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Yang P, Song X, Zhang L, Wang X, Han Z, Wang R, Yang M, Liu P, Zhang Z. Unraveling the molecular landscape of breast muscle development in domestic Yuzhong pigeons and European meat pigeon: Insights from Iso-seq and RNA-seq analysis. PLoS One 2024; 19:e0305907. [PMID: 39052586 PMCID: PMC11271864 DOI: 10.1371/journal.pone.0305907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 06/05/2024] [Indexed: 07/27/2024] Open
Abstract
The mechanisms governing gene regulation in domestic Yuzhong pigeon breast muscle development remain largely elusive. Here, we conducted a comparative analysis using Iso-seq and RNA-seq data from domestic Yuzhong pigeons and European meat pigeons to uncover signaling pathways and genes involved in breast muscle development. The Iso-seq data from domestic Yuzhong pigeons yielded 131,377,075 subreads, resulting in 16,587 non-redundant high-quality full-length transcripts post-correction. Furthermore, utilizing pfam, CPC, PLEK, and CPAT, we predicted 5575, 4973, 2333, and 4336 lncRNAs, respectively. Notably, several genes potentially implicated in breast muscle development were identified, including tropomyosin beta chain, myosin regulatory light chain 2, and myosin binding protein C. KEGG enrichment analysis revealed critical signaling pathways in breast muscle development, spanning carbon metabolism, biosynthesis of amino acids, glycolysis/gluconeogenesis, estrogen signaling, PI3K-AKT signaling, protein processing in the endoplasmic reticulum, oxidative phosphorylation, pentose phosphate pathway, fructose and mannose metabolism, and tight junctions. These findings offer insights into the biological processes driving breast muscle development in domestic Yuzhong pigeon, contributing to our understanding of this complex phenomenon.
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Affiliation(s)
- Pengkun Yang
- College of Animal Science and Technology, Henan University of Animal Husbandry and Economy, Zhengzhou, China
| | - Xinghui Song
- College of Animal Science and Technology, Henan University of Animal Husbandry and Economy, Zhengzhou, China
| | - Liheng Zhang
- College of Animal Science and Technology, Henan University of Animal Husbandry and Economy, Zhengzhou, China
| | - Xinlei Wang
- College of Animal Science and Technology, Henan University of Animal Husbandry and Economy, Zhengzhou, China
| | - Zhanbing Han
- College of Animal Science and Technology, Henan University of Animal Husbandry and Economy, Zhengzhou, China
| | - Runzhi Wang
- Nanjing Institute of Animal Husbandry and Poultry Science, Nanjing, China
| | - Mingjun Yang
- Henan Tiancheng Pigeon Industry Co., Ltd, Pingdingshan, China
| | - Peiyao Liu
- Henan Tiancheng Pigeon Industry Co., Ltd, Pingdingshan, China
| | - Zhen Zhang
- College of Animal Science and Technology, Henan University of Animal Husbandry and Economy, Zhengzhou, China
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Li F, Zhu C, Luo Y, Li S, Wang Q, Han Y, Wu Z, Li X, Liang Y, Chen Y, Shen X, Huang Y, Tian Y, Zhang X. Transcriptomic Analysis on Pectoral Muscle of European Meat Pigeons and Shiqi Pigeons during Embryonic Development. Animals (Basel) 2023; 13:3267. [PMID: 37893991 PMCID: PMC10603743 DOI: 10.3390/ani13203267] [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: 09/04/2023] [Revised: 10/16/2023] [Accepted: 10/18/2023] [Indexed: 10/29/2023] Open
Abstract
In avian muscle development, embryonic muscle development determines the number of myofibers after birth. Therefore, in this study, we investigated the phenotypic differences and the molecular mechanism of pectoral muscle development of the European meat pigeon Mimas strain (later called European meat pigeon) and Shiqi pigeon on embryonic day 6 (E6), day 10 (E10), day 14 (E14) and day 1 after birth (P1). The results showed that the myofiber density of the Shiqi pigeon was significantly higher than that of the European meat pigeon on E6, and myofibers with a diameter in the range of 50~100 μm of the Shiqi pigeon on P1 were significantly higher than those of European meat pigeon. A total of 204 differential expressed genes (DEGs) were obtained from RNA-seq analysis in comparison between pigeon breeds at the same stage. DEGs related to muscle development were found to significantly enrich the cellular amino acid catabolism, carboxylic acid catabolism, extracellular matrix receptor interaction, REDOX enzyme activity, calcium signaling pathway, ECM receptor interaction, PPAR signaling pathway and other pathways. Using Cytoscape software to create mutual mapping, we identified 33 candidate genes. RT-qPCR was performed to verify the 8 DEGs selected-DES, MYOD, MYF6, PTGS1, MYF5, MYH1, MSTN and PPARG-and the results were consistent with RNA-seq. This study provides basic data for revealing the distinct embryonic development mechanism of pectoral muscle between European meat pigeons and Shiqi pigeons.
