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Hou G, Wei L, Li R, Chen F, Yin J, Huang X, Yin Y. Lactobacillus delbrueckii Ameliorated Blood Lipids via Intestinal Microbiota Modulation and Fecal Bile Acid Excretion in a Ningxiang Pig Model. Animals (Basel) 2024; 14:1801. [PMID: 38929420 DOI: 10.3390/ani14121801] [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: 04/26/2024] [Revised: 06/07/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024] Open
Abstract
Lactobacillus delbrueckii intervention can regulate body lipid metabolism, but the underlying mechanism remains unclear. Our study investigated the effects of L. delbrueckii on serum lipid levels, tissular fat metabolism and deposition, bile acid metabolism, and gut microbiota in Ningxiang pigs. Ninety-six pigs were divided into two groups and fed basal diets containing either 0 (CON) or 0.1% L. delbrueckii (LD) for 60 days. Dietary L. delbrueckii promoted fecal total bile acid (TBA) excretion and increased hepatic enzyme activities related to cholesterol and bile synthesis but decreased hepatic and serum lipid concentrations. L. delbrueckii downregulated gene expression associated with fatty acid synthesis but upregulated gene expression related to lipolysis and β-fatty acid oxidation in liver and subcutaneous fat. L. delbrueckii elevated gut Lactobacillus abundance and colonic short-chain fatty acid (SCFA)-producing bacteria but declined the abundance of some pathogenic bacteria. These findings demonstrated that L. delbrueckii modulated intestinal microbiota composition and facilitated fecal TBA excretion to regulate hepatic fat metabolism, which resulted in less lipid deposition in the liver and reduced levels of serum lipids.
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Affiliation(s)
- Gaifeng Hou
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Liangkai Wei
- Hunan Co-Innovation Center of Safety Animal Production, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Rui Li
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Fengming Chen
- Academician Workstation, Changsha Medical University, Changsha 410219, China
| | - Jie Yin
- Hunan Co-Innovation Center of Safety Animal Production, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Xingguo Huang
- Hunan Co-Innovation Center of Safety Animal Production, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Yulong Yin
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
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2
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Wang Y, Gou Y, Yuan R, Zou Q, Zhang X, Zheng T, Fei K, Shi R, Zhang M, Li Y, Gong Z, Luo C, Xiong Y, Shan D, Wei C, Shen L, Tang G, Li M, Zhu L, Li X, Jiang Y. A chromosome-level genome of Chenghua pig provides new insights into the domestication and local adaptation of pigs. Int J Biol Macromol 2024; 270:131796. [PMID: 38677688 DOI: 10.1016/j.ijbiomac.2024.131796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 03/24/2024] [Accepted: 04/04/2024] [Indexed: 04/29/2024]
Abstract
As a country with abundant genetic resources of pigs, the domestication history of pigs in China and the adaptive evolution of Chinese pig breeds at different latitudes have rarely been elucidated at the genome-wide level. To fill this gap, we first assembled a high-quality chromosome-level genome of the Chenghua pig and used it as a benchmark to analyse the genomes of 272 samples from three genera of three continents. The divergence of the three species belonging to three genera, Phacochoerus africanus, Potamochoerus porcus, and Sus scrofa, was assessed. The introgression of pig breeds redefined that the migration routes were basically from southern China to central and southwestern China, then spread to eastern China, arrived in northern China, and finally reached Europe. The domestication of pigs in China occurred ∼12,000 years ago, earlier than the available Chinese archaeological domestication evidence. In addition, FBN1 and NR6A1 were identified in our study as candidate genes related to extreme skin thickness differences in Eurasian pig breeds and adaptive evolution at different latitudes in Chinese pig breeds, respectively. Our study provides a new resource for the pig genomic pool and refines our understanding of pig genetic diversity, domestication, migration, and adaptive evolution at different latitudes.
