Combined transcriptome and metabolome analysis reveals breed-specific regulatory mechanisms in Dorper and Tan sheep.

BACKGROUND: Dorper and Tan sheep are renowned for their rapid growth and exceptional meat quality, respectively. Previous research has provided evidence of the impact of gut microbiota on breed characteristics. The precise correlation between the gastrointestinal tract and peripheral organs in each breed is still unclear. Investigating the metabolic network of the intestinal organ has the potential to improve animal growth performance and enhance economic benefits through the regulation of intestinal metabolites. RESULTS: In this study, we identified the growth advantage of Dorper sheep and the high fat content of Tan sheep. A transcriptome study of the brain, liver, skeletal muscle, and intestinal tissues of both breeds revealed 3,750 differentially expressed genes (DEGs). The genes PPARGC1A, LPL, and PHGDH were found to be highly expressed in Doper, resulting in the up-regulation of pathways related to lipid oxidation, glycerophospholipid metabolism, and amino acid anabolism. Tan sheep highly express the BSEP, LDLR, and ACHE genes, which up-regulate the pathways involved in bile transport and cholesterol homeostasis. Hindgut content analysis identified 200 differentially accumulated metabolites (DAMs). Purines, pyrimidines, bile acids, and fatty acid substances were more abundant in Dorper sheep. Based on combined gene and metabolite analyses, we have identified glycine, serine, and threonine metabolism, tryptophan metabolism, bile secretion, cholesterol metabolism, and neuroactive ligand-receptor interaction as key factors contributing to the differences among the breeds. CONCLUSIONS: This study indicates that different breeds of sheep exhibit unique breed characteristics through various physiological regulatory methods. Dorper sheep upregulate metabolic signals related to glycine, serine, and threonine, resulting in an increase in purine and pyrimidine substances. This, in turn, promotes the synthesis of amino acids and facilitates body development, resulting in a faster rate of weight gain. Tan sheep accelerate bile transport, reduce bile accumulation in the intestine, and upregulate cholesterol homeostasis signals in skeletal muscles. This promotes the accumulation of peripheral and intramuscular fat, resulting in improved meat quality. This work adopts a joint analysis method of multi-tissue transcriptome and gut metabolome, providing a successful case for analyzing the mechanisms underlying the formation of various traits.

Contribution of gut microbiomes and their metabolomes to the performance of Dorper and Tan sheep.

Background: Livestock is an excellent source of high nutritional value protein for humans; breeding livestock is focused on improving meat productivity and quality. Dorper sheep is a distinguished breed with an excellent growth performance, while Tan sheep is a Chinese local breed famous for its delicious meat. Several studies have demonstrated that the composition of gut microbiome and metabolome modulate host phenotype. Methods: In the present study, we performed 16S amplicon sequencing and metabolomic analyses of the rumen and hindgut microbiome of 8-month-old Dorper and Tan sheep, raised under identical feeding and management conditions, to explore the potential effects of gut microbiome and its metabolites on growth performance and meat quality. Results: Our study identified Lactobacillus, a marker genus in the rumen, to be significantly associated with the levels of fumaric acid, nicotinic acid, and 2-deoxyadenosine (P-value < 0.05). Statistical analysis showed that nicotinic acid was significantly negatively correlated with body weight (P-value < 0.01), while 2-deoxyadenosine was significantly positively correlated with fatty acids content (P-value < 0.05). There was a biologically significant negative correlation between Phascolarctobacterium and deoxycytidine levels in the hindgut. Deoxycytidine was significantly positively correlated with body weight, protein, and amino acid content. Differences in rumen fermentation patterns that are distinctive among breeds were identified. Tan sheep mainly used Lactobacillus and fumaric acid-mediated pyruvic acid for energy supply, while Dorper sheep utilize glycogenic amino acids. The difference of iron metabolism in the hindgut of Dorper sheep affects lipid production, while Phascolarctobacterium in Tan sheep is related to roughage tolerance. The accumulation of nucleosides promotes the growth performance of Dorper sheep. Conclusion: These findings provide insights into how the microbiome-metabolome-dependent mechanisms contribute to growth rate and fat contents in different breeds. This fundamental research is vital to identifying the dominant traits of breeds, improving growth rate and meat quality, and establishing principles for precision feeding.

Integrated analysis of the whole transcriptome of skeletal muscle reveals the ceRNA regulatory network related to the formation of muscle fibers in Tan sheep.