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Affiliation(s)
- Fada Li
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510225, China; (F.L.); (C.Z.); (Y.L.); (S.L.); (Q.W.); (Y.H.); (Z.W.); (X.L.); (Y.L.); (Y.C.); (X.S.); (Y.H.)
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Chenyu Zhu
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510225, China; (F.L.); (C.Z.); (Y.L.); (S.L.); (Q.W.); (Y.H.); (Z.W.); (X.L.); (Y.L.); (Y.C.); (X.S.); (Y.H.)
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Yongquan Luo
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510225, China; (F.L.); (C.Z.); (Y.L.); (S.L.); (Q.W.); (Y.H.); (Z.W.); (X.L.); (Y.L.); (Y.C.); (X.S.); (Y.H.)
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Songchao Li
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510225, China; (F.L.); (C.Z.); (Y.L.); (S.L.); (Q.W.); (Y.H.); (Z.W.); (X.L.); (Y.L.); (Y.C.); (X.S.); (Y.H.)
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Qi Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510225, China; (F.L.); (C.Z.); (Y.L.); (S.L.); (Q.W.); (Y.H.); (Z.W.); (X.L.); (Y.L.); (Y.C.); (X.S.); (Y.H.)
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Yuanhao Han
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510225, China; (F.L.); (C.Z.); (Y.L.); (S.L.); (Q.W.); (Y.H.); (Z.W.); (X.L.); (Y.L.); (Y.C.); (X.S.); (Y.H.)
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Zhongping Wu
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510225, China; (F.L.); (C.Z.); (Y.L.); (S.L.); (Q.W.); (Y.H.); (Z.W.); (X.L.); (Y.L.); (Y.C.); (X.S.); (Y.H.)
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Xiujin Li
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510225, China; (F.L.); (C.Z.); (Y.L.); (S.L.); (Q.W.); (Y.H.); (Z.W.); (X.L.); (Y.L.); (Y.C.); (X.S.); (Y.H.)
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Yayan Liang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510225, China; (F.L.); (C.Z.); (Y.L.); (S.L.); (Q.W.); (Y.H.); (Z.W.); (X.L.); (Y.L.); (Y.C.); (X.S.); (Y.H.)
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Yitian Chen
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510225, China; (F.L.); (C.Z.); (Y.L.); (S.L.); (Q.W.); (Y.H.); (Z.W.); (X.L.); (Y.L.); (Y.C.); (X.S.); (Y.H.)
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Xu Shen
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510225, China; (F.L.); (C.Z.); (Y.L.); (S.L.); (Q.W.); (Y.H.); (Z.W.); (X.L.); (Y.L.); (Y.C.); (X.S.); (Y.H.)
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Yunmao Huang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510225, China; (F.L.); (C.Z.); (Y.L.); (S.L.); (Q.W.); (Y.H.); (Z.W.); (X.L.); (Y.L.); (Y.C.); (X.S.); (Y.H.)
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Yunbo Tian
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510225, China; (F.L.); (C.Z.); (Y.L.); (S.L.); (Q.W.); (Y.H.); (Z.W.); (X.L.); (Y.L.); (Y.C.); (X.S.); (Y.H.)
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Xumeng Zhang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510225, China; (F.L.); (C.Z.); (Y.L.); (S.L.); (Q.W.); (Y.H.); (Z.W.); (X.L.); (Y.L.); (Y.C.); (X.S.); (Y.H.)
