Fat deposition is the key factor affecting the efficiency of animal husbandry production. There are many factors affecting fat deposition, in which the gastrointestinal microbiota plays an important role. Therefore, the body mass index (BMI) was introduced into the evaluation of sheep fat deposition, and the different microbiota and functional pathways of the sheep gastrointestinal tract in different BMI groups were analyzed. We selected 5% of individuals with the highest and lowest BMI from a feed test population (357 in whole group). Microorganisms in 10 sites of the gastrointestinal tract in 36 individuals (18 in each group) were evaluated by 16S rRNA V3–V4 region sequencing. There were differences (p < 0.05) in fat deposition traits between different BMI groups. In the 10 parts of the gastrointestinal tract, the diversity and richness of cecal microflora in the high-BMI group were higher than those in low-BMI Hu sheep (p < 0.05). Principal coordinate analysis (PCoA) showed that there was separation of the cecum between groups, and there were differences in the cecal microbial community. Linear discriminant analysis effect size (LEfSe) showed that most biomarkers were in the cecum. On the basis of an indepth study of cecal microorganisms, 26 different bacterial genera were obtained (p < 0.05). Correlation analysis between them and the characteristics of fat deposition in sheep showed that Colidextribacter, Alloprevotella, and Succenivibrio were positively correlated with fat deposition, while Lachnospiraceae_ND3007_Group was negatively correlated (p < 0.05). The above results show that the cecum may be an important part leading to the difference of BMI in sheep, and its microorganisms may affect the level of fat deposition.

Meat quality traits, particularly WHC and tenderness, are pivotal for consumer satisfaction and economic value in the sheep industry. However, their genetic regulatory mechanisms remain unclear. We used RNA-Seq and WGCNA to identify genes regulating WHC and tenderness. Sixty longissimus thoracis samples were classified into high/low WHC (HWHC vs. LWHC) and high/low tenderness (HTN vs. LTN) groups. Comparative transcriptomics identified 270 differentially expressed genes (DEGs) linked to WHC, enriched in pathways like the regulation of the ATP metabolic process and the inhibition of canonical Wnt signaling. Key DEGs (e.g., SORBS1, FOXO1, PDE4B, CDH1) correlated significantly with WHC-associated traits. For tenderness, 165 DEGs were identified, including LEP, FABP4, PLIN1, and GLP1R, enriched in PPAR signaling, fat cell differentiation, and cAMP signaling pathways. WGCNA revealed modules associated with WHC and tenderness, with hub genes (ATP2C1, GSKIP, PATL1, PPARA, CYLD) involved in ATP metabolism, lipid biosynthesis, and myofibril assembly. Tissue-specific gene integration prioritized muscle-enriched candidates (METTL21C and ACTC1) with strong trait correlations. Our findings unveil interconnected gene networks governing WHC and tenderness, highlighting some candidate genes as potential biomarkers for precision breeding. This study provides novel insights into the molecular determinants of meat quality, offering actionable targets to enhance mutton production sustainability and consumer appeal.

Meat quality is a critical determinant of consumer preference and economic value in the livestock industry. However, the relationship between carcass performance and meat quality remains poorly understood. In our study, we conducted an integrative analysis of transcriptomics and metabolomics to investigate the molecular mechanisms underlying meat quality differences in Hu sheep with high (HHS, n = 10) and low (LHS, n = 10) carcass performance. Phenotypic analysis revealed that the HHS group exhibited superior meat quality traits, including higher intramuscular fat (IMF) content (reflected in elevated marbling scores), along with lower shear force, drip loss, and cooking loss, compared to the LHS group. Transcriptomic analysis identified 376 differentially expressed genes (DEGs) enriched in pathways linked to lipid metabolism, such as the PPAR signaling pathway and long-chain fatty acid metabolic process. Weighted gene co-expression network analysis (WGCNA) revealed important modules and key genes (e.g., ELOVL6, PLIN1, and ARHGEF2) associated with meat quality traits. Metabolomic profiling identified 132 differentially accumulated metabolites (DAMs), with significant enrichment in amino acid metabolism pathways, including D-amino acid metabolism, arginine biosynthesis, and glycine, serine, and threonine metabolism. Integrative analysis of transcriptomic and metabolomic data highlighted six co-enriched pathways, such as the mTOR signaling pathway and amino acid metabolism, underscoring their role in regulating meat quality. These findings provide valuable insights into the genetic and metabolic networks driving meat quality variation and offer potential biomarkers for genetic selection and nutritional strategies to enhance both carcass yield and eating quality in Hu sheep. This research enhances knowledge of the molecular basis of meat quality and supports precision breeding in livestock production.

