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Dutta G, Alex R, Singh A, Gowane GR, Vohra V, De S, Verma A, Ludri A. Functional transcriptome analysis revealed upregulation of MAPK-SMAD signalling pathways in chronic heat stress in crossbred cattle. INTERNATIONAL JOURNAL OF BIOMETEOROLOGY 2024; 68:1371-1385. [PMID: 38720050 DOI: 10.1007/s00484-024-02672-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 02/14/2024] [Accepted: 03/01/2024] [Indexed: 07/26/2024]
Abstract
Animal geneticists and breeders have the impending challenge of enhancing the resilience of Indian livestock to heat stress through better selection strategies. Climate change's impact on livestock is more intense in tropical countries like India where dairy cattle crossbreeds are more sensitive to heat stress. The main reason for this study was to find the missing relative changes in transcript levels in thermo-neutral and heat stress conditions in crossbred cattle through whole-transcriptome analysis of RNA-Seq data. Differentially expressed genes (DEGs) identified based on the minimum log twofold change value and false discovery rate 0.05 revealed 468 up-regulated genes and 2273 down-regulated significant genes. Functional annotation and pathway analysis of these significant DEGs were compared based on Gene Ontology (Biological process), Kyoto Encyclopedia of Genes and Genome (KEGG), and Reactome pathways using g: Profiler, ShinyGO v0.76, and iDEP.951 web tools. On finding network visualization, the most over-represented and correlated pathways were neuronal and sensory organ development, calcium signalling pathway, Mitogen-activated protein kinase (MAPK) and Smad signalling pathway, Ras-proximate-1, or Ras-related protein 1 (Rap 1) signalling pathway, apoptosis, and oxidative stress. Similarly, down-regulated genes were most expressed in mRNA processing, immune system, B-cell receptor signalling pathway, Nucleotide oligomerization domain (NOD)-like receptors (NLRs) signalling pathway and nonsense-mediated decay (NMD) pathway. The heat stress-responsive genes identified in this study will facilitate our understanding of the molecular basis for climate resilience and heat tolerance in Indian dairy crossbreeds.
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Affiliation(s)
- Gaurav Dutta
- Animal Genetics and Breeding, ICAR-National Dairy Research Institute, Karnal, Haryana, 132001, India
| | - Rani Alex
- Animal Genetics and Breeding, ICAR-National Dairy Research Institute, Karnal, Haryana, 132001, India.
| | - Ayushi Singh
- Animal Genetics and Breeding, ICAR-National Dairy Research Institute, Karnal, Haryana, 132001, India
| | - Gopal R Gowane
- Animal Genetics and Breeding, ICAR-National Dairy Research Institute, Karnal, Haryana, 132001, India
| | - Vikas Vohra
- Animal Genetics and Breeding, ICAR-National Dairy Research Institute, Karnal, Haryana, 132001, India
| | - Sachidanandan De
- Animal Genetics and Breeding, ICAR-National Dairy Research Institute, Karnal, Haryana, 132001, India
| | - Archana Verma
- Animal Genetics and Breeding, ICAR-National Dairy Research Institute, Karnal, Haryana, 132001, India
| | - Ashutosh Ludri
- Animal Genetics and Breeding, ICAR-National Dairy Research Institute, Karnal, Haryana, 132001, India
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Saini T, Chauhan A, Ahmad SF, Kumar A, Vaishnav S, Singh S, Mehrotra A, Bhushan B, Gaur GK, Dutt T. Elucidation of population stratifying markers and selective sweeps in crossbred Landlly pig population using genome-wide SNP data. Mamm Genome 2024; 35:170-185. [PMID: 38485788 DOI: 10.1007/s00335-024-10029-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 01/23/2024] [Indexed: 05/29/2024]
Abstract
The present study was aimed at the identification of population stratifying markers from the commercial porcine SNP 60K array and elucidate the genome-wide selective sweeps in the crossbred Landlly pig population. Original genotyping data, generated on Landlly pigs, was merged in various combinations with global suid breeds that were grouped as exotic (global pig breeds excluding Indian and Chinese), Chinese (Chinese pig breeds only), and outgroup pig populations. Post quality control, the genome-wide SNPs were ranked for their stratifying power within each dataset in TRES (using three different criteria) and FIFS programs and top-ranked SNPs (0.5K, 1K, 2K, 3K, and 4K densities) were selected. PCA plots were used to assess the stratification power of low-density panels. Selective sweeps were elucidated in the Landlly population using intra- and inter-population haplotype statistics. Additionally, Tajima's D-statistics were calculated to determine the status of balancing selection in the Landlly population. PCA plots showed 0.5K marker density to effectively stratify Landlly from other pig populations. The A-score in DAPC program revealed the Delta statistic of marker selection to outperform other methods (informativeness and FST methods) and that 3000-marker density was suitable for stratification of Landlly animals from exotic pig populations. The results from selective sweep analysis revealed the Landlly population to be under selection for mammary (NAV2), reproductive efficiency (JMY, SERGEF, and MAP3K20), body conformation (FHIT, WNT2, ASRB, DMGDH, and BHMT), feed efficiency (CSRNP1 and ADRA1A), and immunity (U6, MYO3B, RBMS3, and FAM78B) traits. More than two methods suggested sweeps for immunity and feed efficiency traits, thus giving a strong indication for selection in this direction. The study is the first of its kind in Indian pig breeds with a comparison against global breeds. In conclusion, 500 markers were able to effectively stratify the breeds. Different traits under selective sweeps (natural or artificial selection) can be exploited for further improvement.