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
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Yang L, Liu M, Zhu Y, Li Y, Pan T, Li E, Wu X. Candidate Regulatory Genes for Hindlimb Development in the Embryos of the Chinese Alligator ( Alligator sinensis). Animals (Basel) 2023; 13:3126. [PMID: 37835732 PMCID: PMC10571561 DOI: 10.3390/ani13193126] [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: 07/25/2023] [Revised: 09/11/2023] [Accepted: 10/04/2023] [Indexed: 10/15/2023] Open
Abstract
Crocodilians, which are a kind of animal secondary adaptation to an aquatic environment, their hindlimb can provide the power needed to engage in various life activities, even in low-oxygen water environments. The development of limbs is an important aspect of animal growth and development, as it is closely linked to body movement, support, heat production, and other critical functions. For the Chinese alligator, the hindlimb is one of the main sources of power, and its development and differentiation will directly influence the survival ability in the wild. Furthermore, a better understanding of the hindlimb developmental process will provide data support for the comparative evolutionary and functional genomics of crocodilians. In this study, the expression levels of genes related to hindlimb development in the Chinese alligator embryos during fetal development (on days 29, 35, 41, and 46) were investigated through transcriptome analysis. A total of 1675 differentially expressed genes (DEGs) at different stages were identified by using limma software. These DEGs were then analyzed using weighted correlation network analysis (WGCNA), and 4 gene expression modules and 20 hub genes were identified that were associated with the development of hindlimbs in the Chinese alligator at different periods. The results of GO enrichment and hub gene expression showed that the hindlimb development of the Chinese alligator embryos involves the development of the embryonic structure, nervous system, and hindlimb muscle in the early stage (H29) and the development of metabolic capacity occurs in the later stage (H46). Additionally, the enrichment results showed that the AMPK signaling pathway, calcium signaling pathway, HIF-1 signaling pathway, and neuroactive ligand-receptor interaction are involved in the development of the hindlimb of the Chinese alligator. Among these, the HIF-1 signaling pathway and neuroactive ligand-receptor interaction may be related to the adaptation of Chinese alligators to low-oxygen environments. Additionally, five DEGs (CAV1, IRS2, LDHA, LDB3, and MYL3) were randomly selected for qRT-PCR to verify the transcriptome results. It is expected that further research on these genes will help us to better understand the process of embryonic hindlimb development in the Chinese alligator.
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Affiliation(s)
- Liuyang Yang
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (L.Y.); (M.L.); (Y.Z.); (Y.L.); (T.P.)
- Anhui Provincial Key Laboratory of Conservation and Exploitation of Biological Resources, Anhui Normal University, Wuhu 241000, China
| | - Mengqin Liu
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (L.Y.); (M.L.); (Y.Z.); (Y.L.); (T.P.)
- Anhui Provincial Key Laboratory of Conservation and Exploitation of Biological Resources, Anhui Normal University, Wuhu 241000, China
| | - Yunzhen Zhu
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (L.Y.); (M.L.); (Y.Z.); (Y.L.); (T.P.)
- Anhui Provincial Key Laboratory of Conservation and Exploitation of Biological Resources, Anhui Normal University, Wuhu 241000, China
| | - Yanan Li
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (L.Y.); (M.L.); (Y.Z.); (Y.L.); (T.P.)
- Anhui Provincial Key Laboratory of Conservation and Exploitation of Biological Resources, Anhui Normal University, Wuhu 241000, China
| | - Tao Pan
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (L.Y.); (M.L.); (Y.Z.); (Y.L.); (T.P.)
- Anhui Provincial Key Laboratory of Conservation and Exploitation of Biological Resources, Anhui Normal University, Wuhu 241000, China
| | - En Li
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (L.Y.); (M.L.); (Y.Z.); (Y.L.); (T.P.)
- Anhui Provincial Key Laboratory of Conservation and Exploitation of Biological Resources, Anhui Normal University, Wuhu 241000, China
| | - Xiaobing Wu
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (L.Y.); (M.L.); (Y.Z.); (Y.L.); (T.P.)
