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Bai Y, Li J, Wei Y, Chen Z, Liu Z, Guo D, Jia X, Niu Y, Shi B, Zhang X, Zhao Z, Hu J, Han X, Wang J, Liu X, Li S. Proteome Analysis Related to Unsaturated Fatty Acid Synthesis by Interfering with Bovine Adipocyte ACSL1 Gene. Antioxidants (Basel) 2024; 13:641. [PMID: 38929080 PMCID: PMC11200461 DOI: 10.3390/antiox13060641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Revised: 05/21/2024] [Accepted: 05/22/2024] [Indexed: 06/28/2024] Open
Abstract
Unsaturated fatty acids (UFAs) in beef play a vital role in promoting human health. Long-chain fatty acyl-CoA synthase 1 (ACSL1) is a crucial gene for UFA synthesis in bovine adipocytes. To investigate the protein expression profile during UFA synthesis, we performed a proteomic analysis of bovine adipocytes by RNA interference and non-interference with ACSL1 using label-free techniques. A total of 3558 proteins were identified in both the NC and si-treated groups, of which 1428 were differentially expressed proteins (DEPs; fold change ≥ 1.2 or ≤ 0.83 and p-value < 0.05). The enrichment analysis of the DEPs revealed signaling pathways related to UFA synthesis or metabolism, including cAMP, oxytocin, fatty acid degradation, glycerol metabolism, insulin, and the regulation of lipolysis in adipocytes (p-value < 0.05). Furthermore, based on the enrichment analysis of the DEPs, we screened 50 DEPs that potentially influence the synthesis of UFAs and constructed an interaction network. Moreover, by integrating our previously published transcriptome data, this study established a regulatory network involving differentially expressed long non-coding RNAs (DELs), highlighting 21 DEPs and 13 DELs as key genes involved in UFA synthesis. These findings present potential candidate genes for further investigation into the molecular mechanisms underlying UFA synthesis in bovines, thereby offering insights to enhance the quality of beef and contribute to consumer health in future studies.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Zhidong Zhao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (Y.B.); (J.L.); (Y.W.); (Z.C.); (Z.L.); (D.G.); (X.J.); (Y.N.); (B.S.); (X.Z.); (X.H.); (J.W.); (X.L.); (S.L.)
| | - Jiang Hu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (Y.B.); (J.L.); (Y.W.); (Z.C.); (Z.L.); (D.G.); (X.J.); (Y.N.); (B.S.); (X.Z.); (X.H.); (J.W.); (X.L.); (S.L.)
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Li M, Lu Y, Gao Z, Yue D, Hong J, Wu J, Xi D, Deng W, Chong Y. Pan-Omics in Sheep: Unveiling Genetic Landscapes. Animals (Basel) 2024; 14:273. [PMID: 38254442 PMCID: PMC10812798 DOI: 10.3390/ani14020273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/04/2024] [Accepted: 01/14/2024] [Indexed: 01/24/2024] Open
Abstract
Multi-omics-integrated analysis, known as panomics, represents an advanced methodology that harnesses various high-throughput technologies encompassing genomics, epigenomics, transcriptomics, proteomics, and metabolomics. Sheep, playing a pivotal role in agricultural sectors due to their substantial economic importance, have witnessed remarkable advancements in genetic breeding through the amalgamation of multiomics analyses, particularly with the evolution of high-throughput technologies. This integrative approach has established a robust theoretical foundation, enabling a deeper understanding of sheep genetics and fostering improvements in breeding strategies. The comprehensive insights obtained through this approach shed light on diverse facets of sheep development, including growth, reproduction, disease resistance, and the quality of livestock products. This review primarily focuses on the application of principal omics analysis technologies in sheep, emphasizing correlation studies between multiomics data and specific traits such as meat quality, wool characteristics, and reproductive features. Additionally, this paper anticipates forthcoming trends and potential developments in this field.
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Affiliation(s)
- Mengfei Li
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (M.L.); (Y.L.); (Z.G.); (D.Y.); (J.H.); (J.W.); (D.X.); (W.D.)
| | - Ying Lu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (M.L.); (Y.L.); (Z.G.); (D.Y.); (J.H.); (J.W.); (D.X.); (W.D.)
| | - Zhendong Gao
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (M.L.); (Y.L.); (Z.G.); (D.Y.); (J.H.); (J.W.); (D.X.); (W.D.)
| | - Dan Yue
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (M.L.); (Y.L.); (Z.G.); (D.Y.); (J.H.); (J.W.); (D.X.); (W.D.)