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Affiliation(s)
- Tapendra Saini
- Animal Genetics Division, ICAR-Indian Veterinary Research Institute, Izatnagar, 243122, India
| | - Anuj Chauhan
- Swine Production Farm, LPM Section, ICAR-Indian Veterinary Research Institute, Izatnagar, 243122, India.
| | - Sheikh Firdous Ahmad
- Animal Genetics Division, ICAR-Indian Veterinary Research Institute, Izatnagar, 243122, India
| | - Amit Kumar
- Animal Genetics Division, ICAR-Indian Veterinary Research Institute, Izatnagar, 243122, India
| | - Sakshi Vaishnav
- Animal Genetics Division, ICAR-Indian Veterinary Research Institute, Izatnagar, 243122, India
| | - Shivani Singh
- Swine Production Farm, LPM Section, ICAR-Indian Veterinary Research Institute, Izatnagar, 243122, India
| | | | - Bharat Bhushan
- Animal Genetics Division, ICAR-Indian Veterinary Research Institute, Izatnagar, 243122, India
| | - G K Gaur
- Swine Production Farm, LPM Section, ICAR-Indian Veterinary Research Institute, Izatnagar, 243122, India
- ADG Animal Production & Breeding, ICAR, New Delhi, 110001, India
| | - Triveni Dutt
- Indian Veterinary Research Institute, Izatnagar, 243122, India
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Hu Y, Li Q, Qian Z, BeiXiao, Luo K, Luo N. Joint Analysis of Genome-wide DNA Methylation and Transcription Sequencing Identifies the Role of BAX Gene in Heat Stress-Induced-Sertoli Cells Apoptosis. Reprod Sci 2024; 31:1311-1322. [PMID: 38180610 DOI: 10.1007/s43032-023-01430-6] [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: 10/05/2023] [Accepted: 12/12/2023] [Indexed: 01/06/2024]
Abstract
The problem of male infertility is a global health crisis and poses a serious threat to the well-being of families. Under heat stress (HS), the reduction of Sertoli cells (SCs) inhibits energy transport and nutrient supply to germ cells, leading to spermatogenesis failure. DNA methylation of genes is a central epigenetic regulatory mechanism in mammalian reproduction. However, it remains unclear how DNA methylation regulates gene expression in heat-stressed SCs. In this study, we investigated whether the decrease in SC levels during HS could be related to epigenetic DNA modifications. The cells exposed to HS showed changes in differential methylation cytosines and regions (DMCs/DMRs) and differential expression genes (DEGs), but not in global DNA methylations. One of the most important biological processes affected by HS is cell apoptosis induced by the intrinsic apoptotic signaling pathway (GO: 2,001,244, P < 0.05) by enrichment in the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). The joint analysis showed that several gene expressions in RNA-seq and WGBS overlapped and the shortlisted genes BAX, HSPH1, HSF1B, and BAG were strongly correlated with stress response and apoptosis. Methylation-specific PCR (MSP) and flow cytometry (FCM) analyzes showed that reduced promoter methylation and enhanced gene expression of BAX with a consequence of apoptosis. The activity of BAX, as well as an increase in its expression, is likely to result in a reduction of SCs population which could further impair ATP supply and adversely affect membrane integrity. These findings provide novel insights into the molecular mechanisms through which stressors cause male reproductive dysfunction and a new molecular etiology of male infertility.
