Isobaric Tags for Relative and Absolute Quantification-Based Proteomics Reveals Candidate Proteins of Fat Deposition in Chinese Indigenous Sheep With Morphologically Different Tails

Abstract

Background: Chinese indigenous sheep can be classified into two types according to their tail morphology: fat-rumped and thin-tailed sheep, of which the typical breeds are Altay sheep and Tibetan sheep, respectively.Methods: To identify the differentially expressed proteins (DEPs) underlying the phenotypic differences between tail types, we used isobaric tags for relative and absolute quantification (iTRAQ) combined with multi-dimensional liquid chromatography tandem-mass spectrometry (LC-MS/MS) technology to detect candidate proteins. We then subjected these to a database search and identified the DEPs. Finally, bioinformatics technology was used to carry out Gene Ontology (GO) functional and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses.Results: A total of 3,248 proteins were identified, of which 44 were up-regulated and 40 were down-regulated DEPs. Analyzing their GO function terms and KEGG pathways revealed that the functions of these DEPs are mainly binding, catalytic activity, structural molecule activity, molecular function regulator, and transporter activity. Among the genes encoding the DEPs, APOA2, GALK1, ADIPOQ, and NDUFS4 are associated with fat formation and metabolism.Conclusion: The APOA2, GALK1, ADIPOQ, and NDUFS4 genes may be involved in the deposition of fat in the tail of sheep. This study provides a scientific basis for the breeding of thin-tailed sheep.

Proteome Analysis Related to Unsaturated Fatty Acid Synthesis by Interfering with Bovine Adipocyte ACSL1 Gene

“…Additionally, the peptide length distribution, number of unique peptides, and protein molecular weight distribution in the proteome analysis met the research conditions. Notably, this study detected a higher number of DEPs (1428) compared to previous studies [ 17 , 27 , 28 , 47 ], which can be attributed to variations in the screening thresholds employed for the differential analysis. The screening threshold used in some studies may be too high, resulting in the exclusion of important genes or proteins [ 20 , 27 ].…”

“…Conversely, setting the screening threshold too low for differential analysis may prolong the filtration process of irrelevant information during analysis. Nevertheless, this approach could potentially unveil a greater number of key genes or proteins [ 17 , 47 ]. Furthermore, the expression pattern of the DEPs observed in this study aligns with previous research findings, suggesting that differential proteins between different species have comparable expression patterns.…”

“…Proteomic analysis is a robust technique for the investigation of protein expression patterns and has been extensively employed in studies involving sheep [ 17 , 18 ], chickens [ 19 , 20 , 21 ], and pigs [ 22 , 23 ]. It is worth noting that research on bovine FA metabolism from the perspective of transcriptomics or proteomics is still in its nascent stage.…”

Pan-Omics in Sheep: Unveiling Genetic Landscapes

“…To discern differentially expressed proteins (DEPs) associated with tail phenotypes, advanced proteomics technology identified 3248 proteins, among which 44 were upregulated and 40 were downregulated DEPs. Notably, APOA2, GALK1, ADIPOQ, and NDUFS4 were implicated in sheep tail fat deposition and metabolism [59]. A comparative proteomic analysis of rumen epithelial tissues across different sheep ages revealed 4523 proteins, indicating the involvement of processes like glutathione, the Wnt signaling pathway, and the Notch signaling pathway in rumen epithelial cell growth [60].…”

Development and Application of a High-Resolution Melting Analysis with Unlabeled Probes for the Screening of Short-Tailed Sheep TBXT Heterozygotes

“…The tails of most animals serve multiple functions in nature [1], including balance, movement, information exchange with peers [1,2], and swatting flies to remove them from the animals. After a long period of domestication, sheep with different tail length phenotypes have been developed [3,4], including the fat-long-tail, fat-short-tail, fat-waisttail, slender tail, and thin-short-tail phenotypes. There is evidence [5,6] that the ancestors of sheep had a narrow tail phenotype that evolved into a fat-tail phenotype as they adapted to their frigid living environment.…”