Bovine embryonic stem cells (bESCs) can greatly enhance the understanding of bovine embryonic development and applications for disease-resistance, biomedical, and zoonotic pre-clinical models. However, formative bESCs with distinct morphology and complete differentiation capacity are still unreported. We document here the generation of formative bESCs (bFSCs) which are pluripotent both in vitro and in vivo, and efficiently converted into neural progenitor cells (NPCs) and primordial germ cell-like cells (PGCLCs) by direct differentiation. Transcriptomic analysis reveals these cells exhibited distinct metabolic features from human and mouse ESCs and early embryos. bFSCs contributed to a wide range of cell types within embryonic and extraembryonic tissues after aggregating with mouse and bovine embryos, as confirmed by chimeric experiment and single cell RNA-seq (scRNA-seq). The establishment of bFSCs with dual developmental plasticity represents a milestone for agricultural biotechnology and decoding the underlying mechanism of bona fide bovine pluripotency.

Accurate pedigree reconstruction is critical for genetic evaluation in admixed cattle populations, yet the relative performance of microsatellite and genome-wide SNP markers in twin-rich herds with incomplete pedigree records remains unclear. We compared 12 ISAG-recommended microsatellite markers with whole-genome SNP data for dam–calf assignment in a Simmental crossbred population (n = 43, 13 dam–calf groups) from southern China. Twin zygosity was determined from SNP identity-by-descent (PI_HAT) values: nine calf pairs were dizygotic, one pair was monozygotic (20A/21A), and one adult pair was composed of dizygotic twin sisters (31A/34A). Admixture analysis at K = 3 revealed ancestry proportions of 50.7% European taurine, 28.9% Chinese indicine and 20.4% East Asian taurine. The SNP-based neighbor-joining tree correctly recovered 12 of 13 groups (92.3%, 95% CI: 64.0–99.8%), whereas the microsatellite-based tree recovered 11 (84.6%, 95% CI: 54.6–98.1%); the difference was not statistically significant (exact McNemar test, p = 1.0). Locus INRA023 was monomorphic (PIC = 0), reducing the effective number of markers to 11. These results indicate that genome-wide SNPs show a favourable trend in accuracy and are less prone to false-positive clustering than a standard microsatellite panel in admixed, twin-rich cattle populations.

In the Hong Kong Special Administrative Region of China, there is a feral cattle population that has not been well characterized genetically. In this study, we used high-coverage (∼30×) whole-genome sequencing from 30 Hong Kong feral (HKF) cattle and compared them to 116 individuals from four representative populations worldwide. Our analyses revealed that the HKF cattle have high genetic diversity in the face of a declining effective population size, suggesting their substantial and yet untapped genetic potential. We also identified introgression events that occurred prior to the divergence between HKF cattle and other East Asian indicine populations, which shaped the adaptation of HKF cattle in Asian agro-ecologies. Moreover, we identified positive selection in HKF cattle for environmental adaptation, particularly in traits related to heat tolerance, bone strength, and coat color. Our findings provide insights into the genetic origin and unique adaptation of HKF cattle.

We studied the worldwide differentiation of Y-chromosomal haplotypes of cattle in order to clarify their origin and migrations. Previous studies of Y-chromosomal single-nucleotide polymorphisms (Y-SNPs) have defined five Y-chromosomal haplogroups and 10 sub-haplogroups of global cattle. In this study, we collected genomic data for 560 male cattle from Europe, America, Africa and Asia, including 71 Central Chinese cattle (CCC) of mixed taurindicine ancestry. We identified 1418 Y-SNPs, which defined 11 Y-chromosomal sub-haplogroups. Their geographic distributions indicate two paternal founder effects in Europe and Africa, respectively, whereas two other founder effects occurred relatively recently within China in the CCC (Y2B haplogroup) and the South Chinese indicine (Y3A3 sub-haplogroup). This suggests that the environmental adaptation of Chinese cattle was accompanied by consequential paternal founder effects due to population bottlenecks, which is relevant for the conservation and management of the Chinese cattle breeds.