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Affiliation(s)
- Yu Hu
- Department of Reproductive Medicine, Department of Obstetrics and Gynecology, Affiliated Hospital of Zunyi Medical University, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, China
| | - QingHan Li
- Department of Reproductive Medicine, Department of Obstetrics and Gynecology, Affiliated Hospital of Zunyi Medical University, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, China
| | - ZhengLi Qian
- Department of Reproductive Medicine, Department of Obstetrics and Gynecology, Affiliated Hospital of Zunyi Medical University, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, China
| | - BeiXiao
- Department of Reproductive Medicine, Department of Obstetrics and Gynecology, Affiliated Hospital of Zunyi Medical University, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, China
| | - KeYan Luo
- Department of Reproductive Medicine, Department of Obstetrics and Gynecology, Affiliated Hospital of Zunyi Medical University, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, China.
| | - NanJian Luo
- Department of Preclinical Medicine, Zunyi Medical University, Zunyi, 563000, China.
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Yang C, He J, Mao J, Ren Y, Liu G, Wei C, Zhang G, Tian K, Huang X. Genome-Wide DNA Methylation Analysis and Functional Validation of Litter Size Traits in Jining Grey Goats. Genes (Basel) 2024; 15:353. [PMID: 38540412 PMCID: PMC10970512 DOI: 10.3390/genes15030353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 03/07/2024] [Accepted: 03/07/2024] [Indexed: 06/14/2024] Open
Abstract
DNA methylation (DNAm) is associated with the reproductive system. However, the genetic mechanism through which DNAm regulates gene expression and thus affects litter size in goats is unclear. Therefore, in the present work, genome-wide DNAm profiles of HP and LP Jining Grey goat ovary tissues were comprehensively analyzed via WGBS, and RNA-Seq data were combined to identify candidate genes associated with litter size traits in the Jining Grey goat. Finally, BSP and RT-qPCR were used to verify the sequencing results of the key genes. Notably, the DNMT genes were downregulated at the expression level in the HP group. Both groups exhibited comparable levels of methylation. A total of 976 differentially methylated regions (DMRs) (973 DMRs for CG and 3 DMRs for CHG) and 310 differentially methylated genes (DMGs) were identified in this study. Through integration of WGBS and RNA-Seq data, we identified 59 differentially methylated and differentially expressed genes (DEGs) and ultimately screened 8 key DMGs (9 DMRS) associated with litter size traits in Jining Grey goats (SERPINB2: chr24_62258801_62259000, NDRG4: chr18_27599201_27599400, CFAP43: chr26_27046601_27046800, LRP1B. chr2_79720201_79720400, EPHA6: chr1_40088601_40088800, TTC29: chr17_59385801_59386000, PDE11A: chr2_117418601_117418800 and PGF: chr10_ 16913801_16914000 and chr10_16916401_16916600). In summary, our research comprehensively analyzed the genome-wide DNAm profiles of HP and LP Jining Grey goat ovary tissues. The data findings suggest that DNAm in goat ovaries may play an important role in determining litter size.
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Affiliation(s)
- Cunming Yang
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China; (C.Y.); (Y.R.)
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (J.H.); (J.M.); (G.L.); (C.W.); (G.Z.)
| | - Junmin He
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (J.H.); (J.M.); (G.L.); (C.W.); (G.Z.)
| | - Jingyi Mao
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (J.H.); (J.M.); (G.L.); (C.W.); (G.Z.)
| | - Yifan Ren
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China; (C.Y.); (Y.R.)
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (J.H.); (J.M.); (G.L.); (C.W.); (G.Z.)
| | - Guifen Liu
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (J.H.); (J.M.); (G.L.); (C.W.); (G.Z.)
| | - Chen Wei
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (J.H.); (J.M.); (G.L.); (C.W.); (G.Z.)
| | - Guoping Zhang
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (J.H.); (J.M.); (G.L.); (C.W.); (G.Z.)
| | - Kechuan Tian
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (J.H.); (J.M.); (G.L.); (C.W.); (G.Z.)
| | - Xixia Huang
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China; (C.Y.); (Y.R.)
