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Cai S, Duo T, Wang X, Tong X, Luo C, Chen Y, Li J, Mo D. A Comparative Analysis of Metabolic Profiles of Embryonic Skeletal Muscle from Lantang and Landrace Pigs. Animals (Basel) 2022; 12:ani12040420. [PMID: 35203128 PMCID: PMC8868109 DOI: 10.3390/ani12040420] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/25/2022] [Accepted: 01/31/2022] [Indexed: 02/06/2023] Open
Abstract
Simple Summary The pig is one of the most important domesticated meat animals. Some studies have revealed that pigs with low meat production show more intense myogenesis at the early stage of embryonic muscle development than pigs with high meat production. Here, by gas chromatography–mass spectrometry GC–MS based metabolomics, we concluded that the nucleotide metabolism and energy metabolism of the longissimuslumborum (LL) were increased in Lantang pigs compared with Landrace pigs, indicating rapid synthesis of nucleic acids and ATP to meet the material and energy requirements of rapid cell proliferation and differentiation in Lantang pigs. Abstract Elucidation of the complex regulation of porcine muscle development is key to increasing pork output and improving pork quality. However, the molecular mechanisms involved in early porcine embryonic muscle development in different pig breeds remain largely unknown. Here, GC–MS based metabolomics and metabolomic profiling was used to examine the longissimus lumborum (LL) of the Lantang (LT) and the Landrace (LR) pig at embryonic day 35 (E35). Metabolites showed clear separation between LT and LR, with 40 metabolites having higher abundances in LT and 14 metabolites having lower abundances in LT compared with LR. In addition, these metabolic changes were mainly associated with nucleotide metabolism and energy metabolism, such as purine metabolism, pyrimidine metabolism, the pentose phosphate pathway, and the TCA cycle. More interestingly, the contents of DNA, RNA, and ATP per unit mass of LL tissues were higher in LT, indicating rapid synthesis of nucleic acids and ATP, to meet both the material and energy requirements of rapid cell proliferation and differentiation. Furthermore, enzyme activity associated with the TCA cycle and pentose phosphate pathway, including α-ketoglutaric dehydrogenase (KGDH), malate dehydrogenase (MDH), pyruvate dehydrogenase (PDH), succinate dehydrogenase (SDH), and glucose-6-phosphate dehydrogenase (G6PDH), were higher in LT. Based on these results, we conclude that there are significant differences in nucleotide metabolism and energy metabolism of LL between LT and LR, and we speculate that the enhanced nucleic acid metabolism and energy metabolism in LT can meet the material and energy requirements of rapid cell proliferation and differentiation, making myogenesis more intense in LT compared to LR which might be the metabolic mechanism underlying the distinct skeletal muscle development in the two breeds.
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Affiliation(s)
- Shufang Cai
- State Key Laboratory of Livestock and Poultry Breeding & Guangdong Public Laboratory of Animal Breeding and Nutrition & Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (S.C.); (C.L.)
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, China; (T.D.); (X.W.); (X.T.); (Y.C.)
| | - Tianqi Duo
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, China; (T.D.); (X.W.); (X.T.); (Y.C.)
| | - Xiaoyu Wang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, China; (T.D.); (X.W.); (X.T.); (Y.C.)
| | - Xian Tong
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, China; (T.D.); (X.W.); (X.T.); (Y.C.)
| | - Chenglong Luo
- State Key Laboratory of Livestock and Poultry Breeding & Guangdong Public Laboratory of Animal Breeding and Nutrition & Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (S.C.); (C.L.)
| | - Yaosheng Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, China; (T.D.); (X.W.); (X.T.); (Y.C.)
| | - Jianhao Li
- State Key Laboratory of Livestock and Poultry Breeding & Guangdong Public Laboratory of Animal Breeding and Nutrition & Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (S.C.); (C.L.)
- Correspondence: (J.L.); (D.M.); Tel.: +86-020-38765361 (J.L.); +86-020-39332991 (D.M.)
| | - Delin Mo
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, China; (T.D.); (X.W.); (X.T.); (Y.C.)
- Correspondence: (J.L.); (D.M.); Tel.: +86-020-38765361 (J.L.); +86-020-39332991 (D.M.)