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Affiliation(s)
- Yifei Wang
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Yuwei Gou
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Rong Yuan
- Chengdu Livestock and Poultry Genetic Resources Protection Center, Chengdu, Sichuan 610081, China
| | - Qin Zou
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Xukun Zhang
- Academy for Engineering and Technology, Fudan University, Shanghai 200433, China
| | - Ting Zheng
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Kaixin Fei
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Rui Shi
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Mei Zhang
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Yujing Li
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Zhengyin Gong
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Chenggang Luo
- Chengdu Livestock and Poultry Genetic Resources Protection Center, Chengdu, Sichuan 610081, China
| | - Ying Xiong
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Dai Shan
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Chenyang Wei
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Linyuan Shen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Guoqing Tang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Mingzhou Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Li Zhu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Xuewei Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Yanzhi Jiang
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China.
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3
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Song Q, Li J, Li S, Cao H, Jin X, Zeng Y, Chen W. Full-Length Transcriptome Analysis of Skeletal Muscle of Jiangquan Black Pig at Different Developmental Stages. Int J Mol Sci 2024; 25:6095. [PMID: 38892283 PMCID: PMC11172715 DOI: 10.3390/ijms25116095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 05/22/2024] [Accepted: 05/24/2024] [Indexed: 06/21/2024] Open
Abstract
Skeletal muscle grows in response to a combination of genetic and environmental factors, and its growth and development influence the quality of pork. Elucidating the molecular mechanisms regulating the growth and development of skeletal muscle is of great significance to both animal husbandry and farm management. The Jiangquan black pig is an excellent pig breed based on the original Yimeng black pig, importing the genes of the Duroc pig for meat traits, and cultivated through years of scientific selection and breeding. In this study, full-length transcriptome sequencing was performed on three growth stages of Jiangquan black pigs, aiming to study the developmental changes in Jiangquan black pigs at different developmental stages at the molecular level and to screen the key genes affecting the growth of skeletal muscle in Jiangquan black pigs. We performed an enrichment analysis of genes showing differential expression and constructed a protein-protein interaction network with the aim of identifying core genes involved in the development of Jiangquan black pigs. Notably, genes such as TNNI2, TMOD4, PLDIM3, MYOZ1, and MYH1 may be potential regulators of muscle development in Jiangquan black pigs. Our results contribute to the understanding of the molecular mechanisms of skeletal muscle development in this pig breed, which will facilitate molecular breeding efforts and the development of pig breeds to meet the needs of the livestock industry.
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Affiliation(s)
- Qi Song
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai’an 271017, China; (Q.S.); (J.L.); (S.L.); (H.C.); (X.J.); (Y.Z.)
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Tai’an 271017, China
| | - Jinbao Li
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai’an 271017, China; (Q.S.); (J.L.); (S.L.); (H.C.); (X.J.); (Y.Z.)
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Tai’an 271017, China
| | - Shiyin Li
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai’an 271017, China; (Q.S.); (J.L.); (S.L.); (H.C.); (X.J.); (Y.Z.)
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Tai’an 271017, China
| | - Hongzhen Cao
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai’an 271017, China; (Q.S.); (J.L.); (S.L.); (H.C.); (X.J.); (Y.Z.)
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Tai’an 271017, China
| | - Xinlin Jin
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai’an 271017, China; (Q.S.); (J.L.); (S.L.); (H.C.); (X.J.); (Y.Z.)
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Tai’an 271017, China
| | - Yongqing Zeng
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai’an 271017, China; (Q.S.); (J.L.); (S.L.); (H.C.); (X.J.); (Y.Z.)
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Tai’an 271017, China
| | - Wei Chen
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai’an 271017, China; (Q.S.); (J.L.); (S.L.); (H.C.); (X.J.); (Y.Z.)