The golden yak lives on the Qinghai-Xizang Plateau with a golden coat and adapts to high altitudes and strong ultraviolet environment. The golden coat is a prominent phenotype in many domesticated species, contributing to the breeding of new strains and the promotion of national culture. However, the genetic basis underlying the phenotype of the golden yak remains unknown. This study collected 21 golden yak samples from the Yushu population in Qinghai Province (Golden Yushu yak) and 17 samples from the Jila population in the Xizang Autonomous Region (Golden Jila yak) and combined 45 published data of black, white, and wild yak. The genetic diversity of the golden yak was high, but the genomic runs of homozygosity coverage revealed inbreeding. Selective sweep analysis of Golden Jila yak highlighted the ABCC12, MARK1, FANCA, and TCF25 genes, which are involved in energy metabolism, hypoxia adaptation, and reproduction. Moreover, some genes involved in immune response and adaptation were of wild yak origin. In addition, an F-ST, GWAS, and candidate gene sequencing revealed the previously reported MC1R mutation p.Gln34*, CM016709.1: c.100C > T, which is homozygous or heterozygous in all golden yak but not in black, white, or wild yak. The mutation took place in an MC1R sequence that originated from wild yak. Transcriptome analysis of skin samples revealed substantial differences between golden and black yak with a clear decrease in MC1R expression in golden yak.

Fetal skeletal muscle development involves coordinated interactions among myogenic, stromal, vascular, and immune compartments, yet the cellular and molecular programs guiding tissue maturation remain incompletely understood. To address this, we generated a high-resolution single-cell atlas of fetal female goat skeletal muscle and performed trajectory analysis, transcription factor activity profiling, and intercellular communication mapping. Unsupervised clustering identified RUNX2 mesenchymal progenitors, fibro-adipogenic progenitors (FAPs), myofibroblasts, endothelial cells, macrophages, differentiating myocytes, and mature skeletal muscle fibers, revealing a heterogeneous ecosystem in which stromal populations support myogenic progression and vascular and immune cells contribute to tissue organization. Pseudotime analysis traced a maturation continuum from differentiation-competent myocytes to contractile fibers, marked by sequential activation of extracellular matrix remodeling, cytoskeletal stabilization, and sarcomere assembly. KEGG and GO enrichment highlighted stage-specific engagement of ErbB, Hedgehog, and Hippo signaling, as well as cell cycle and ubiquitin-mediated proteolysis pathways, linking proliferation, differentiation, and structural maturation. Transcription factor profiling revealed early-stage proliferative and morphogenetically permissive states driven by E2F4/5, HMGA2, and HAND2, transitioning to late-stage differentiation, ECM remodeling, and tissue stabilization orchestrated by CEBPB, CREB3L1, ELK1, and E2F2. Cell-cell communication analysis showed a developmental redistribution of signaling authority, from ECM-driven, progenitor-centered networks to modular, structurally stabilized interactions. These findings define the cellular, transcriptional, and signaling framework orchestrating fetal skeletal muscle maturation.

BACKGROUND:Cattle have undergone complex evolutionary trajectories shaped by domestication, migration, and selection. Although runs of homozygosity (ROH) are a ubiquitous genomic feature, their full potential to decipher the evolutionary history and functional consequences in global cattle populations remains underexplored. We analyzed whole-genome sequences from 102 breeds across 17 geographic regions to conduct a global investigation of ROH landscapes, population structure, genomic inbreeding, and functional variants. RESULTS:ROH patterns revealed elevated homozygosity burdens in intensively selected European breeds, whereas South Chinese indicine showed a high short ROH burden, suggestive of a unique ancient demography. ROH-based principal component analysis (PCA) and admixture delineated taurine-indicine lineages, region-specific ancestries, inbreeding, and breeding effects. ROH-based inbreeding coefficient (FROH) exhibited greater stability for cross-population inbreeding assessment, showing a high correlation with excess of homozygosity-based inbreeding coefficient (FHOM) and a negative association with heterozygosity. Region-specific ROH hotspots, identified via permutation test, reflected a combination of local adaptation and demographic legacies. Trait-focused analyses, cross-validated with multiple selection scans, identified genes underlying growth, milk, and climate adaptation. Notably, we found missense mutations in CHEK2, SPG7, FANCA, and MSRB3, whose frequencies were significantly correlated with temperature and humidity. CONCLUSION:This study establishes ROH as a pivotal genomic marker for illuminating the dynamics of domestication, migration, inbreeding, and selection. Our findings offer valuable resources and insights for advancing genetic conservation and precision breeding in cattle under the pressures of climate change.