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Wang Y, Wang J, Hu H, Wang H, Wang C, Lin H, Zhao X. Dynamic transcriptome profiles of postnatal porcine skeletal muscle growth and development. BMC Genom Data 2021; 22:32. [PMID: 34488628 PMCID: PMC8419915 DOI: 10.1186/s12863-021-00984-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 08/02/2021] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Skeletal muscle growth and development are closely associated with the quantity and quality of pork production. We performed a transcriptomic analysis of 12 Longissimus dorsi muscle samples from Tibetan piglets at four postnatal stages of 0, 14, 30, and 60 days using RNA sequencing. RESULTS According to the pairwise comparisons between the libraries of the muscle samples at the four postnatal stages, a total of 4115 differentially expressed genes (DEGs) were identified in terms of |log2(fold change)| ≥ 1 and an adjusted P value < 0.01. Short-time series expression miner (STEM) analysis of the DEGs identified eight significantly different expression profiles, which were divided into two clusters based on the expression pattern. DEGs in cluster I displayed a pattern of decreasing to a nadir, and then a rise, and the significantly enriched gene ontology (GO) terms detected using them were involved in multiple processes, of which the cell cycle, immunocyte activation and proliferation, as well as actin cytoskeleton organization, were the top three overrepresented processes based on the GO terms functional classification. DEGs in cluster II displayed a pattern of increasing to a peak, then declining, which mainly contributed to protein metabolism. Furthermore, besides the pathways related to immune system, a few diseases, and protein metabolism, the DEGs in clusters I and II were significantly enriched in pathways related to muscle growth and development, such as the Rap1, PI3K-Akt, AMPK, and mTOR signaling pathways. CONCLUSIONS This study revealed GO terms and pathways that could affect the postnatal muscle growth and development in piglets. In addition, this study provides crucial information concerning the molecular mechanisms of muscle growth and development as well as an overview of the piglet transcriptome dynamics throughout the postnatal period in terms of growth and development.
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Affiliation(s)
- Yanping Wang
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong Province, China
| | - Jiying Wang
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong Province, China
| | - Hongmei Hu
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong Province, China
| | - Huaizhong Wang
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong Province, China
| | - Cheng Wang
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong Province, China
| | - Haichao Lin
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong Province, China
| | - Xueyan Zhao
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong Province, China.
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3
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Poklukar K, Čandek-Potokar M, Batorek Lukač N, Tomažin U, Škrlep M. Lipid Deposition and Metabolism in Local and Modern Pig Breeds: A Review. Animals (Basel) 2020; 10:E424. [PMID: 32138208 PMCID: PMC7142902 DOI: 10.3390/ani10030424] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 02/28/2020] [Accepted: 02/29/2020] [Indexed: 12/25/2022] Open
Abstract
Modern pig breeds, which have been genetically improved to achieve fast growth and a lean meat deposition, differ from local pig breeds with respect to fat deposition, fat specific metabolic characteristics and various other properties. The present review aimed to elucidate the mechanisms underlying the differences between fatty local and modern lean pig breeds in adipose tissue deposition and lipid metabolism, taking into consideration morphological, cellular, biochemical, transcriptomic and proteomic perspectives. Compared to modern breeds, local pig breeds accumulate larger amounts of fat, which generally contains more monounsaturated and saturated fatty acids; they exhibit a higher adipocyte size and higher activity of lipogenic enzymes. Studies using transcriptomic and proteomic approaches highlighted several processes like immune response, fatty-acid turn-over, oxidoreductase activity, mitochondrial function, etc. which differ between local and modern pig breeds.
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Affiliation(s)
- Klavdija Poklukar
- Agricultural Institute of Slovenia, Ljubljana SI-1000, Slovenia; (K.P.); (M.Č.-P.); (N.B.L.); (U.T.)
| | - Marjeta Čandek-Potokar
- Agricultural Institute of Slovenia, Ljubljana SI-1000, Slovenia; (K.P.); (M.Č.-P.); (N.B.L.); (U.T.)
