Background: Copy number variation (CNV) is an important source of structural variation in the mammalian genome. CNV assays present a new method to explore the genomic diversity of environmental adaptations in animals and plants and genes associated with complex traits. In this study, the genome-wide CNV distribution characteristics of 20 Tibetan sheep from two breeds (10 Oula sheep and 10 Panou sheep) were analysed using whole-genome resequencing to investigate the variation in the genomic structure of Tibetan sheep during breeding. Results: CNVs were detected using CNVnator, and the overlapping regions of CNVs between individual sheep were combined. Among them, a total of 60,429 CNV events were detected between the indigenous sheep breed (Oula) and the synthetic sheep breed (Panou). After merging the overlapping CNVs, 4927 CNV regions (CNVRs) were finally obtained. Of these, 4559 CNVRs were shared by two breeds, and there were 368 differential CNVRs. Deletion events have a higher percentage of occurrences than duplication events. Functional enrichment analysis showed that the shared CNVRs were significantly enriched in 163 GO terms and 62 KEGG pathways, which were mainly associated with organ development, neural regulation, immune regulation, digestion and metabolism. In addition, 140 QTLs overlapped with some of the CNVRs at more than 1 kb, such as average daily gain QTL, body weight QTL, and total lambs born QTL. Many of the CNV-overlapping genes such as PPP3CA, SSTR1 and FASN, overlap with the average daily weight gain and carcass weight QTL regions. Moreover, V_ST analysis showed that XIRP2, ABCB1, CA1, ASPA and EEF2 differed significantly between the synthetic breed and local sheep breed. The duplication of the ABCB1 gene may be closely related to adaptation to the plateau environment in Panou sheep, which deserves further study. Additionally, cluster analysis, based on all individuals, showed that the CNV clustering could be divided into two origins, indicating that some Tibetan sheep CNVs are likely to arise independently in different populations and contribute to population differences. Conclusions: Collectively, we demonstrated the genome-wide distribution characteristics of CNVs in Panou sheep by whole genome resequencing. The results provides a valuable genetic variation resource and help to understand the genetic characteristics of Tibetan sheep. This study also provides useful information for the improvement and breeding of Tibetan sheep in the future.

Yeast products (YP) are commonly used as rumen regulators, but their mechanisms of action are still unclear. Based on our previous studies, we questioned whether yeast products would have an impact on rumen solid-associated (SA) and liquid-associated (LA) microorganisms and alter rumen fermentation patterns. Thirty 3-month-old male sheep weighing 19.27 ± 0.45 kg were selected and randomized into three groups for 60 days: (1) basal diet group (CON group), (2) basal diet add 20 g YP per day (low YP, LYP group) and (3) basal diet add 40 g YP per day (high YP, HYP group). The results demonstrated that the addition of YP increased rumen cellulase activity, butyrate and total volatile fatty acid (TVFA) concentrations (p < 0.05), while it decreased rumen amylase activity and abnormal metabolites, such as lactate, lipopolysaccharides (LPS) and histamine (HIS) (p < 0.05). Metagenomic analysis of rumen microorganisms in three groups revealed that YP mainly influenced the microbial profiles of the SA system. YP increased the relative abundance of R. flavefaciens and decreased methanogens in the SA system (p < 0.05). With the addition of YP, the abundance of only a few lactate-producing bacteria increased in the SA system, including Streptococcus and Lactobacillus (p < 0.05). However, almost all lactate-utilizing bacteria increased in the LA system, including Megasphaera, Selenomonas, Fusobacterium and Veillonella (p < 0.05). In addition, YP increased the abundance of certain GHs family members, including GH43 and GH98 (p < 0.05), but decreased the abundance of some KEGG metabolic pathways involved in starch and sucrose metabolism, biosynthesis of antibiotics and purine metabolism, among others. In conclusion, the addition of YP to high-concentrate diets can change the abundance of major functional microbiota in the rumen, especially in the solid fraction, which in turn affects rumen fermentation patterns and improves rumen digestibility.

To address the bottleneck in meat production efficiency within China’s mutton sheep industry, this study established a two-generation crossbreeding program between WHS rams and STH ewes. Hybrid offspring (F1 and BC1) were evaluated for growth performance, slaughter traits, meat quality, and reproductive performance. The F1 generation exhibited significant improvements over STH in 6-month body weight (52.3 kg, +27.3%), dressing percentage (56.1%, +6.3%), and feed efficiency ratio (FER) of 4.6 (p < 0.05). The BC1 generation shows a mixed state of paternal and maternal characteristics and further enhanced these traits, achieving a 6-month body weight of 55.2 kg (+5.4% vs. F1), a dressing percentage of 58.3%, and an optimized gain-to-feed ratio (G:F) of 4.2 (−8.7%). Meat quality parameters, including shear force (32.5 N vs. 41.6 N in F1 vs. STH) and intramuscular fat content (4.5% vs. 3.8% in F1 vs. STH), demonstrated superior tenderness and marbling. Despite a decline in lambing rate (F1: 178%; BC1: 142%), the hybrids combined the dam’s adaptability with the sire’s meat traits, forming a novel germplasm for sustainable mutton production. This study provides a replicable model for balancing genetic improvement and ecological sustainability in central China.