- Anhui Provincial Key Laboratory of Conservation and Exploitation of Biological Resources, Anhui Normal University, Wuhu 241000, China
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Yu B, Cai Z, Liu J, Zhao W, Fu X, Gu Y, Zhang J. Transcriptome and co-expression network analysis reveals the molecular mechanism of inosine monophosphate-specific deposition in chicken muscle. Front Physiol 2023; 14:1199311. [PMID: 37265843 PMCID: PMC10229883 DOI: 10.3389/fphys.2023.1199311] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 05/05/2023] [Indexed: 06/03/2023] Open
Abstract
The inosine monophosphate (IMP) content in chicken meat is closely related to muscle quality and is an important factor affecting meat flavor. However, the molecular regulatory mechanisms underlying the IMP-specific deposition in muscle remain unclear. This study performed transcriptome analysis of muscle tissues from different parts, feeding methods, sexes, and breeds of 180-day-old Jingyuan chickens, combined with differential expression and weighted gene co-expression network analysis (WGCNA), to identify the functional genes that regulate IMP deposition. Out of the four comparison groups, 1,775, 409, 102, and 60 differentially expressed genes (DEGs) were identified, of which PDHA2, ACSS2, PGAM1, GAPDH, PGM1, GPI, and TPI1 may be involved in the anabolic process of muscle IMP in the form of energy metabolism or amino acid metabolism. WGCNA identified 11 biofunctional modules associated with IMP deposition. The brown, midnight blue, red, and yellow modules were strongly correlated with IMP and cooking loss (p < 0.05). Functional enrichment analysis showed that glycolysis/gluconeogenesis, arginine and proline metabolism, and pyruvate metabolism, regulated by PYCR1, SMOX, and ACSS2, were necessary for muscle IMP-specific deposition. In addition, combined analyses of DEGs and four WGCNA modules identified TGIF1 and THBS1 as potential candidate genes affecting IMP deposition in muscle. This study explored the functional genes that regulate muscle development and IMP synthesis from multiple perspectives, providing an important theoretical basis for improving the meat quality and molecular breeding of Jingyuan chickens.
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Jin CL, He YA, Jiang SG, Wang XQ, Yan HC, Tan HZ, Gao CQ. Chemical Composition of Pigeon Crop Milk and Factors Affecting Its Production: A Review. Poult Sci 2023; 102:102681. [PMID: 37098298 PMCID: PMC10149254 DOI: 10.1016/j.psj.2023.102681] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 03/18/2023] [Accepted: 03/26/2023] [Indexed: 03/31/2023] Open
Abstract
Pigeons are important commercial poultry in addition to being ornamental birds. In 2021, more than 111 million pairs of breeding pigeons were kept in stock and 1.6 billion squabs were slaughtered for meat in China. However, in many countries, pigeons are not domestic birds; thus, it is necessary to elucidate the factors involved in their growth and feeding strategy due to their economic importance. Pigeons are altricial birds, so feedstuffs cannot be digested by squabs, which instead are fed a mediator named pigeon crop milk. During lactation, breeding pigeons (both female and male) ingest diets and generate crop milk to feed squabs. Thus, research on squab growth is more complex than that on chicken and other poultry. To date, research on the measurement of crop milk composition and estimation of the factors affecting its production has not ceased, and these results are worth reviewing to guide production. Moreover, some studies have focused on the formation mechanism of crop milk, reporting that the synthesis of crop milk is controlled by prolactin and insulin-activated pathways. Furthermore, the Janus kinase 2 (JAK2)-signal transducer and activator of transcription 5 (STAT5) pathway, target of rapamycin (TOR) pathway and AMP-activated protein kinase (AMPK) pathway were also reported to be involved in crop milk synthesis. Therefore, this review focuses on the chemical composition of pigeon crop milk and factors affecting its production during lactation. This work explores novel mechanisms and provides a theoretical reference for improving production in the pigeon industry, including for racing, ornamental purposes, and production of meat products.
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Zhu J, Teng X, Wang L, Zheng M, Meng Y, Liu T, Liu Y, Huan H, Gong D, Xie P. Prolactin promotes crop epithelial proliferation of domestic pigeons (Columba livia) through the Hippo signaling pathway. J Anim Sci 2023; 101:skad312. [PMID: 37721785 PMCID: PMC10576522 DOI: 10.1093/jas/skad312] [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: 07/26/2023] [Accepted: 09/15/2023] [Indexed: 09/19/2023] Open
Abstract
The purpose of this study was to investigate whether prolactin (PRL) regulates the proliferation of pigeon crop epithelium through the Hippo signaling pathway during the breeding cycle. Twenty-four pairs of adult pigeons were allotted to four groups by different breeding stages, and their crops and serum were sampled. Eighteen pairs of young pigeons were selected and divided into three groups for the injection experiments. The results showed that the serum PRL content and crop epithelial thickness of pigeons increased significantly at day 17 of incubation (I17) and day 1 of chick-rearing (R1). In males, the mRNA levels of yes-associated transcriptional regulator (YAP) and snail family transcriptional repressor 2 (SNAI2) were peaked at I17, and the gene levels of large tumor suppressor kinase 1 (LATS1), serine/threonine kinase 3 (STK3), TEA domain transcription factor 3 (TEAD3), connective tissue growth factor (CTGF), MYC proto-oncogene (c-Myc) and SRY-box transcription factor 2 (SOX2) reached the maximum value at R1. In females, the gene expression of YAP, STK3, TEAD3, and SOX2 reached the greatest level at I17, the expression profile of SAV1, CTGF, and c-Myc were maximized at R1. In males, the protein levels of LATS1 and YAP were maximized at R1 and the CTGF expression was upregulated at I17. In females, LATS1, YAP, and CTGF reached a maximum value at I17, and the expression level of phosphorylated YAP was minimized at I17 in males and females. Subcutaneous injection of prolactin (injected for 6 d, 10 μg per kg body weight every day) on the left crop of pigeons can promote the proliferation of crop epithelium by increasing the CTGF level and reducing the phosphorylation level of YAP. YAP-TEAD inhibitor verteporfin (injection for 6 d, 2.5 mg per kg body weight every day) can inhibit the proliferation of crop epithelium induced by prolactin by inhibiting YAP and CTGF expression. In conclusion, PRL can participate in crop cell proliferation of pigeons by promoting the expression of YAP and CTGF in Hippo pathway.