- University of Maribor, Faculty of Agriculture and Life Sciences, Hoče SI-2311, Slovenia
| | - Nina Batorek Lukač
- Agricultural Institute of Slovenia, Ljubljana SI-1000, Slovenia; (K.P.); (M.Č.-P.); (N.B.L.); (U.T.)
| | - Urška Tomažin
- Agricultural Institute of Slovenia, Ljubljana SI-1000, Slovenia; (K.P.); (M.Č.-P.); (N.B.L.); (U.T.)
| | - Martin Škrlep
- Agricultural Institute of Slovenia, Ljubljana SI-1000, Slovenia; (K.P.); (M.Č.-P.); (N.B.L.); (U.T.)
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Liang Y, Wang Y, Ma L, Zhong Z, Yang X, Tao X, Chen X, He Z, Yang Y, Zeng K, Kang R, Gong J, Ying S, Lei Y, Pang J, Lv X, Gu Y. Comparison of microRNAs in adipose and muscle tissue from seven indigenous Chinese breeds and Yorkshire pigs. Anim Genet 2019; 50:439-448. [PMID: 31328299 DOI: 10.1111/age.12826] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2019] [Indexed: 01/29/2023]
Abstract
Elucidation of the pig microRNAome is essential for interpreting functional elements of the genome and understanding the genetic architecture of complex traits. Here, we extracted small RNAs from skeletal muscle and adipose tissue, and we compared their expression levels between one Western breed (Yorkshire) and seven indigenous Chinese breeds. We detected the expression of 172 known porcine microRNAs (miRNAs) and 181 novel miRNAs. Differential expression analysis found 92 and 12 differentially expressed miRNAs in adipose and muscle tissue respectively. We found that different Chinese breeds shared common directional miRNA expression changes compared to Yorkshire pigs. Some miRNAs differentially expressed across multiple Chinese breeds, including ssc-miR-129-5p, ssc-miR-30 and ssc-miR-150, are involved in adipose tissue function. Functional enrichment analysis revealed that the target genes of the differentially expressed miRNAs are associated mainly with signaling pathways rather than metabolic and biosynthetic processes. The miRNA-target gene and miRNA-phenotypic traits networks identified many hub miRNAs that regulate a large number of target genes or phenotypic traits. Specifically, we found that intramuscular fat content is regulated by the greatest number of miRNAs in muscle tissue. This study provides valuable new candidate miRNAs that will aid in the improvement of meat quality and production.
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Affiliation(s)
- Y Liang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, Sichuan Province China
| | - Y Wang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, Sichuan Province China
| | - L Ma
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences, Chengdu, 610052, Sichuan Province China
| | - Z Zhong
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, Sichuan Province China
| | - X Yang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, Sichuan Province China
| | - X Tao
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, Sichuan Province China
| | - X Chen
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, Sichuan Province China
| | - Z He
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, Sichuan Province China
| | - Y Yang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, Sichuan Province China
| | - K Zeng
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, Sichuan Province China
| | - R Kang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, Sichuan Province China
| | - J Gong
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, Sichuan Province China
| | - S Ying
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, Sichuan Province China
| | - Y Lei
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, Sichuan Province China
| | - J Pang
- Chengdu Biotechservice Institute, Chengdu, 610041, Sichuan Province China
| | - X Lv
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, Sichuan Province China
| | - Y Gu
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, Sichuan Province China
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Liu X, Gong J, Wang L, Hou X, Gao H, Yan H, Zhao F, Zhang L, Wang L. Genome-Wide Profiling of the Microrna Transcriptome Regulatory Network to Identify Putative Candidate Genes Associated with Backfat Deposition in Pigs. Animals (Basel) 2019; 9:ani9060313. [PMID: 31159441 PMCID: PMC6617047 DOI: 10.3390/ani9060313] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 05/27/2019] [Accepted: 05/30/2019] [Indexed: 12/27/2022] Open
Abstract
Simple Summary Backfat thickness is an important characteristic in pig breeding. In this study, the key microRNAs (miRNAs) and genes associated with pig backfat deposition were detected and characterized using RNA sequencing between adipose tissues of high-backfat and low-backfat pigs. Strong candidate mRNA‒miRNA interaction pairs were identified to affect backfat deposition through the regulation of target genes by miRNAs. These results provide novel insights into the backfat deposition mechanism in pigs. Abstract Backfat deposition is strongly related to carcass traits, growth rate, feed conversion rate, and reproductive performance in pig production. To understand the molecular mechanisms underlying porcine backfat thickness phenotypes, transcriptome and miRNA profiling of backfat from high-backfat thickness and low-backfat thickness pigs were performed by RNA sequencing. Twenty genes encoding for miRNAs and 126 genes encoding for protein-coding genes were found to be differentially expressed between the two libraries. After integrative analysis of DEMs targets and DEGs, a total of 33 mRNA‒miRNA interaction pairs were identified, and the regulatory networks of these pairs were determined. Among these genes, five (AQP9, DKK3, GLYCTK, GLIPR1, and DUSP2) related to fat deposition were found to be strong candidate genes, and mir-31-5p/AQP9 and mir-31-5p/GLIPR1 may play important roles in fat deposition. Additionally, potential adipogenesis-related genes and miRNAs were identified. These findings improve the current understanding of the molecular genetic mechanisms of subcutaneous fat deposition in pigs and provide a foundation for further studies.