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Tai’an 271017, China
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Miao J, Wei X, Cao C, Sun J, Xu Y, Zhang Z, Wang Q, Pan Y, Wang Z. Pig pangenome graph reveals functional features of non-reference sequences. J Anim Sci Biotechnol 2024; 15:32. [PMID: 38389084 PMCID: PMC10882747 DOI: 10.1186/s40104-023-00984-4] [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: 08/29/2023] [Accepted: 12/22/2023] [Indexed: 02/24/2024] Open
Abstract
BACKGROUND The reliance on a solitary linear reference genome has imposed a significant constraint on our comprehensive understanding of genetic variation in animals. This constraint is particularly pronounced for non-reference sequences (NRSs), which have not been extensively studied. RESULTS In this study, we constructed a pig pangenome graph using 21 pig assemblies and identified 23,831 NRSs with a total length of 105 Mb. Our findings revealed that NRSs were more prevalent in breeds exhibiting greater genetic divergence from the reference genome. Furthermore, we observed that NRSs were rarely found within coding sequences, while NRS insertions were enriched in immune-related Gene Ontology terms. Notably, our investigation also unveiled a close association between novel genes and the immune capacity of pigs. We observed substantial differences in terms of frequencies of NRSs between Eastern and Western pigs, and the heat-resistant pigs exhibited a substantial number of NRS insertions in an 11.6 Mb interval on chromosome X. Additionally, we discovered a 665 bp insertion in the fourth intron of the TNFRSF19 gene that may be associated with the ability of heat tolerance in Southern Chinese pigs. CONCLUSIONS Our findings demonstrate the potential of a graph genome approach to reveal important functional features of NRSs in pig populations.
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Affiliation(s)
- Jian Miao
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Xingyu Wei
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Caiyun Cao
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Jiabao Sun
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Yuejin Xu
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Zhe Zhang
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Qishan Wang
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
- Yazhou Bay Science and Technology City, Hainan Institute of Zhejiang University, Yazhou District, Building 11, Yongyou Industrial Park, Sanya, 572025, Hainan, China
| | - Yuchun Pan
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
- Yazhou Bay Science and Technology City, Hainan Institute of Zhejiang University, Yazhou District, Building 11, Yongyou Industrial Park, Sanya, 572025, Hainan, China.
| | - Zhen Wang
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
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Ren Y, Wang F, Sun R, Zheng X, Liu Y, Lin Y, Hong L, Huang X, Chao Z. The Genetic Selection of HSPD1 and HSPE1 Reduce Inflammation of Liver and Spleen While Restraining the Growth and Development of Skeletal Muscle in Wuzhishan Pigs. Animals (Basel) 2024; 14:174. [PMID: 38200905 PMCID: PMC10777996 DOI: 10.3390/ani14010174] [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: 11/21/2023] [Revised: 12/25/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
Wuzhishan (WZS) pigs, which are minipigs native to Hainan Province in China, are characterized by strong resistance to extreme hot temperatures and humidity. The relationship between their immune response and growth still needs to be clarified. In this study, we used whole genome sequencing (WGS) to detect variations within 37 WZS pigs, 32 Large White (LW) pigs, and 22 Xiangxi black (XXB) pigs, and ~2.49 GB of SNPs were obtained. These data were combined with those of two other pig breeds, and it was found that most of the genes detected (354) were located within the distinct genetic regions between WZS pigs and LW pigs. The network that was constructed using these genes represented a center including 12 hub genes, five of which had structural variations (SVs) within their regulatory regions. Furthermore, RNA-seq and RT-qPCR data for 12 genes were primarily consistent in liver, spleen, and LDM tissues. Notably, the expression of HSPs (HSPD1 and HSPE1) was higher while that of most genes involved in the JAK3-STAT pathway were lower in liver tissue of WZS pigs, compared with LW pigs. This likely not only reduced inflammation-related immune response but also impaired their growth. Our findings demonstrated the role of HSPs in the connection between inflammation and growth rate, while also providing the fundamental genetic selection of the adaptability of WZS pigs.
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Affiliation(s)
- Yuwei Ren
- Key Laboratory of Tropical Animal Breeding and Disease Research, Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou 571100, China; (Y.R.)
| | - Feng Wang
- Key Laboratory of Tropical Animal Breeding and Disease Research, Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou 571100, China; (Y.R.)
| | - Ruiping Sun
- Key Laboratory of Tropical Animal Breeding and Disease Research, Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou 571100, China; (Y.R.)
| | - Xinli Zheng
- Key Laboratory of Tropical Animal Breeding and Disease Research, Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou 571100, China; (Y.R.)
| | - Yuanyuan Liu
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, China
| | - Yanning Lin
- Key Laboratory of Tropical Animal Breeding and Disease Research, Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou 571100, China; (Y.R.)
| | - Lingling Hong
- Key Laboratory of Tropical Animal Breeding and Disease Research, Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou 571100, China; (Y.R.)
| | - Xiaoxian Huang
- Key Laboratory of Tropical Animal Breeding and Disease Research, Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou 571100, China; (Y.R.)
| | - Zhe Chao
- Key Laboratory of Tropical Animal Breeding and Disease Research, Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou 571100, China; (Y.R.)