[This retracts the article DOI: 10.1016/j.omtn.2018.02.012.].

Neuropeptide B/W receptor-2 (NPBWR2) is a G protein-coupled receptor which is related to the regulation of feeding behavior, energy homeostasis, neuroendocrine function, and inflammatory pain. In addition, it plays a potential role in the regulation of stress, emotion, anxiety and fear responses. Interestingly, previous genomic analyses revealed variable levels of Bos javanicus introgression into Chinese indicine cattle, including a key adaptive region encompassing the NPBWR2 gene. By integrating introgression analysis with the Bovine Genome Variation Database, a banteng introgressed missense mutation (NC_083880.1: c.14C > G,Thr5Ser) of NPBWR2 was identified. The current study explored the allele frequency of this mutation in 1648 individuals representing 63 Chinese cattle breeds/populations using polymerase chain reaction amplification and whole genome resequencing methods. Here, we explored the prevalence of this variant in native Chinese cattle to instigate the introgression influence of B. javanicus on Chinese cattle.

The domestication and selective breeding of horses have profoundly influenced the emergence of adaptive traits and stress resistance mechanisms, shaping modern equine populations. This comprehensive review examines the genomic foundations of these traits, emphasizing recent advancements in high-throughput sequencing technologies and bioinformatics. These tools have elucidated the genetic underpinnings of key characteristics such as endurance, speed, metabolic efficiency, and disease resistance. Importantly, the review identifies and connects gene variants associated with thermoregulation, immune function, and cellular repair mechanisms, shedding light on their synergistic roles in enabling horses to adapt to diverse environmental challenges and physiological stressors. By establishing these causal links, this review enhances the coherence between genomic findings and their implications for equine biology. Furthermore, the integration of genomic insights provides a framework for addressing contemporary challenges in horse management and conservation. Issues such as climate change, disease outbreaks, and the preservation of genetic diversity demand innovative strategies grounded in genomics. By bridging the findings on equine adaptation and stress resistance mechanisms with practical applications in breeding and management, this review highlights the potential of genomics to ensure the sustainability and resilience of equine populations in the face of evolving environmental and societal pressures. This expanded perspective underscores the critical role of genomics in both understanding the evolutionary trajectory of horses and guiding future practices in equine health and conservation.

Skeletal muscle cellular heterogeneity and molecular regulation are fundamental to understanding exercise physiology in Equus species. However, these mechanisms remain incompletely characterized in donkeys (Equus asinus) and horses (Equus caballus). Here, we integrated single-nucleus transcriptomics and metabolomics to systematically compare the longissimus dorsi muscle across developmental stages in both species. We identified nine and twelve distinct skeletal muscle cell types in donkeys and horses, respectively. Muscle fiber composition exhibited species-specific age-related changes: in adult horses, the proportion of both type I and II fibers increased; in adult donkeys, by contrast, the proportion of type I fibers decreased while that of type II fibers increased. The predominance of type II fibers in horses likely reflects a species-specific adaptation to high-intensity locomotor demands. Pseudotime analysis delineated muscle fiber trajectories and revealed dynamic gene expression profiles along these paths. Subpopulation analysis of immune cells revealed the activation of pro-inflammatory signaling pathways (TNF and NOD-like receptor pathways) in adult groups, coupled with diminished anti-inflammatory capacity in dendritic cells, collectively indicating an age-associated pro-inflammatory shift. Intercellular communication analysis further indicated age-related dysregulation in key signaling pathways, including BMP (adipogenic differentiation), Notch (immune regulation), and IGF (tissue repair), which may contribute to impaired muscle metabolism and regenerative capacity. Cross-species comparison revealed that skeletal muscle transcriptomes of donkeys and horses are highly conserved (Pearson correlation coefficient 0.87), although species-specific marker gene expression, such as SLC29A1 in endothelial cells, was observed. Metabolomic profiling identified distinct differences in overall metabolite category composition and revealed significantly divergent gene-metabolite networks between the two species. Together, these findings comprehensively illuminate the cellular dynamics, metabolic remodeling, and evolutionary conservation of skeletal muscle development in Equus species, providing valuable insights into mammalian muscle adaptation and identifying potential targets for enhancing locomotor performance or managing myopathies in equids.