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Affiliation(s)
- Jianguo Zhu
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Huaian 223300, P.R.China
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, P.R.China
| | - Xingyi Teng
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao 266000, P.R.China
| | - Liuxiong Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, P.R.China
| | - Mingde Zheng
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, P.R.China
| | - Yu Meng
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, P.R.China
| | - Tingwu Liu
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Huaian 223300, P.R.China
| | - Ying Liu
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Huaian 223300, P.R.China
| | - Haixia Huan
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Huaian 223300, P.R.China
| | - Daoqing Gong
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, P.R.China
| | - Peng Xie
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Huaian 223300, P.R.China
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Luo Y, Hu S, Yan P, Wu J, Guo H, Zhao L, Tang Q, Ma J, Long K, Jin L, Jiang A, Li M, Li X, Wang X. Analysis of mRNA and lncRNA Expression Profiles of Breast Muscle during Pigeon ( Columbalivia) Development. Genes (Basel) 2022; 13:genes13122314. [PMID: 36553580 PMCID: PMC9777807 DOI: 10.3390/genes13122314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/04/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022] Open
Abstract
The breast muscle is essential for flight and determines the meat yield and quality of the meat type in pigeons. At present, studies about long non-coding RNA (lncRNA) expression profiles in skeletal muscles across the postnatal development of pigeons have not been reported. Here, we used transcriptome sequencing to examine the White-King pigeon breast muscle at four different ages (1 day, 14 days, 28 days, and 2 years old). We identified 12,918 mRNAs and 9158 lncRNAs (5492 known lncRNAs and 3666 novel lncRNAs) in the breast muscle, and 7352 mRNAs and 4494 lncRNAs were differentially expressed in the process of development. We found that highly expressed mRNAs were mainly related to cell-basic and muscle-specific functions. Differential expression and time-series analysis showed that differentially expressed genes were primarily associated with muscle development and functions, blood vessel development, cell cycle, and energy metabolism. To further predict the possible role of lncRNAs, we also conducted the WGCNA and trans/cis analyses. We found that differentially expressed lncRNAs such as lncRNA-LOC102093252, lncRNA-G12653, lncRNA-LOC110357465, lncRNA-G14790, and lncRNA-LOC110360188 might respectively target UBE2B, Pax7, AGTR2, HDAC1, Sox8 and participate in the development of the muscle. Our study provides a valuable resource for studying the lncRNAs and mRNAs of pigeon muscles and for improving the understanding of molecular mechanisms in muscle development.
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Affiliation(s)
- Yi Luo
- Livestock and Poultry Multi-Omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, China
| | - Silu Hu
- Livestock and Poultry Multi-Omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Peiqi Yan
- Livestock and Poultry Multi-Omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jie Wu
- Livestock and Poultry Multi-Omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Hongrui Guo
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Ling Zhao
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Qianzi Tang
- Livestock and Poultry Multi-Omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, China
| | - Jideng Ma
- Livestock and Poultry Multi-Omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, China
| | - Keren Long
- Livestock and Poultry Multi-Omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, China
| | - Long Jin
- Livestock and Poultry Multi-Omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, China
| | - Anan Jiang
- Livestock and Poultry Multi-Omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, China
| | - Mingzhou Li
- Livestock and Poultry Multi-Omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, China
| | - Xuewei Li
- Livestock and Poultry Multi-Omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Correspondence: (X.L.); (X.W.)
| | - Xun Wang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, China
- Correspondence: (X.L.); (X.W.)
