Understanding the genetic mechanisms of phenotypic variation in hybrids between domestic animals and their wild relatives may aid germplasm innovation. Here, we report the high-quality genome assemblies of a male Pamir argali (O. ammon polii, 2n = 56), a female Tibetan sheep (O. aries, 2n = 54), and a male hybrid of Pamir argali and domestic sheep, and the high-throughput sequencing of 425 ovine animals, including the hybrids of argali and domestic sheep. We detected genomic synteny between Chromosome 2 of sheep and two acrocentric chromosomes of argali. We revealed consistent satellite repeats around the chromosome breakpoints, which could have resulted in chromosome fusion. We observed many more hybrids with karyotype 2n = 54 than with 2n = 55, which could be explained by the selfish centromeres, the possible decreased rate of normal/balanced sperm, and the increased incidence of early pregnancy loss in the aneuploid ewes or rams. We identified genes and variants associated with important morphological and production traits (e.g., body weight, cannon circumference, hip height, and tail length) that show significant variations. We revealed a strong selective signature at the mutation (c.334C > A, p.G112W) in TBXT and confirmed its association with tail length among sheep populations of wide geographic and genetic origins. We produced an intercross population of 110 F₂ offspring with varied number of vertebrae and validated the causal mutation by whole-genome association analysis. We verified its function using CRISPR-Cas9 genome editing. Our results provide insights into chromosomal speciation and phenotypic evolution and a foundation of genetic variants for the breeding of sheep and other animals.

The high concentration of secondary branched wool follicles is a distinctive feature of the Merino sheep. At present, the molecular control of the development and branching of secondary wool follicles (SF) remains elusive. To reveal the potential genes associated with the development of hair follicles, we investigated the characteristics of prenatal and postnatal development of wool follicles, and the transcriptional expression profile in fetuses/lambs from dams under either maternal maintenance or sub-maintenance (75% maintenance) nutrition. The density of SF and the ratio of SF to primary wool follicles (PF) were reduced (p < 0.05) in fetuses from day 105 to 135 of gestation under sub-maintenance nutrition. Differentially expressed genes were enriched in the binding, single-organism process, cellular process, cell and cell part Gene Ontology (GO) functional categories and metabolism, apoptosis, and ribosome pathways. Four candidate genes, SFRP4, PITX1, BAMBI, and KRT16, which were involved in secondary wool follicles branching and development, were identified. Our results indicate that nutritional intervention imposed on pregnant ewes by short-term sub-maintenance nutrition could provide a strategy for the study of wool follicle development. Overall insight into the global gene expression associated with SF development can be used to investigate the underlying mechanisms of SF branching in Merino sheep.

Background: Various regulators coregulate muscle development in animals. MicroRNAs (miRNAs) are crucial regulators that participate in multiple aspects of myofiber formation. Method: To identify key miRNAs and target genes associated with muscle development, embryos or longissimus dorsi of Chinese Merino sheep were collected for whole-transcriptome sequencing across 11 gestation periods: 26 days (D26), D29, D32, D35, D40, D45, D55, D75, D85, D105, and D135. The functions of key miRNAs and target genes were determined by qRT-PCR, Western blot, dual-luciferase reporter gene assay, and Immunofluorescence staining.Results: A total of 284 differentially expressed miRNAs (DE-miRNAs) were screened by comparing the transcriptome data across all 11 periods. DE-miRNAs were divided into two developmental stages (stage A and stage B) based on heat map clustering analysis. Functional enrichment analysis revealed that DE-miRNAs in stage A were closely related to myofiber formation, whereas those in stage B were closely related to myofiber growth and maturation. Differential expression and functional enrichment analysis of target genes of DE-miRNAs obtained from stage A revealed the target relationships between 159 DE-miRNAs and 21 differentially expressed target genes associated with myofiber formation. In vitro assays revealed that myoblast differentiation and myotube formation were significantly inhibited by MYH3 knockdown via siMYH3 and that novel-miR-766 targets and decreases the expression of MYH3. In addition, the expression levels of marker genes related to myoblast differentiation and myofiber types were altered after the overexpression and inhibition of novel-miR-766 in sheep myoblasts.Discussion: This research not only elucidates the core temporal expression patterns of miRNAs but also suggests that novel-miR-766 influences myoblast differentiation and myofiber-type formation. This provides an important theoretical foundation for a deeper understanding of the molecular mechanisms by which miRNAs regulate myofiber development.