Testicular development and spermatogenesis are critical for male reproduction, but their molecular mechanisms in Dezhou donkeys remain understudied. This study used single-cell RNA sequencing (scRNA-seq) to analyze testicular tissues from Dezhou donkeys at juvenile (2 months), pre-pubertal (12 months), and mature (24 months) stages. A total of 24,606 high-quality cells were profiled, constructing a comprehensive single-cell transcriptional atlas. Unsupervised clustering identified nine major cell types: three germ cell subtypes (spermatogonia, spermatocytes, spermatids) and six somatic cell subtypes (Leydig cells, Sertoli cells, peritubular muscle cells, macrophages, endothelial cells, T cells). Key marker genes (AMH, TNP1, UTF1, ZMYND10) were validated by immunofluorescence. Pseudotemporal trajectory analysis revealed sequential germ cell differentiation (spermatogonia → spermatocytes → spermatids) and Sertoli cell maturation (immature → mature), while Leydig cells and peritubular muscle cells shared common progenitors. CellChat analysis identified critical ligand–receptor pairs in BMP, IGF, WNT, and FSH pathways, which regulate testicular development. This study provides the comprehensive single-cell transcriptional map of Dezhou donkey testicular development, elucidating key molecular mechanisms of germ and somatic cell maturation. The findings offer valuable insights into donkey reproductive biology, supporting breeding improvement and male infertility research.

Lufeng cattle ( Bos indicus ) are a representative indigenous indicine breed from southern China with extensive variation in background pigmentation and white-pattern distribution. However, the evolutionary history and genetic architecture underlying these traits remain largely uncharacterized. We integrated whole-genome resequencing data from 291 Lufeng cattle with 213 publicly available bovine genomes and employed genome-wide association studies, haplotype characterization, introgression inference, and epigenomic profiling. Population genomic analyses demonstrated a predominantly East Asian indicine genetic background with detectable Gaur and Banteng ancestry. D-statistics, local ancestry inference, and haplotype analyses supported historical introgression and retention of wild bovine-related haplotypes. GWAS identified two regions associated with distinct coat-color components: a chromosome 10 locus related to white-pattern distribution and a chromosome 18 locus influencing background pigmentation. The chromosome 10 region exhibited extended linkage disequilibrium, differentiated haplotypes, wild bovine-related ancestry, and active regulatory epigenomic features, suggesting that introgression and regulatory variation contributed to white-pattern distribution. In contrast, the chromosome 18 locus showed a dosage-dependent effect on pigmentation and harbored candidate genes, including SPIRE2 , FANCA , and MC1R . These findings support a dual-component model in which background pigmentation and white-pattern distribution are influenced by partially independent genetic mechanisms. More broadly, historical introgression, haplotype variation, regulatory mechanisms, and multilocus architecture may collectively shape complex phenotypic diversity in indigenous cattle. This study advances our understanding of coat-color evolution and the evolutionary history of southern Chinese cattle and provides a genomic framework for conserving and sustainably utilizing indigenous cattle genetic resources.

