, with the T allele frequency rising at higher altitudes (p < 0.05). At 2500 m, TT genotype goats showed significantly higher RBC and HGB levels than AA genotypes (p < 0.05). Protein modeling revealed structural instability caused by the polymorphism, highlighting its role in enhancing hypoxia adaptation. These findings provide a foundation for improving high-altitude livestock genetics.

The Gayal (Bos frontalis) is a rare semi-wild Bovine species that inhabits the harsh environments of Indo-China. Although the origins of the Gayal remain largely enigmatic, addressing the lack of comprehensive transcriptomic data is critical for understanding its genetic and molecular characteristics, which are essential for formulating effective conservation and management plans. In this study, an integrated PacBio Iso-seq and RNA-seq analysis was conducted on samples from 10 different organs and tissues of the Gayal, with each being sequenced in triplicate. The samples analyzed included the heart, liver, spleen, lung, kidney, rumen, abomasum, duodenum, ileum, and rectum. This comprehensive analysis resulted in the identification of 30,760 full-length transcripts ranging from 363 bp to 7,157 bp, with transcript information matched to seven commonly used databases. Gene family clustering and phylogenetic analyses encompassed a comprehensive dataset of 9 Bovine species, including the Gayal. Additionally, long non-coding RNAs (lncRNAs) were identified across all sampled tissues, and comprehensive gene expression profiles and differential expression gene analyses were performed. These findings provide a rich repository of genetic information, laying the foundation for comprehensive functional genomics studies and paving the way for deeper insights into the molecular mechanisms of the Gayal, thereby advancing our understanding of its transcriptome architecture and offering crucial data for conservation efforts and practical applications.

Sheep (Ovis aries) were domesticated around 10,000 years ago and have since become an integral part of human agriculture, providing essential resources, such as wool, meat, and milk. Over the past century, advances in communication and agricultural productivity have driven the evolution of selective breeding practices, further enhancing the value of sheep in the global economy. Recently, the rapid development of whole-genome resequencing (WGR) technologies has significantly accelerated research in sheep molecular biology, facilitating the discovery of genetic underpinnings for critical traits. This review offers a comprehensive overview of the evolution of whole-genome resequencing and its application to sheep genetics. It explores the domestication and genetic origins of sheep, examines the genetic structure and differentiation of various sheep populations, and discusses the use of WGR in the development of genetic maps. In particular, the review highlights how WGR technology has advanced our understanding of key traits, such as wool production, lactation, reproductive performance, disease resistance, and environmental adaptability. The review also covers the use of WGR technology in the conservation and sustainable utilization of sheep genetic resources, offering valuable insights for future breeding programs aimed at enhancing the genetic diversity and resilience of sheep populations.