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Xu X, Yu Z, Ai N, Liufu S, Liu X, Chen B, Li X, Jiang J, Zhang Y, Ma H, Yin Y. Molecular Mechanism of MYL4 Regulation of Skeletal Muscle Development in Pigs. Genes (Basel) 2023; 14:1267. [PMID: 37372447 DOI: 10.3390/genes14061267] [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: 05/17/2023] [Revised: 06/11/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
The processes of muscle growth and development, including myoblast proliferation, migration, differentiation, and fusion, are modified by a variety of regulatory factors. MYL4 plays an important role in atrial development, atrial cardiomyopathy, muscle-fiber size, and muscle development. The structural variation (SV) of MYL4 was found via the de novo sequencing of Ningxiang pigs, and the existence of SV was verified in the experiments. The genotype distribution of Ningxiang pigs and Large White pigs was detected, and it was found that Ningxiang pigs were mainly of the BB genotype and that Large White pigs were mainly of the AB genotype. However, the molecular mechanisms behind the MYL4-mediated regulation of skeletal muscle development need to be deeply explored. Therefore, RT-qPCR, 3'RACE, CCK8, EdU, Western blot, immunofluorescence, flow cytometry, and bioinformation analysis were used to explore the function of MYL4 in myoblast development. The cDNA of MYL4 was successfully cloned from Ningxiang pigs, and its physicochemical properties were predicted. The expression profiles in six tissues and four stages of Ningxiang pigs and Large White pigs were found to be the highest in the lungs and 30 days after birth. The expression of MYL4 increased gradually with the extension of the myogenic differentiation time. The myoblast function test showed that the overexpression of MYL4 inhibited proliferation and promoted apoptosis and differentiation. The knockdown of MYL4 showed the opposite result. These results enhance our understanding of the molecular mechanisms of muscle development and provide a solid theoretical foundation for further exploring the role of the MYL4 gene in muscle development.
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Affiliation(s)
- Xueli Xu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Zonggang Yu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Nini Ai
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Sui Liufu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Xiaolin Liu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Bohe Chen
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Xintong Li
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Jun Jiang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Yuebo Zhang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Haiming Ma
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Yulong Yin
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
- Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
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Liufu S, Lan Q, Liu X, Chen B, Xu X, Ai N, Li X, Yu Z, Ma H. Transcriptome Analysis Reveals the Age-Related Developmental Dynamics Pattern of the Longissimus Dorsi Muscle in Ningxiang Pigs. Genes (Basel) 2023; 14:genes14051050. [PMID: 37239410 DOI: 10.3390/genes14051050] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 05/02/2023] [Accepted: 05/04/2023] [Indexed: 05/28/2023] Open
Abstract
The growth and development of the Longissimus Dorsi muscle are complex, playing an important role in the determination of pork quality. The study of the Longissimus Dorsi muscle at the mRNA level is particularly crucial for finding molecular approaches to improving meat quality in pig breeding. The current study utilized transcriptome technology to explore the regulatory mechanisms of muscle growth and intramuscular fat (IMF) deposition in the Longissimus Dorsi muscle at three core developmental stages (natal stage on day 1, growing stage on day 60, and finishing stage on day 210) in Ningxiang pigs. Our results revealed 441 differentially expressed genes (DEGs) in common for day 1 vs. day 60 and day 60 vs. day 210, and GO (Gene Ontology) analysis showed that candidate genes RIPOR2, MEGF10, KLHL40, PLEC, TBX3, FBP2, and HOMER1 may be closely related to muscle growth and development, while KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis showed that DEGs (UBC, SLC27A5, RXRG, PRKCQ, PRKAG2, PPARGC1A, PLIN5, PLIN4, IRS2, and CPT1B) involved the PPAR (Peroxisome Proliferator-Activated Receptor) signaling pathway and adipocytokine signaling pathway, which might play a pivotal role in the regulation of IMF deposition. PPI (Protein-Protein Interaction Networks) analysis found that the STAT1 gene was the top hub gene. Taken together, our results provide evidence for the molecular mechanisms of growth and development and IMF deposition in Longissimus Dorsi muscle to optimize carcass mass.