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Affiliation(s)
- Xin Liu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Jianfei Gong
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao 266109, China.
| | - Ligang Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Xinhua Hou
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Hongmei Gao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Hua Yan
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Fuping Zhao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Longchao Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Lixian Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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Gao Z, Sun L, Dai K, Du Y, Wu S, Bao W. Effects of mutations in porcine miRNA-215 precursor sequences on miRNA-215 regulatory function. Gene 2019; 701:131-138. [PMID: 30905811 DOI: 10.1016/j.gene.2019.03.044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 03/12/2019] [Accepted: 03/20/2019] [Indexed: 01/21/2023]
Abstract
MicroRNAs (miRNAs) play an important role in animal growth and disease development, and sequence variation in microRNAs can alter their functions. Herein, we explored the effects of mutations in the miRNA-215 precursor sequence on the miRNA-215 regulatory network and resistance to Escherichia coli (E. coli). Polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) was used to detect sequence variations in Sutai and Meishan pigs. The miR-192 precursor sequence was not mutated, but the miR-215 precursor included an AT insertion mutation at position 6 (start from the first base of the miR-215 precursor) and a C/T mutation at position 43. Wild-type (WT) and mutant miR-215 precursor expression vectors were constructed to investigate the effects of sequence variation on expression of miR-215 and its target genes DLG5 and ALCAM, cytokine levels and E. coli adhesion. Compared with the WT control group, cells harbouring the C/T mutant vector displayed reduced miR-215 expression, increased target gene expression, elevated cytokine levels and rising E. coli adhesion, whereas cells harbouring the AT insertion mutant vector were not significantly changed. The sequence variation in the miRNA-215 precursor may affect the miRNA-215 regulatory network, and alter the stability of intestinal epithelial cells (IPEC-J2 cells) and resistance to E. coli. Our findings provide guidance for future research on the regulatory mechanisms of miR-215 in porcine resistance to E. coli F18, and identifying effective genetic markers against this organism.
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Affiliation(s)
- Zhongcheng Gao
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Li Sun
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Kaiyu Dai
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Yulu Du
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Shenglong Wu
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Jiangsu, Yangzhou, 225009, China
| | - Wenbin Bao
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Jiangsu, Yangzhou, 225009, China.
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Zhang Q, Wang Q, Zhang Y, Cheng S, Hu J, Ma Y, Zhao X. Comprehensive Analysis of MicroRNA⁻Messenger RNA from White Yak Testis Reveals the Differentially Expressed Molecules Involved in Development and Reproduction. Int J Mol Sci 2018; 19:ijms19103083. [PMID: 30304826 PMCID: PMC6213350 DOI: 10.3390/ijms19103083] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 09/30/2018] [Accepted: 10/02/2018] [Indexed: 01/31/2023] Open
Abstract
Testis development is a vital and tightly regulated process in mammals. Understanding the biological mechanisms underlying testis development will benefit the animal reproduction industry. Expression changes in microRNA and messenger RNA in response to dynamic regulation effects have been associated with this process. However, very little is known about the roles of these molecules in yak development. Using whole-genome small RNA and messenger RNA sequencing, we performed a comprehensive analysis of the microRNA–messenger RNA interaction network expression in the testicles of Tianzhu white yaks during three developmental stages. Using Short Time-series Expression Miner analysis we identified 589 differentially expressed microRNAs (DERs) and 3383 differentially expressed messenger RNAs (DEGs) in the three age groups. A total of 93 unique DEGs are primarily involved in reproduction and testis development. Subsequently, four integration networks were constructed according to the DEGs and DERs in three biological processes. Nineteen DEGs were potentially regulated by 60 DERs, of which miR-574 and target gene AURKA played a crucial role in yak testis development and reproduction. The results of this study provide a basis for further exploration of the microRNA–messenger RNA interactions in testis development and reproduction and aid in uncovering the molecular mechanisms of spermatogenesis in male mammals.