Meat quality is highly influenced by the kind of muscle fiber, and it can be significantly improved by increasing the percentage of slow-twitch fibers. It is still not known which genes control the formation of muscle fibers or how those genes control the process of forming in sheep until now. In this study, we used high-throughput RNA sequencing to assess the expression profiles of coding and noncoding RNAs in muscle tissue of Tan sheep and Dorper sheep. To investigate the molecular processes involved in the formation of muscle fibers, we collected two different muscle tissues, longissimus dorsi and biceps femoris, from Tan sheep and Dorper sheep. The longissimus dorsi of Tan sheep and Dorper sheep displayed significantly differential expression levels for 214 lncRNAs, 25 mRNAs, 4 miRNAs, and 91 circRNAs. Similarly, 172 lncRNAs, 35 mRNAs, 12 miRNAs, and 95 circRNAs were differentially expressed in the biceps femoris of Tan sheep and Dorper sheep according to the expression profiling. GO and KEGG annotation revealed that these differentially expressed genes and noncoding RNAs were related to pathways of the formation of muscle fiber, such as the Ca2+, FoxO, and AMPK signaling pathways. Several key genes are involved in the formation of muscle fibers, including ACACB, ATP6V0A1, ASAH1, EFHB, MYL3, C1QTNF7, SFSWAP, and FBXL5. RT-qPCR verified that the expression patterns of randomly selected differentially expressed transcripts were highly consistent with those obtained by RNA sequencing. A total of 10 lncRNAs, 12 miRNAs, 20 circRNAs, and 19 genes formed lncRNA/circRNA-miRNA-gene networks, indicating that the formation of muscle fiber in Tan sheep is controlled by intricate regulatory networks of coding and noncoding genes. Our findings suggested that specific ceRNA subnetworks, such as circ_0017336-miR-23a-FBXL5, may be critical in the regulation of the development of muscle fibers, offering a valuable resource for future study of the development of muscle fibers in this animal species. The findings increase our understanding of the variety in how muscle fibers originate in various domestic animals and lay the groundwork for future research into new systems that regulate the development of muscle.

Dynamic changes of genomic methylation profiles at different growth stages in Chinese Tan sheep.

BACKGROUND: Tan sheep, an important local sheep breed in China, is famous for their fur quality. One-month-old Tan sheep have white, curly hair with beautiful flower spikes, commonly known as "nine bends", which has high economic value. However, the "nine bends" characteristic gradually disappears with age; consequently, the economic value of the Tan sheep decreases. Age-related changes in DNA methylation have been reported and may be responsible for age-induced changes in gene expression. Until now, no genome-wide surveys have been conducted to identify potential DNA methylation sites involved in different sheep growth stages. In this study we investigated the dynamic changes of genome-wide DNA methylation profiles in Tan sheep using DNA from skin and deep whole-genome bisulfite sequencing, and compared the DNA methylation levels at three different growth stages: 1, 24, and 48 months old (mon1, mon24, and mon48, respectively). RESULTS: In this study, 11 skin samples from three growth stages (four for mon1, four for mon24, and three for mon48) were used for DNA methylation analysis and gene expression profiling. There were 52, 288 and 236 differentially methylated genes (DMGs) identified between mon1 and mon24, mon1 and mon48, and mon24 and mon48, respectively. Of the differentially methylated regions, 1.11%, 7.61%, and 7.65% were in the promoter in mon1 vs. mon24, mon24 vs. mon48, and mon1 vs. mon48, respectively. DMGs were enriched in the MAPK and WNT signaling pathways, which are related to age growth and hair follicle morphogenesis processes. There were 51 DMGs associated with age growth and curly fleece formation. Four DMGs between mon1 and mon48 (KRT71, CD44, ROR2 and ZDHHC13) were further validated by bisulfite sequencing. CONCLUSIONS: This study revealed dynamic changes in the genomic methylation profiles of mon1, mon24, and mon48 sheep, and the percentages of methylated cytosines were 3.38%, 2.85% and 4.17%, respectively. Of the DMGs, KRT71 and CD44 were highly methylated in mon1, and ROR2 and ZDHHC13 were highly methylated in mon48. These findings provide foundational information that may be used to develop strategies for potentially retaining the lamb fur and thus improving the economic value of Tan sheep.

Cloning and polymorphism analysis of prion protein gene in domestic bactrian camel in China.

Up to now, little is known about the prion protein gene (PRNP) of domestic bactrian camels, and no polymorphisms of the bactrian camel PRNP have been analyzed or reported. In this study, we cloned and analyzed the PRNP sequences of 89 domestic bactrian camels. The results showed that the amino acid sequence of bactrian camel PrP starts with the consensus sequence MVKSH, with almost identical amino acid sequence to the PrP of dromedary camels. A four octapeptide PHGGGWGQ repeat region follows a nonapeptide (PQGGGGWGQ) in the N-terminal of deduced amino acid sequence from residues 54 to 95. Polymorphisms of PRNP in both species of camels were observed in codons 16(A→V), 17(M→T), 120(N→S), 176(R→K), 215(I→V), 234(S→Y), 237(Y→S), and 239(Q→G) by comparing with other ruminants. The PrP gene nucleotide sequence alignments of bactrian camels (HQ204566.1 and HQ204567.1) showed high identity with dromedary camel (99.2%, 99.1%), sheep (91.9%, 91.8%) and cattle (91.8%, 91.6%). This study provides valuable data for future research on susceptibility or resistance of camels to prion diseases.