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Affiliation(s)
- Sui Liufu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Qun Lan
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Xiaolin Liu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Bohe Chen
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Xueli Xu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Nini Ai
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Xintong Li
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Zonggang Yu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Haiming Ma
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
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8
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Li X, Zhang X, Luo Y, Liu R, Sun Y, Zhao S, Yu M, Cao J. Large Fragment InDels Reshape Genome Structure of Porcine Alveolar Macrophage 3D4/21 Cells. Genes (Basel) 2022; 13:genes13091515. [PMID: 36140681 PMCID: PMC9498719 DOI: 10.3390/genes13091515] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/17/2022] [Accepted: 08/20/2022] [Indexed: 11/25/2022] Open
Abstract
The porcine monomyeloid cell line, or 3D4/21 cells, is an effective tool to study the immune characteristics and virus infection mechanism of pigs. Due to the introduction of the neomycin resistance gene and the SV40 large T antigen gene, its genome has undergone essential changes, which are still unknown. Studying the variation in genome structure, especially the large fragments of insertions and deletions (InDels), is one of the proper ways to reveal these issues. In this study, an All-seq method was established by combining Mate-pair and Shotgun sequencing methods, and the detection and verification of large fragments of InDels were performed on 3D4/21 cells. The results showed that there were 844 InDels with a length of more than 1 kb, of which 12 regions were deletions of more than 100 kb in the 3D4/21 cell genome. In addition, compared with porcine primary alveolar macrophages, 82 genes including the CD163 had lost transcription in 3D4/21 cells, and 72 genes gained transcription as well. Further referring to the Hi-C structure, it was found that the fusion of the topologically associated domains (TADs) caused by the deletion may lead to abnormal gene function. The results of this study provide a basis for elaborating the genome structure and functional variation in 3D4/21 cells, provide a method for rapid and convenient detection of large-scale InDels, and provide useful clues for the study of the porcine immune function genome and the molecular mechanism of virus infection.
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Affiliation(s)
- Xiaolong Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaoqian Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yandong Luo
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ru Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yan Sun
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Shuhong Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- The Cooperative Innovation Center for Sustainable Pig Production, Swine Breeding and Reproduction Innovation Platform, Huazhong Agricultural University, Wuhan 430070, China
| | - Mei Yu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- The Cooperative Innovation Center for Sustainable Pig Production, Swine Breeding and Reproduction Innovation Platform, Huazhong Agricultural University, Wuhan 430070, China
| | - Jianhua Cao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- The Cooperative Innovation Center for Sustainable Pig Production, Swine Breeding and Reproduction Innovation Platform, Huazhong Agricultural University, Wuhan 430070, China
- 3D Genomics Research Center, Huazhong Agricultural University, Wuhan 430070, China
- Correspondence:
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Gao Y, Ma L, Liu GE. Initial Analysis of Structural Variation Detections in Cattle Using Long-Read Sequencing Methods. Genes (Basel) 2022; 13:genes13050828. [PMID: 35627213 PMCID: PMC9142105 DOI: 10.3390/genes13050828] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/01/2022] [Accepted: 05/04/2022] [Indexed: 02/01/2023] Open
Abstract
Structural variations (SVs), as a great source of genetic variation, are widely distributed in the genome. SVs involve longer genomic sequences and potentially have stronger effects than SNPs, but they are not well captured by short-read sequencing owing to their size and relevance to repeats. Improved characterization of SVs can provide more advanced insight into complex traits. With the availability of long-read sequencing, it has become feasible to uncover the full range of SVs. Here, we sequenced one cattle individual using 10× Genomics (10 × G) linked read, Pacific Biosciences (PacBio) continuous long reads (CLR) and circular consensus sequencing (CCS), as well as Oxford Nanopore Technologies (ONT) PromethION. We evaluated the ability of various methods for SV detection. We identified 21,164 SVs, which amount to 186 Mb covering 7.07% of the whole genome. The number of SVs inferred from long-read-based inferences was greater than that from short reads. The PacBio CLR identified the most of large SVs and covered the most genomes. SVs called with PacBio CCS and ONT data showed high uniformity. The one with the most overlap with the results obtained by short-read data was PB CCS. Together, we found that long reads outperformed short reads in terms of SV detections.