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Affiliation(s)
- Quanwei Zhang
- College of Veterinary Medicine, Gansu Agriculture University, Lanzhou 730070, China.
- College of Life science and Technology, Gansu Agriculture University, Lanzhou 730070, China.
| | - Qi Wang
- College of Veterinary Medicine, Gansu Agriculture University, Lanzhou 730070, China.
| | - Yong Zhang
- College of Veterinary Medicine, Gansu Agriculture University, Lanzhou 730070, China.
- College of Life science and Technology, Gansu Agriculture University, Lanzhou 730070, China.
| | - Shuru Cheng
- College of Animal Science and Technology, Gansu Agriculture University, Lanzhou 730070, China.
| | - Junjie Hu
- College of Veterinary Medicine, Gansu Agriculture University, Lanzhou 730070, China.
| | - Youji Ma
- College of Animal Science and Technology, Gansu Agriculture University, Lanzhou 730070, China.
| | - Xingxu Zhao
- College of Veterinary Medicine, Gansu Agriculture University, Lanzhou 730070, China.
- College of Life science and Technology, Gansu Agriculture University, Lanzhou 730070, China.
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Shu Y, Xia J, Yu Q, Wang G, Zhang J, He J, Wang H, Zhang L, Wu H. Integrated analysis of mRNA and miRNA expression profiles reveals muscle growth differences between adult female and male Chinese concave-eared frogs (Odorrana tormota). Gene 2018; 678:241-251. [PMID: 30103010 DOI: 10.1016/j.gene.2018.08.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Revised: 07/24/2018] [Accepted: 08/02/2018] [Indexed: 02/07/2023]
Abstract
The Chinese concave-eared torrent frog (Odorrana tormota) is the first known non-mammalian vertebrate that can communicate using ultrasound. In this species, females are approximately four times as large as males, in which the female growth rate is obviously higher than that of male. Until now, the molecular mechanisms underlying muscle growth development differences between male and female frogs have not been reported. Here, we integrated mRNA and miRNA expression profiles to reveal growth differences in the hindlimb muscles of 2-year-old frogs. Among 569 differentially expressed genes (DEGs), 69 were associated with muscle growth and regeneration. Fifty-one up-regulated genes in females were potentially involved in promoting muscle growth and regeneration, whereas 18 up-regulated genes in males may lead to muscle growth inhibition and fast-twitch muscle fiber contraction. 244 DEGs were enriched in mTOR and other protein synthesis signaling pathways, and protein degradation pathways, including lysosomal protease, calpain, caspase, and ubiquitin-proteasome system pathways. It may interpret why female muscles grow faster than males. Based on expression differences of genes involved in glycolysis and oxidative metabolism, we speculated that the proportion of slow muscle fiber was higher and that of fast muscle fiber was lower in female compared with male muscle. Additionally, 767 miRNAs were identified, including 217 new miRNAs, and 6248 miRNA-negatively regulated mRNAs were predicted. The miRNA target genes were enriched in pathways related to muscle growth, protein synthesis, and degradation. Thus, in addition to the identified mRNA differential expressions, miRNAs may play other important roles in the differential regulation of hindlimb muscle growth between female and male O. tormota.
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Affiliation(s)
- Yilin Shu
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu 241000, China; College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Jinquan Xia
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu 241000, China; College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Qiang Yu
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu 241000, China; College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Gang Wang
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu 241000, China; College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Jihui Zhang
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu 241000, China; College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Jun He
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu 241000, China; College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Huan Wang
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu 241000, China; College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Ling Zhang
- Department of Occupational and Environmental Health, School of Public Health, Wuhan University of Science and Technology, China; Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Wuhan University of Science and Technology, China.
| | - Hailong Wu
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu 241000, China; College of Life Sciences, Anhui Normal University, Wuhu 241000, China.
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