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Wang J, Li B, Yang X, Liang C, Raza SHA, Pan Y, Zhang K, Zan L. Integration of RNA-seq and ATAC-seq identifies muscle-regulated hub genes in cattle. Front Vet Sci 2022; 9:925590. [PMID: 36032309 PMCID: PMC9404375 DOI: 10.3389/fvets.2022.925590] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
As the main product of livestock, muscle itself plays an irreplaceable role in maintaining animal body movement and regulating metabolism. Therefore, it is of great significance to explore its growth, development and regeneration to improve the meat yield and quality of livestock. In this study, we attempted to use RNA-seq and ATAC-seq techniques to identify differentially expressed genes (DEGs) specifically expressed in bovine skeletal muscle as potential candidates for studying the regulatory mechanisms of muscle development. Microarray data from 8 tissue samples were selected from the GEO database for analysis. First, we obtained gene modules related to each tissue through WGCNA analysis. Through Gene Ontology (GO) functional annotation, the module of lightyellow (MElightyellow) was closely related to muscle development, and 213 hub genes were screened as follow-up research targets. Further, the difference analysis showed that, except for PREB, all other candidate hub genes were up-regulated (muscle group vs. other-group). ATAC-seq analysis showed that muscle-specific accessible chromatin regions were mainly located in promoter of genes related to muscle structure development (GO:0061061), muscle cell development (GO:0055001) and muscle system process (GO:0003012), which were involved in cAMP, CGMP-PKG, MAPK, and other signaling pathways. Next, we integrated the results of RNA-seq and ATAC-seq analysis, and 54 of the 212 candidate hub genes were identified as key regulatory genes in skeletal muscle development. Finally, through motif analysis, 22 of the 54 key genes were found to be potential target genes of transcription factor MEF2C. Including CAPN3, ACTN2, MB, MYOM3, SRL, CKM, ALPK3, MAP3K20, UBE2G1, NEURL2, CAND2, DOT1L, HRC, MAMSTR, FSD2, LRRC2, LSMEM1, SLC29A2, FHL3, KLHL41, ATXN7L2, and PDRG1. This provides a potential reference for studying the molecular mechanism of skeletal muscle development in mammals.
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Affiliation(s)
- Jianfang Wang
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Bingzhi Li
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Xinran Yang
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Chengcheng Liang
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | | | - Yueting Pan
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Ke Zhang
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
- National Beef Cattle Improvement Center, Northwest A&F University, Xianyang, China
- *Correspondence: Linsen Zan
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Transcriptome Sequencing Analysis Reveals Dynamic Changes in Major Biological Functions during the Early Development of Clearhead Icefish, Protosalanx chinensis. FISHES 2022. [DOI: 10.3390/fishes7030115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Early development, when many important developmental events occur, is a critical period for fish. However, research on the early development of clearhead icefish is very limited, especially in molecular research. In this study, we aimed to explore the dynamic changes in the biological functions of five key periods in clearhead icefish early development, namely the YL (embryonic), PM (first day after hatching), KK (fourth day after hatching), LC (seventh day after hatching), and SL (tenth day after hatching) stages, through transcriptome sequencing and different analysis strategies. A trend expression analysis and an enrichment analysis revealed that the expression ofgenes encoding G protein-coupled receptors and their ligands, i.e., prss1_2_3, pomc, npy, npb, sst, rln3, crh, gh, and prl that are associated with digestion and feeding regulation gradually increased during early development. In addition, a weighted gene co-expression network analysis (WGCNA) showed that eleven modules were significantly associated with early development, among which nine modules were significantly positively correlated. Through the enrichment analysis and hub gene identification results of these nine modules, it was found that the pathways related to eye, bone, and heart development were significantly enriched in the YL stage, and the ccnd2, seh1l, kdm6a, arf4, and ankrd28 genes that are associated with cell proliferation and differentiation played important roles in these developmental processes; the pak3, dlx3, dgat2, and tas1r1 genes that are associated with jaw and tooth development, TG (triacylglycerol) synthesis, and umami amino acid receptors were identified as hub genes for the PM stage; the pathways associated with aerobic metabolism and unsaturated fatty acid synthesis were significantly enriched in the KK stage, with the foxk, slc13a2_3_5, ndufa5, and lsc2 genes playing important roles; the pathways related to visual perception were significantly enriched in the LC stage; and the bile acid biosynthetic and serine-type peptidase activity pathways were significantly enriched in the SL stage. These results provide a more detailed understanding of the processes of early development of clearhead icefish.
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