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Affiliation(s)
- Yahui Gao
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD 20705, USA;
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA;
| | - Li Ma
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA;
| | - George E. Liu
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD 20705, USA;
- Correspondence: ; Tel.: +1-301-504-9843
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Chen W, Ma H, Li B, Yang F, Xiao Y, Gong Y, Li Z, Li T, Zeng Q, Xu K, Duan Y. Spatiotemporal Regulation of Circular RNA Expression during Liver Development of Chinese Indigenous Ningxiang Pigs. Genes (Basel) 2022; 13:746. [PMID: 35627131 PMCID: PMC9141790 DOI: 10.3390/genes13050746] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/22/2022] [Accepted: 04/22/2022] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND There have been many studies on the relationship between circRNAs and fat deposition. Although the liver is a central organ for fat metabolism, there are few reports on the relationship between circRNAs in the liver and fat deposition. METHODS In this study, we systematically analyzed circular RNAs in the liver of Ningxiang pigs, at four time points after birth (30 days, 90 days, 150 days and 210 days). RESULTS A total of 3705 circRNAs were coexpressed in four time periods were found, and KEGG analysis showed that the significantly upregulated pathways were mainly enriched in lipid metabolism and amino acid metabolism, while significantly downregulated pathways were mainly related to signal transduction, such as ECM-receptor interaction, MAPK signaling pathway, etc. Short time-series expression miner (STEM) analysis showed multiple model spectra that were significantly enriched over time in the liver. By constructing a competing endogenous RNA (ceRNA) regulatory network, 9187 pairs of networks related to the change in development time were screened. CONCLUSIONS The expression profiles of circRNAs in Ningxiang pig liver were revealed at different development periods, and it was determined that there is differential coexpression. Through enrichment analysis of these circRNAs, it was revealed that host genes were involved in metabolism-related signaling pathways and fatty acid anabolism. Through STEM analysis, many circRNAs involved in fat metabolism, transport, and deposition pathways were screened, and the first circRNA-miRNA-mRNA regulation network map in Ningxiang pig liver was constructed. The highly expressed circRNAs related to fat deposition were verified and were consistent with RNA-Seq results.
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Affiliation(s)
- Wenwu Chen
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (W.C.); (F.Y.); (Y.X.); (Y.G.); (Z.L.); (T.L.); (Q.Z.)
| | - Haiming Ma
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (W.C.); (F.Y.); (Y.X.); (Y.G.); (Z.L.); (T.L.); (Q.Z.)
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Biao Li
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (W.C.); (F.Y.); (Y.X.); (Y.G.); (Z.L.); (T.L.); (Q.Z.)
- College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu 610000, China
| | - Fang Yang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (W.C.); (F.Y.); (Y.X.); (Y.G.); (Z.L.); (T.L.); (Q.Z.)
| | - Yu Xiao
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (W.C.); (F.Y.); (Y.X.); (Y.G.); (Z.L.); (T.L.); (Q.Z.)
| | - Yan Gong
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (W.C.); (F.Y.); (Y.X.); (Y.G.); (Z.L.); (T.L.); (Q.Z.)
| | - Zhi Li
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (W.C.); (F.Y.); (Y.X.); (Y.G.); (Z.L.); (T.L.); (Q.Z.)
| | - Ting Li
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (W.C.); (F.Y.); (Y.X.); (Y.G.); (Z.L.); (T.L.); (Q.Z.)
| | - Qinghua Zeng
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (W.C.); (F.Y.); (Y.X.); (Y.G.); (Z.L.); (T.L.); (Q.Z.)
- Laboratory of Animal Nutritional Physiology and Metabolic Process, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Kang Xu
- Ningxiang Pig Farm of Dalong Livestock Technology Co., Ltd., Ningxiang 410600, China; (K.X.); (Y.D.)
| | - Yehui Duan
- Ningxiang Pig Farm of Dalong Livestock Technology Co., Ltd., Ningxiang 410600, China; (K.X.); (Y.D.)
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