|
1
|
Xu Y, Wang H, Cheng F, Chen K, Lei G, Deng Z, Wu X, Liu C, Si J, Liang J. Screening for Genes Related to Meat Production Traits in Duroc × Bama Xiang Crossbred Pigs by Whole Transcriptome Sequencing. Animals (Basel) 2024; 14:2347. [PMID: 39199880 PMCID: PMC11350711 DOI: 10.3390/ani14162347] [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: 06/30/2024] [Revised: 08/02/2024] [Accepted: 08/11/2024] [Indexed: 09/01/2024] Open
Abstract
The meat production traits of pigs are influenced by the expression regulation of multiple gene types, including mRNAs, miRNAs, and lncRNAs. To study the differences in meat production traits at the transcriptional level among individuals with different growth rates, the longissimus dorsi samples from eight Duroc × Bama Xiang F2 crossbred pigs with a fast growth rate (high gTroup) or a slow growth rate (low group) were selected to perform whole transcriptome sequencing and ceRNA regulatory network construction. This study first analyzed the differences in physiological and biochemical indicators, muscle histological characteristics, and muscle fiber types. A total of 248 mRNAs, 25 miRNAs, and 432 lncRNAs were identified as differentially expressed by whole transcriptome sequencing. Key genes that may influence meat production traits include MTMR14, PPP1R3A, PYGM, PGAM2, MYH1, and MYH7. The ceRNA regulatory network map showed that ENSSSCG00000042061-ssc-mir-208b-MYH7, ENSSSCG00000042223-ssc-mir-146a-MTMR14, ENSSSCG00000045539-ssc-mir-9-3-MYH1, and ENSSSCG00000047852-ssc-mir-103-1-PPP1R3A may be the key factors affecting meat production traits through their regulatory relationships. This study provides valuable insights into the molecular mechanisms underlying porcine muscle development and can aid in improving meat production traits.
Collapse
Affiliation(s)
- Yupei Xu
- College of Animal Science & Technology, Guangxi University, Nanning 530004, China; (Y.X.); (H.W.); (F.C.); (K.C.); (G.L.); (Z.D.); (X.W.); (C.L.)
| | - Hui Wang
- College of Animal Science & Technology, Guangxi University, Nanning 530004, China; (Y.X.); (H.W.); (F.C.); (K.C.); (G.L.); (Z.D.); (X.W.); (C.L.)
| | - Feng Cheng
- College of Animal Science & Technology, Guangxi University, Nanning 530004, China; (Y.X.); (H.W.); (F.C.); (K.C.); (G.L.); (Z.D.); (X.W.); (C.L.)
| | - Kuirong Chen
- College of Animal Science & Technology, Guangxi University, Nanning 530004, China; (Y.X.); (H.W.); (F.C.); (K.C.); (G.L.); (Z.D.); (X.W.); (C.L.)
| | - Guofeng Lei
- College of Animal Science & Technology, Guangxi University, Nanning 530004, China; (Y.X.); (H.W.); (F.C.); (K.C.); (G.L.); (Z.D.); (X.W.); (C.L.)
| | - Zhongrong Deng
- College of Animal Science & Technology, Guangxi University, Nanning 530004, China; (Y.X.); (H.W.); (F.C.); (K.C.); (G.L.); (Z.D.); (X.W.); (C.L.)
| | - Xiaoxiao Wu
- College of Animal Science & Technology, Guangxi University, Nanning 530004, China; (Y.X.); (H.W.); (F.C.); (K.C.); (G.L.); (Z.D.); (X.W.); (C.L.)
| | - Cong Liu
- College of Animal Science & Technology, Guangxi University, Nanning 530004, China; (Y.X.); (H.W.); (F.C.); (K.C.); (G.L.); (Z.D.); (X.W.); (C.L.)
| | - Jinglei Si
- College of Animal Science & Technology, Guangxi University, Nanning 530004, China; (Y.X.); (H.W.); (F.C.); (K.C.); (G.L.); (Z.D.); (X.W.); (C.L.)
- Guangxi State Farms Yongxin Animal Husbandry Group Co., Ltd., Nanning 530022, China
| | - Jing Liang
- College of Animal Science & Technology, Guangxi University, Nanning 530004, China; (Y.X.); (H.W.); (F.C.); (K.C.); (G.L.); (Z.D.); (X.W.); (C.L.)