Coat color variation in domestic animals provides important insights into the genetic mechanisms of phenotypic diversity. The gray coat of Hetian gray donkeys is a distinctive breed characteristic, yet its genetic basis remains elusive. We integrated multiomics data from 175 domestic donkeys, including whole-genome sequencing, RNA-seq (n = 6), and Oxford Nanopore Technologies (ONT) sequencing (n = 8). Genome-wide association study (GWAS) and selection signature analyses identified the agouti signaling protein (ASIP) locus as the top candidate associated with the gray coat phenotype. Transcriptomic analysis revealed a 6.17-fold increase in ASIP expression in Hetian gray donkeys, suggesting that elevated ASIP levels may inhibit eumelanin synthesis. Further, comparative ONT analysis identified a 30 bp deletion in the second intron of ASIP. Dual-luciferase assays demonstrated that this deletion significantly enhances transcriptional activity. The increased ASIP expression appears to prevent melanocyte maturation, resulting in hypopigmentation in the skin and hair of Hetian gray donkeys. Our study provides functional evidence that this structural variant in ASIP modulates pigmentation by enhancing its expression, thereby offering mechanistic insight into both a distinctive donkey breed phenotype and the evolutionary processes shaping coat color diversity in equids.

Alternative polyadenylation within the 3' untranslated region (3' UTR-APA) is a post-transcriptional mechanism that influences mRNA stability and translation. Here, we investigated the role of 3' UTR-APA in regulating proteasome 26S subunit, ATPase 6 (PSMC6) in bovine Sertoli cells (BSCs). BSCs generated two PSMC6 mRNA isoforms through 3' UTR-APA, and the long 3' UTR isoform exhibited higher mRNA and protein levels than the short isoform. Further analyses revealed that cleavage and polyadenylation specificity factor 6 (CPSF6)-mediated APA regulation results in lower expression of the short isoform. Mechanistically, CPSF6 targets the UGUA motif upstream of the proximal polyadenylation signal (PAS) within the PSMC6 3' UTR, thereby biasing APA toward proximal PAS usage. This shift alters isoform ratios and mRNA stability, regulating BSC function. Collectively, our findings highlight the critical role of CPSF6-mediated PSMC6 3' UTR-APA in BSC function and provide a basis for marker-assisted breeding of male reproductive traits in cattle.

BACKGROUND: Guanling cattle is a vital livestock resource in Guizhou Province, China. Characterizing their genetic diversity provides a foundation for developing effective breeding and conservation strategies. This study employed whole-genome sequencing to analyse the population genetic structure and adaptive evolution of Guanling cattle. RESULTS: The results revealed that Guanling cattle are hybrids of East Asian indicine (EAI, 50%) and East Asian taurine (EAT, 35%) ancestry, exhibiting high genetic diversity and low inbreeding levels. Through local ancestry inference and selection signature analyses, several genes associated with disease resistance, heat tolerance, reproduction, and meat quality (such as STAT6, DNAJC8, HSPA4, PPP1R8, and BASP1) were identified. Notably, DNAJC8 and HSPA4, detected within selection-signal regions showing excessive EAI ancestry, were mainly related to immune and adaptive traits, whereas BASP1, identified in selection-signal regions enriched for EAT ancestry, was associated with muscle development and meat quality. CONCLUSIONS: Our findings reveal that Guanling cattle, composed of both indicine and taurine ancestries, represent a newly recognized and highly valuable genetic resource. The results provide important molecular insights for the conservation and breeding of Guanling cattle.