Hybridization effectively enhances breeding efficiency and significantly boosts sheep productivity. However, the epigenetic mechanisms underlying the superior production performance of crossbreds remain largely elusive. In this study, Hu sheep were crossbred with Suffolk rams used as the paternal line. We integrated RNA-seq, ATAC-seq, and CUT&Tag (H3K4me3, H3K4me1, H3K27ac, and H3K27me3) techniques to characterize epigenetic regulatory differences in the longissimus dorsi muscle between Hu sheep (HU) and crossbred progeny (SH). Phenotypic and transcriptomic analyses revealed that SH crossbred sheep exhibited superior growth performance (p < 0.05), and the upregulated genes in the Apelin signaling pathway were significantly correlated with eye muscle area (p < 0.05). Utilizing a Hidden Markov Model, we annotated 15 distinct chromatin states in both HU and SH sheep, systematically characterizing the dynamic epigenomic landscapes across the two breeds. In contrast to SH sheep, the genome of HU sheep exhibited enrichment of repressive chromatin modifications typified by H3K27me3. Strong active enhancers (EnhA) were significantly enriched within upregulated genes in SH. A total of 1862 SH-specific and 691 HU-specific EnhA elements were characterized in this study. Motif analysis revealed that SH-specific EnhA were enriched for myogenic MEF2 family motifs (p < 0.05), which promote muscle and vascular development. By integrating multi-omics data, we constructed a putative regulatory network potentially modulated by SH-specific enhancers, identifying CMKLR1, PPARGC1A, and TLE3 as the core hub genes. Collectively, this study provides a robust data resource, identifying candidate genes and regulatory elements associated with crossbreeding-related muscle phenotypes.

Body weight (BW) is a critical economic trait closely linked to livestock meat production performance and producer profitability. In the present study, we measured individual BW of 1070 male Hu sheep at six growth stages (80, 100, 120, 140, 160, and 180 days of age) and conducted descriptive statistical analyses. Results showed that the coefficient of variation (CV) for BW at each stage was higher than 13%. Additionally, we investigated the expression patterns of the FGF9 gene and its associations with single nucleotide polymorphisms (SNPs) and BW. Quantitative real-time PCR (qRT-PCR) revealed FGF9 is significantly higher expressed in the hypophysis tissues that in the other tested tissues. Association analyses indicated that the SNP FGF9:c.382-1264C>T was significantly associated with BW across different measurement periods. Finally, we performed assay for transposase-accessible chromatin using sequencing (ATAC-seq) and cleavage under targets and tagmentation (CUT&Tag) techniques to identify the OCRs (open chromatin regions) and regulatory regions in the hypophysis tissues of Hu sheep, and we obtained an average of 221243, 52692, and 20957.5 peaks in the ATAC-seq, H3K27ac, and H3K4me3 data per sample. Simultaneously, by integrating the SNPs of FGF9 and hypophysis tissue’s epigenomic data, we found that the SNP FGF9:c.382-1264C>T was located in the adjacent OCR- and H3K27ac-modified peaks. Therefore, we propose that the SNP FGF9:c.382-1264C>T plays an important role in regulating body weight in sheep. Overall, this study generated a valuable epigenetic dataset (ATAC-seq, H3K27ac, and H3K4me3) in sheep hypophysis tissue and identified a novel functional regulatory variant for improving body weight in sheep.