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Li N, Wang J, Li K, Yang P, Wang Y, Xu C, He N, Ji K, Song H, Zhang M, Du L, Liu Q. Influence of e-waste exposure on DNA damage and DNA methylation in people living near recycling sites. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:88744-88756. [PMID: 37442932 DOI: 10.1007/s11356-023-28591-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 06/30/2023] [Indexed: 07/15/2023]
Abstract
The association between long-term exposure to e-waste and poor health is well established, but how e-waste exposure affects DNA methylation is understudied. In this study, we measured the DNA damage levels and the alternation of DNA methylation in peripheral blood mononuclear cells (PBMCs) collected from a population exposed to e-waste. The concentration of 28 PCB congeners in the blood samples of e-waste recycling workers was elevated than those of the reference group. DNA damage levels were significantly higher than that of samples from the reference group by detecting the SCGE, CA, and CBMN assays. Eventually, we found that the methylation level of 1233 gene loci was changed in the exposure group. Bioinformatic analysis of differential genes revealed that the hypermethylated genes were enriched in cell component movement and regulation of cell function, and hypomethylated genes were involved in the cellular metabolic process. Among the 30 genes we tested, 14 genes showed a negative correlation between methylation level and expression level. Therefore, e-waste exposure potentially increased the levels of DNA damage and alters DNA methylation, which would likely impact human health.
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Affiliation(s)
- Na Li
- Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin Key Laboratory of Molecular Nuclear Medicine, Tianjin, China
| | - Jinhan Wang
- Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin Key Laboratory of Molecular Nuclear Medicine, Tianjin, China
| | - Kejun Li
- Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin Key Laboratory of Molecular Nuclear Medicine, Tianjin, China
| | - Ping Yang
- Tianjin Institute of Medical and Pharmaceutical Science, Tianjin, China
| | - Yan Wang
- Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin Key Laboratory of Molecular Nuclear Medicine, Tianjin, China
| | - Chang Xu
- Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin Key Laboratory of Molecular Nuclear Medicine, Tianjin, China
| | - Ningning He
- Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin Key Laboratory of Molecular Nuclear Medicine, Tianjin, China
| | - Kaihua Ji
- Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin Key Laboratory of Molecular Nuclear Medicine, Tianjin, China
| | - Huijuan Song
- Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin Key Laboratory of Molecular Nuclear Medicine, Tianjin, China
| | - Manman Zhang
- Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin Key Laboratory of Molecular Nuclear Medicine, Tianjin, China
| | - Liqing Du
- Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin Key Laboratory of Molecular Nuclear Medicine, Tianjin, China
| | - Qiang Liu
- Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin Key Laboratory of Molecular Nuclear Medicine, Tianjin, China.
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Zhu W, Yang C, Liu Q, Peng M, Li Q, Wang H, Chen X, Zhang B, Feng P, Chen T, Zeng D, Zhao Y. Integrated Analysis of DNA Methylome and Transcriptome Reveals Epigenetic Regulation of Cold Tolerance in Litopenaeus vannamei. Int J Mol Sci 2023; 24:11573. [PMID: 37511332 PMCID: PMC10380378 DOI: 10.3390/ijms241411573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/05/2023] [Accepted: 07/09/2023] [Indexed: 07/30/2023] Open
Abstract
DNA methylation is an important epigenetic modification that has been shown to be associated with responses to non-biological stressors. However, there is currently no research on DNA methylation in response to environmental signals in shrimp. In this study, we conducted a comprehensive comparative analysis of DNA methylation profiles and differentially expressed genes between two strains of Litopenaeus vannamei with significantly different cold tolerance through whole genome bisulfite sequencing (WGBS) and transcriptome sequencing. Between Lv-C and Lv-T (constant temperature of 28 °C and low temperatures of 18 °C and 10 °C) under cytosine-guanine (CG) environments, 39,100 differentially methylated regions (DMRs) were identified, corresponding to 9302 DMR-related genes (DMRGs). The DMRs were mainly located in the gene body (exons and introns). Gene Ontology (GO) analysis showed that these DMRGs were significantly enriched in cell parts, catalytic activity, and metabolic processes. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed significant enrichment of these DMRGs in pathways such as proteasome (ko03050), oxidative phosphorylation (ko00190), mTOR signaling pathway (ko04150), fatty acid metabolism (ko01212), and fatty acid degradation (ko00071). The comprehensive results suggested that L. vannamei mainly regulates gene expression in response to low temperatures through hypermethylation or demethylation of some genes involved in thermogenesis, glycolysis, the autophagy pathway, the peroxisome, and drug metabolism pathways. These results provide important clues for studying DNA methylation patterns and identifying cold tolerance genes in shrimp.
