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Wang J, Fan H, Li M, Zhao K, Xia S, Chen Y, Shao J, Tang T, Bai X, Liu Z, Lu Y, Chen X, Sun W, Jia X, Lai S. Integration of Non-Coding RNA and mRNA Profiles Reveals the Mechanisms of Rumen Development Induced by Different Types of Diet in Calves. Genes (Basel) 2023; 14:genes14051093. [PMID: 37239453 DOI: 10.3390/genes14051093] [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: 03/27/2023] [Revised: 05/10/2023] [Accepted: 05/12/2023] [Indexed: 05/28/2023] Open
Abstract
Selecting suitable feed types and understanding the gastrointestinal digestive mechanism are helpful for the growth and health of calves in intensive dairy farming. However, the effects on rumen development of changing the molecular genetic basis and the regulatory mechanism by using different feed types are still unclear. Nine 7-day-old Holstein bull calves were randomly divided into GF (concentrate), GFF (alfalfa: oat grass = 3:2) and TMR (concentrate: alfalfa grass: oat grass: water = 0.30:0.12:0.08:0.50) diet experiment groups. Rumen tissue and serum samples were collected for physiological and transcriptomic analysis after 80 days. The results showed that serum α-amylase content and ceruloplasmin activity were significantly higher in the TMR group, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis ncRNAs and mRNAs were significantly enriched in the pathways of rumen epithelial development and stimulated rumen cell growth, including the Hippo signaling pathway, Wnt signaling pathway, thyroid hormone signaling pathway, ECM-receptor interaction and the absorption of protein and fat. The circRNAs/lncRNA-miRNAs-mRNA networks constructed, including novel_circ_0002471, novel_circ_0012104, TCONS_00946152, TCONS_00960915, bta-miR-11975, bta-miR-2890, PADI3 and CLEC6A, participated in metabolic pathways of lipid, immune system, oxidative stress and muscle development. In conclusion, the TMR diet could improve rumen digestive enzyme activities, stimulate rumen nutrient absorption and stimulate the DEGs related to energy homeostasis and microenvironment balance, and is thus better than the GF and GFF diets for promoting rumen growth and development.
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Affiliation(s)
- Jie Wang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Huimei Fan
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Mianying Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Kaisen Zhao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Siqi Xia
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yang Chen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jiahao Shao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Tao Tang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xue Bai
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Zheliang Liu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yusheng Lu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiangrui Chen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Wenqiang Sun
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xianbo Jia
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Songjia Lai
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
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Wang Q, Gao B, Yue X, Cui Y, Loor JJ, Dai X, Wei X, Xu C. Weighted Gene Co-expression Network Analysis Identifies Specific Modules and Hub Genes Related to Subacute Ruminal Acidosis. Front Vet Sci 2022; 9:897714. [PMID: 35754546 PMCID: PMC9226770 DOI: 10.3389/fvets.2022.897714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 04/26/2022] [Indexed: 11/13/2022] Open
Abstract
Weighted gene co-expression network analysis (WGCNA) was used to understand the pathogenesis of subacute ruminal acidosis (SARA) and identify potential genes related to the disease. Microarray data from dataset GSE143765, which included 22 cows with and nine cows without SARA, were downloaded from the NCBI Gene Expression Omnibus (GEO). Results of WGCNA identified highly correlated modules of sample genes, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses allowed further biological insights into SARA-related modules. The protein-protein interaction (PPI) network, modules from the PPI network, and cistron annotation enrichment of modules were also analyzed. A total of 14,590 DEGs were used for the WGCNA. Construction of a protein-protein network identified DCXR, MMP15, and MMP17 as hub genes. Functional annotation showed that DCXR mainly exhibited L-xylulose reductase (NADP+) activity, glucose metabolic process, xylulose metabolic process, and carbonyl reductase (NADPH) activity, which are involved in the pentose and glucuronate interconversion pathways. MMP15 and MMP17 mainly have a collagen catabolic process. Overall, the results of this study aid the clarification of the biological and metabolic processes associated with SARA at the molecular level. The data highlight potential mechanisms for the future development of intervention strategies to reduce or alleviate the risk of SARA.
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Affiliation(s)
- Qiuju Wang
- College of Animal Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China.,Key Laboratory of Low-Carbon Green Agriculture in Northeastern China, Ministry of Agriculture and Rural Affairs P. R. China, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Bingnan Gao
- College of Animal Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Xueqing Yue
- College of Animal Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Yizhe Cui
- College of Animal Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Juan J Loor
- Department of Animal Sciences, Division of Nutritional Sciences, University of Illinois, Urbana, IL, United States
| | - Xiaoxia Dai
- The Royal Veterinary College, University of London, London, United Kingdom
| | - Xu Wei
- Department of Biosystems, Division of Animal and Human Health Engineering, KU Leuven, Leuven, Belgium
| | - Chuang Xu
- College of Animal Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China.,Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, Daqing, China
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