- Faculty of Animal Science and Technology, Yuxi Agricultural Vocational and Technical College, Yuxi 653106, China
| | - Jieyun Hong
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (M.L.); (Y.L.); (Z.G.); (D.Y.); (J.H.); (J.W.); (D.X.); (W.D.)
| | - Jiao Wu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (M.L.); (Y.L.); (Z.G.); (D.Y.); (J.H.); (J.W.); (D.X.); (W.D.)
| | - Dongmei Xi
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (M.L.); (Y.L.); (Z.G.); (D.Y.); (J.H.); (J.W.); (D.X.); (W.D.)
| | - Weidong Deng
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (M.L.); (Y.L.); (Z.G.); (D.Y.); (J.H.); (J.W.); (D.X.); (W.D.)
| | - Yuqing Chong
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (M.L.); (Y.L.); (Z.G.); (D.Y.); (J.H.); (J.W.); (D.X.); (W.D.)
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Kalds P, Zhou S, Gao Y, Cai B, Huang S, Chen Y, Wang X. Genetics of the phenotypic evolution in sheep: a molecular look at diversity-driving genes. Genet Sel Evol 2022; 54:61. [PMID: 36085023 PMCID: PMC9463822 DOI: 10.1186/s12711-022-00753-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 08/29/2022] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND After domestication, the evolution of phenotypically-varied sheep breeds has generated rich biodiversity. This wide phenotypic variation arises as a result of hidden genomic changes that range from a single nucleotide to several thousands of nucleotides. Thus, it is of interest and significance to reveal and understand the genomic changes underlying the phenotypic variation of sheep breeds in order to drive selection towards economically important traits. REVIEW Various traits contribute to the emergence of variation in sheep phenotypic characteristics, including coat color, horns, tail, wool, ears, udder, vertebrae, among others. The genes that determine most of these phenotypic traits have been investigated, which has generated knowledge regarding the genetic determinism of several agriculturally-relevant traits in sheep. In this review, we discuss the genomic knowledge that has emerged in the past few decades regarding the phenotypic traits in sheep, and our ultimate aim is to encourage its practical application in sheep breeding. In addition, in order to expand the current understanding of the sheep genome, we shed light on research gaps that require further investigation. CONCLUSIONS Although significant research efforts have been conducted in the past few decades, several aspects of the sheep genome remain unexplored. For the full utilization of the current knowledge of the sheep genome, a wide practical application is still required in order to boost sheep productive performance and contribute to the generation of improved sheep breeds. The accumulated knowledge on the sheep genome will help advance and strengthen sheep breeding programs to face future challenges in the sector, such as climate change, global human population growth, and the increasing demand for products of animal origin.
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Affiliation(s)
- Peter Kalds
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
- Department of Animal and Poultry Production, Faculty of Environmental Agricultural Sciences, Arish University, El-Arish, 45511 Egypt
| | - Shiwei Zhou
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100 China
| | - Yawei Gao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Bei Cai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Shuhong Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Yulin Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs, Yangling, 712100 China
| | - Xiaolong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs, Yangling, 712100 China
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Development and Application of a High-Resolution Melting Analysis with Unlabeled Probes for the Screening of Short-Tailed Sheep TBXT Heterozygotes. Animals (Basel) 2022; 12:ani12060792. [PMID: 35327188 PMCID: PMC8944613 DOI: 10.3390/ani12060792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/17/2022] [Accepted: 03/17/2022] [Indexed: 12/04/2022] Open
Abstract
Simple Summary TBXT (c.333G > C; c.334G > T) has been identified as a molecular genetic marker in short-tailed sheep. This paper describes a high-resolution melting (HRM) analysis using unlabeled probes and asymmetric PCR for the detection of genetic variants of TBXT in short-tailed sheep populations. The detection results of this method are consistent with those of Sanger sequencing and can help farmers with marker-assisted breeding. Abstract The short-tailed phenotype has long been considered one of the best traits for population genetic improvement in sheep breeding. In short-tailed sheep, not only is tail fat eliminated but also the pubic area is exposed due to the lack of a tail covering, giving them an advantage in reproduction. Recent studies have shown that two linked mutations in sheep TBXT at nucleotides 333 and 334 are associated with the short-tailed phenotype. In the population of short-tailed sheep, several heterozygous mutants of this gene are found. In our research, we used high-resolution melting (HRM) to identify homozygous and heterozygous genotypes in a flock of short-tailed sheep and compared the results with those of Sanger sequencing, which were identical. This demonstrates that our established HRM method, a rapid and inexpensive genotyping method, can be used to identify homozygous and heterozygous individuals in short-tailed sheep flocks.
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