| |
Collapse
|
|
2
|
Jiao Y, Hao L, Xia P, Cheng Y, Song J, Chen X, Wang Z, Ma Z, Zheng S, Chen T, Zhang Y, Yu H. Identification of Potential miRNA-mRNA Regulatory Network Associated with Pig Growth Performance in the Pituitaries of Bama Minipigs and Landrace Pigs. Animals (Basel) 2022; 12:3058. [PMID: 36359184 PMCID: PMC9657654 DOI: 10.3390/ani12213058] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/02/2022] [Accepted: 11/03/2022] [Indexed: 08/27/2023] Open
Abstract
Pig growth performance is one of the criteria for judging pork production and is influenced by genotype and external environmental factors such as feeding conditions. The growth performance of miniature pigs, such as Bama minipigs, differs considerably from that of the larger body size pigs, such as Landrace pigs, and can be regarded as good models in pig growth studies. In this research, we identified differentially expressed genes in the pituitary gland of Bama minipigs and Landrace pigs. Through the pathway enrichment analysis, we screened the growth-related pathways and the genes enriched in the pathways and established the protein-protein interaction network. The RNAHybrid algorithm was used to predict the interaction between differentially expressed microRNAs and differentially expressed mRNAs. Four regulatory pathways (Y-82-ULK1/CDKN1A, miR-4334-5p-STAT3/PIK3R1/RPS6KA3/CAB39L, miR-4331-SCR/BCL2L1, and miR-133a-3p-BCL2L1) were identified via quantitative real-time PCR to detect the expression and correlation of candidate miRNAs and mRNAs. In conclusion, we revealed potential miRNA-mRNA regulatory networks associated with pig growth performance in the pituitary glands of Bama minipigs and Landrace pigs, which may help to elucidate the underlying molecular mechanisms of growth differences in pigs of different body sizes.
Collapse
Affiliation(s)
- Yingying Jiao
- College of Animal Science, Jilin University, Changchun 130061, China
| | - Linlin Hao
- College of Animal Science, Jilin University, Changchun 130061, China
| | - Peijun Xia
- College of Animal Science, Jilin University, Changchun 130061, China
| | - Yunyun Cheng
- Ministry of Health Key Laboratory of Radiobiology, College of Public Health, Jilin University, Changchun 130061, China
| | - Jie Song
- College of Animal Science, Jilin University, Changchun 130061, China
| | - Xi Chen
- College of Animal Science, Jilin University, Changchun 130061, China
| | - Zhaoguo Wang
- College of Animal Science, Jilin University, Changchun 130061, China
| | - Ze Ma
- College of Animal Science, Jilin University, Changchun 130061, China
| | - Shuo Zheng
- College of Animal Science, Jilin University, Changchun 130061, China
| | - Ting Chen
- Chinese National Engineering Research Center for Breeding Swine Industry, SCAU-Alltech Research Joint Alliance, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Ying Zhang
- College of Animal Science, Jilin University, Changchun 130061, China
| | - Hao Yu
- College of Animal Science, Jilin University, Changchun 130061, China
| |
Collapse
|
|
3
|
Muroya S. An insight into farm animal skeletal muscle metabolism based on a metabolomics approach. Meat Sci 2022; 195:108995. [DOI: 10.1016/j.meatsci.2022.108995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 09/21/2022] [Accepted: 09/23/2022] [Indexed: 01/10/2023]
|
|
4
|
Zhang J, Liu P, He M, Wang Y, Kui H, Jin L, Li D, Li M. Reorganization of 3D genome architecture across wild boar and Bama pig adipose tissues. J Anim Sci Biotechnol 2022; 13:32. [PMID: 35277200 PMCID: PMC8917667 DOI: 10.1186/s40104-022-00679-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 01/10/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A growing body of evidence has revealed that the mammalian genome is organized into hierarchical layers that are closely correlated with and may even be causally linked with variations in gene expression. Recent studies have characterized chromatin organization in various porcine tissues and cell types and compared them among species and during the early development of pigs. However, how chromatin organization differs among pig breeds is poorly understood. RESULTS In this study, we investigated the 3D genome organization and performed transcriptome characterization of two adipose depots (upper layer of backfat [ULB] and greater omentum [GOM]) in wild boars and Bama pigs; the latter is a typical indigenous pig in China. We found that over 95% of the A/B compartments and topologically associating domains (TADs) are stable between wild boars and Bama pigs. In contrast, more than 70% of promoter-enhancer interactions (PEIs) are dynamic and widespread, involving over a thousand genes. Alterations in chromatin structure are associated with changes in the expression of genes that are involved in widespread biological functions such as basic cellular functions, endocrine function, energy metabolism and the immune response. Approximately 95% and 97% of the genes associated with reorganized A/B compartments and PEIs in the two pig breeds differed between GOM and ULB, respectively. CONCLUSIONS We reported 3D genome organization in adipose depots from different pig breeds. In a comparison of Bama pigs and wild boar, large-scale compartments and TADs were mostly conserved, while fine-scale PEIs were extensively reorganized. The chromatin architecture in these two pig breeds was reorganized in an adipose depot-specific manner. These results contribute to determining the regulatory mechanism of phenotypic differences between Bama pigs and wild boar.
Collapse
Affiliation(s)
- Jiaman Zhang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130 China
| | - Pengliang Liu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130 China
| | - Mengnan He
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130 China
| | - Yujie Wang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130 China
| | - Hua Kui
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130 China
| | - Long Jin
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130 China
| | - Diyan Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130 China
| | - Mingzhou Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130 China
| |
Collapse
|