While traveling through the epididymis, immature sheep spermatozoa undergo a sequence of processes that ultimately give them the capacity to swim and fertilize an egg. Different gene expression patterns may be found in the epididymal caput, corpus, and cauda, conferring variant or unique biological roles during epididymis development and sperm maturation. To search for candidate genes associated with ovine sperm maturation and assess their possible modulating mechanisms, we characterized gene expression in each epididymal segment derived from pre- and post-pubertal Tibetan sheep by RNA sequencing. Compared with pre-puberty, 7730 (3724 upregulated and 4006 downregulated), 7516 (3909 upregulated and 3607 downregulated), and 7586 (4115 elevated and 3471 downregulated) genes were found to be differentially expressed in the post-pubertal caput, corpus, and cauda epididymis, respectively, and real-time quantitative PCR verified the validity of the gathered expression patterns. Based on their functional annotations, most differential genes were assigned to the biological processes and pathways associated with cellular proliferation, differentiation, immune response, or metabolic activities. As for the post-pubertal epididymis, 2801, 197, and 186 genes were specifically expressed in the caput, corpus, and cauda, respectively. Functional annotation revealed that they were mainly enriched to various distinct biological processes associated with reproduction (including the caput binding of sperm to the zona pellucida; fertilization in the caput and corpus; and meiosis in the caput and cauda) and development (such as cell differentiation and developmental maturation in the caput; cell proliferation and metabolism in the corpus; and regulation of tube size and cell division/cell cycle in the cauda). Additionally, we focused on the identification of genes implicated in immunity and sperm maturation, and subsequent functional enrichment analysis revealed that immune-related genes mainly participated in the biological processes or pathways associated with the immune barrier (such as JAM3 and ITGA4/6/9) and immunosuppression (such as TGFB2, TGFBR1, TGFBR2, and SMAD3), thus protecting auto-immunogenic spermatozoa. Additionally, sperm maturation was mostly controlled by genes linked with cellular processes, including cell growth, proliferation, division, migration, morphogenesis, and junction. Altogether, these results suggest that most genes were differentially expressed in developmental epididymal regions to contribute to microenvironment development and sperm maturation. These findings help us better understand the epididymal biology, including sperm maturation pathways and functional differences between the epididymal regions in Tibetan sheep and other sheep breeds.

To address global protein shortages, black soldier fly (Hermetia illucens L.) larvae (BSFL) can be used as a sustainable feed alternative, with nutritional quality dependent on rearing substrates. This study compared quail feed (QF), food waste (FW), and quail manure (QM) for BSFL cultivation. Larvae raised on FW and QM had higher crude protein content (47.5–48.3%) than the QF group, while QF-reared larvae contained more fat (33.2%) than the other groups. QM led to larvae with the highest mineral content, and larvae from the FW group showed elevated calcium levels (5.6%). The FW-reared larvae also demonstrated superior growth, with a yield of 186.3 g/kg and a dry-matter conversion rate of 13.7%. Multi-omics analyses indicated substrate-specific differences in gut microbiota and metabolic pathways. FW promoted beneficial bacteria such as Lactobacillus, enhancing nutrient assimilation, while QF and QM upregulated lipid and mineral processing. For sustainable protein production through BSFL rearing, FW was the most suitable substrate among the three tested, offering a balanced combination of high larval protein content and efficient growth.

This study investigated the variations in the fecal microbiota and serum metabolome of prolific Hu sheep across different gestational stages to understand their physiological relationships. Fecal and blood samples were collected from 24 multiparous ewes across four stages: non-pregnant and gestational days 55, 85, and 110. Fecal microbial communities were analyzed via 16S rRNA gene sequencing, and serum metabolic profiles were assessed using liquid chromatography–tandem mass spectrometry (LC-MS)-based untargeted metabolomics. Serum biochemical analysis showed that pregnant ewes had decreased urea concentrations (p < 0.05), an early-gestation peak in total cholesterol, and a mid-gestation peak in triglycerides (p < 0.05). Fecal microbiota analysis indicated higher alpha diversity during gestation than in the non-pregnant stage (p < 0.05), with Firmicutes as the dominant phylum and stage-specific variations in genera such as Negativibacillus and Monoglobus. Metabolomics analysis identified 68 differential metabolites primarily assigned to lipid, amino acid, and steroid hormone pathways. Procrustes and Spearman correlation analyses showed statistical concordance between the fecal microbial community structure and the serum metabolome. Specific genera, including UCG-005, Alistipes, and unclassified Lachnospiraceae, correlated positively with metabolites such as pregnanediol 3-O-glucuronide and specific sphingomyelins. In conclusion, the progression of pregnancy in Hu sheep is characterized by concurrent shifts in the fecal microbiota and serum metabolites. These concurrent variations correlate with host nitrogen reallocation and lipid parameters, providing baseline reference data for the nutritional management of gestating ewes. These results provide a useful reference for future studies investigating maternal physiology, nutrition, and microbiome dynamics in prolific sheep breeds.