Mongolian horses are famous for their lactation traits. Their milk contains a high protein content and low levels of fatty acids. Given their superior milk composition and historical use in dairy production across Inner Mongolia and Central Asia, Mongolian horses serve as a valuable model for understanding lactational biology. Multiple factors regulate the lactation process; however, a detailed study of this biological process has not been performed with single-nucleus RNA sequencing (snRNA-seq) technology. Insights gained from snRNA-seq of their mammary glands can inform molecular strategies to enhance milk production both in Mongolian horses and in other less productive equine breeds. These findings may aid in selective breeding, nutritional interventions, and health management practices aimed at improving lactational efficiency, as snRNA-seq of frozen mammary gland tissue samples from young fillies and adult Mongolian mares provides high-resolution insights into the transcriptional dynamics and cellular heterogeneity associated with mammary gland development. In this study, we employed snRNA-seq and histological analyses to map the cellular landscape of the mammary gland in Mongolian mares across 4 physiological stages: 6-mo-old weanlings (6M), 2-yr-old yearlings (2Y), 4-yr-old lactating adults (LT), and 4-yr-old nonlactating adults (NL). Frozen parenchymal mammary gland tissues were surgically collected and processed for snRNA-seq via iodixanol gradient-based nuclei isolation, enabling high-resolution transcriptomic profiling, and complementary tissues were processed for histology. This study employed integrated analysis to reveal stage-specific shifts in epithelial, stromal, and immune cell populations, to highlight dynamic changes in mammary gland development and function. A total of 28,287 nuclei were profiled via transcriptome sequencing and categorized into 8 major cell types: basal myoepithelial, luminal secretory, luminal hormone-sensing, endothelial, fibroblasts, macrophages, T cells, and B cells. The LT-group samples (11,136) exhibited the greatest nuclei diversity and expansion, particularly in the luminal compartments, compared with the other stages, 6M (3,067 nuclei), 2Y (5,654 nuclei), and adult NL (8,430 nuclei), which shows the structure and maturation of the mammary gland. Hematoxylin and eosin staining confirmed structural remodeling during lactation, including increased epithelial thickness and ductal complexity. Pseudotime analysis revealed a dynamic transition from basal progenitors to differentiated luminal cells, identifying 3 major epithelial branches. Expression analysis of key genes and functional enrichment (Gene Ontology [GO] and Kyoto Encyclopedia of Genes and Genomes [KEGG]) was performed using the entire dataset across all physiological stages to capture shared transcriptional programs. To further investigate stage-specific responses, pathway enrichment and intercellular signaling analyses were conducted separately for each stage, enabling identification of both common and unique regulatory events. Key genes such as TP63 (basal identity), ERBB4 and NRG1 (epithelial signaling), and SORBS1, SLPI, SLC12A2, KCNMA1, and TAGLN (cytoskeletal and immune remodeling) were differentially expressed across stages, reflecting their roles in epithelial maintenance, lactational function, and structural adaptation. The GO and KEGG analyses identified differentially expressed genes in each cluster, mainly enriched in the TGF-β and VEGF signaling pathways, suggesting coordinated regulation of tissue remodeling, vascular development, and immune modulation. These findings deepen our understanding of mammary gland maturation and offer insights into the cellular and molecular architecture of equine mammary biology and its relevance to reproductive health and lactation studies.

Skeletal muscle is a crucial tissue involved in body movement and energy metabolism, and its growth and development directly influence the economic value of livestock. This study investigates the effects of the TEX10 gene on the proliferation, differentiation, and apoptosis of bovine myoblasts, as well as the underlying molecular mechanisms. Using techniques such as CCK-8, EdU incorporation, qPCR, Western blotting, and immunofluorescence, we observed that TEX10 significantly promotes the expression of cell cycle factors, including CDK2 and PCNA, thereby increasing cell proliferation and the proportion of cells in the S phase. Overexpression and knockdown experiments demonstrated that TEX10 enhances the differentiation and myotube formation of myoblasts, while upregulating key genes such as MYOG and MYOD. Additionally, flow cytometry analysis of the cell cycle revealed that TEX10 inhibits apoptosis in bovine myoblasts. Transcriptomic analysis showed that TEX10 regulates several signaling pathways associated with proliferation, differentiation, and apoptosis, including PI3K-Akt, cAMP, and IL-17. Overall, these findings suggest that TEX10 plays a significant regulatory role in bovine muscle growth, providing a theoretical foundation for molecular breeding strategies aimed at improving yellow cattle.