Background: Originating from the cold and arid regions of northwestern China, Kazakh sheep are dual-purpose breeds optimized for both meat and fat production. In contrast, Texel sheep are internationally recognized for their high-quality meat and exceptional flavor. Previous studies have indicated that the hybrids of Texel and Kazakh sheep exhibit significant quality advantages. Additionally, body weight is a crucial indicator of sheep production performance, directly correlating with meat yield and economic returns. Objective: This study aims to identify genetic variations and related genes associated with the body weight traits of hybrid lambs, thereby revealing their genetic mechanisms. Methods: This study genotyped hybrid lambs using a 50K chip and performed rigorous quality control on both genotypic and phenotypic data. The traits examined include body weight traits of lambs at various stages such as birth, pre-weaning, and post-weaning. Various genome-wide association study (GWAS) models were utilized to analyze the association between lamb body weight traits and genetic markers. The study then employed an Ensemble-like GWAS (E-GWAS) strategy to integrate these models, achieving a stable list of SNPs, rather than a mere aggregation. Multiple annotation databases were consulted to further investigate the mechanisms by which genetic markers affect body weight traits. All study results were validated through an extensive literature review. Results: Analyses with multiple statistical models revealed that 48 SNPs were significantly associated with body weight traits. The annotation process identified 24 related genes (including 4 unknown genes) and 9 quantitative trait loci (QTLs). Additionally, 6 Gene Ontology (GO) terms and 22 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were determined. Conclusions: This study identified key genes and pathways in the body weight traits of hybrids between Texel and Kazakh sheep, enhancing our understanding of their genetic mechanisms.

Background: The composition of skeletal muscle fiber types is a crucial determinant of meat quality in livestock. While the transition from embryonic to mature fiber types is known to occur during late gestation, the precise temporal dynamics and molecular mechanisms underlying this process in sheep remain poorly understood. A comprehensive, multi-technique approach is needed to elucidate the critical developmental transitions in myofiber specification.Methods: We systematically investigated muscle fiber type differentiation in the longissimus thoracis et lumborum (LTL) muscle of sheep fetuses at 85, 105, 115, and 135 days of gestation (D85-D135) using an integrated approach combining histological (ATPase staining), protein biochemical (SDS-PAGE and Western blotting), and transcriptomic (RNA-seq) analyses. This multi-omics strategy enabled comprehensive characterization of fiber type composition, myosin heavy chain (MHC) isoform expression, and associated molecular pathways.Results: Our findings revealed distinct stage-specific developmental patterns. Prior to D105, the number of muscle fibres increased progressively, with fibres predominantly expressing embryonic (MHC-emb) and neonatal (MHC-neo) isoforms. After D105, fibre numbers stabilized and underwent maturation, transitioning to predominantly type I, IIA, and IIB fibres, with type IIA fibres becoming the most abundant (61.2%) by D135. Transcriptome analysis identified D105 as a critical transition point, characterized by the significant downregulation of MYH3 (MHC-emb) and MYH8 (MHC-neo), and the upregulation of mature fibre genes (MYH7, MYH2, and MYH4). Concurrently, we observed increased expression of oxidative metabolism genes (COX7A1, NDUFB6) and enhanced aerobic metabolic capacity in maturing fibers.Discussion: This study provides the first integrated multi-omics characterization of muscle fiber type development in late-gestation sheep, identifying D105 as a pivotal transition point in myofiber specification. Our findings reveal coordinated molecular and metabolic changes underlying the transition from embryonic to mature fibre types, with significant implications for understanding ruminant muscle development. These results establish a scientific foundation for improving meat quality through targeted molecular breeding strategies and prenatal nutritional interventions in sheep production systems.

Background: Inbreeding and genetic diversity are critical factors influencing the adaptability, productivity, and sustainability of livestock populations. Teha sheep, a crossbred line between Texel and Kazakh sheep, are an important meat-producing breed in China, yet their genetic structure and inbreeding status remain underexplored. In this study, we aim to evaluate inbreeding coefficients, genetic diversity, and selection signatures in Teha sheep by integrating pedigree and genomic data.Results: Analysis of pedigree data from 2,652 individuals revealed a low inbreeding coefficient (FPED = 0.001), whereas analysis of genomic data from 1,271 individuals indicated slightly higher inbreeding coefficients, with the FROH averaging 0.044. Genetic diversity metrics, including Ho = 0.347 and PIC = 0.345, confirmed moderate variability within the population. A significant region of runs of homozygosity (ROH) hotspot was identified on chromosome 2 (112.01–119.89 Mb), encompassing genes such as MSTN, TUBGCP5, and NIPA2, which are associated with muscle growth, fat metabolism, and skeletal development. Notably, CYFIP1, SAP130, and UGGT1 were identified as key genes shared across ROH hotspots, QTL regions, and LD blocks, implicating their roles in growth efficiency, carcass quality, and protein regulation under stress. These findings reveal critical genomic regions contributing to the breed’s productivity and adaptability.Conclusion: In this study, we highlight the low inbreeding levels and moderate genetic diversity of Teha sheep, emphasizing the integration of pedigree and genomic analyses for sustainable breeding programs. The identification of key genes provides a foundation for optimizing productivity and maintaining genetic variability in this important livestock population.