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Affiliation(s)
- Weilin Zhu
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery Huazhong Agricultural University, Wuhan 430070, China
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
| | - Chunling Yang
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
| | - Qingyun Liu
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
| | - Min Peng
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
| | - Qiangyong Li
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
| | - Huanling Wang
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery Huazhong Agricultural University, Wuhan 430070, China
| | - Xiuli Chen
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
| | - Bin Zhang
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
| | - Pengfei Feng
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
| | - Tiancong Chen
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
| | - Digang Zeng
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
| | - Yongzhen Zhao
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
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Corbett RJ, Ford LM, Raney NE, Grabowski JM, Ernst CW. Pig fetal skeletal muscle development is associated with genome-wide DNA hypomethylation and corresponding alterations in transcript and microRNA expression. Genome 2023; 66:68-79. [PMID: 36876850 DOI: 10.1139/gen-2022-0008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
Fetal myogenesis represents a critical period of porcine skeletal muscle development and requires coordinated expression of thousands of genes. Epigenetic mechanisms, including DNA methylation, drive transcriptional regulation during development; however, these processes are understudied in developing porcine tissues. We performed bisulfite sequencing to assess DNA methylation in pig longissimus dorsi muscle at 41- and 70-days gestation (dg), as well as RNA- and small RNA-sequencing to identify coordinated changes in methylation and expression between myogenic stages. We identified 45 739 differentially methylated regions (DMRs) between stages, and the majority (N = 34 232) were hypomethylated at 70 versus 41 dg. Integration of methylation and transcriptomic data revealed strong associations between differential gene methylation and expression. Differential miRNA methylation was significantly negatively correlated with abundance, and dynamic expression of assayed miRNAs persisted postnatally. Motif analysis revealed significant enrichment of myogenic regulatory factor motifs among hypomethylated regions, suggesting that DNA hypomethylation may function to increase accessibility of muscle-specific transcription factors. We show that developmental DMRs are enriched for GWAS SNPs for muscle- and meat-related traits, demonstrating the potential for epigenetic processes to influence phenotypic diversity. Our results enhance understanding of DNA methylation dynamics of porcine myogenesis and reveal putative cis-regulatory elements governed by epigenetic processes.
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Affiliation(s)
- R J Corbett
- Genetics & Genome Sciences Graduate Program, Michigan State University, East Lansing, MI 48824, USA
| | - L M Ford
- Genetics & Genome Sciences Graduate Program, Michigan State University, East Lansing, MI 48824, USA
| | - N E Raney
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA
| | - J M Grabowski
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA
| | - C W Ernst
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA
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8
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Lin YL, Zhu ZX, Ai CH, Xiong YY, De Liu T, Lin HR, Xia JH. Transcriptome and DNA Methylation Responses in the Liver of Yellowfin Seabream Under Starvation Stress. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2023; 25:150-160. [PMID: 36445545 DOI: 10.1007/s10126-022-10188-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 11/23/2022] [Indexed: 06/16/2023]
Abstract
Fish suffer from starvation due to environmental risks such as extreme weather in the wild and due to insufficient feedings in farms. Nutrient problems from short-term or long-term starvation conditions can result in stress-related health problems for fish. Yellowfin seabream (Acanthopagrus latus) is an important marine economic fish in China. Understanding the molecular responses to starvation stress is vital for propagation and culturing yellowfin seabream. In this study, the transcriptome and genome-wide DNA methylation levels in the livers of yellowfin seabream under 14-days starvation stress were analyzed. One hundred sixty differentially expressed genes (DEGs) by RNA-Seq analysis and 737 differentially methylated-related genes by whole genome bisulfite sequencing analysis were identified. GO and KEGG pathway enrichment analysis found that energy metabolism-related pathways such as glucose metabolism and lipid metabolism were in response to starvation. Using bisulfite sequencing PCR, we confirmed the presence of CpG methylation differences within the regulatory region of a DEG ppargc1a in response to 14-days starvation stress. This study revealed the molecular responses of livers in response to starvation stress at the transcriptomic and whole genome DNA methylation levels in yellowfin seabream.
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Affiliation(s)
- Yi Long Lin
- College of Life Sciences, State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Zong Xian Zhu
- College of Life Sciences, State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Chun Hui Ai
- College of Life Sciences, State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Ying Ying Xiong
- College of Life Sciences, State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Tong De Liu
- College of Life Sciences, State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Hao Ran Lin
- College of Life Sciences, State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Jun Hong Xia
- College of Life Sciences, State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, 525000, People's Republic of China.
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9
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RNA-Seq Analysis Identifies Differentially Expressed Genes in the Longissimus dorsi of Wagyu and Chinese Red Steppe Cattle. Int J Mol Sci 2022; 24:ijms24010387. [PMID: 36613828 PMCID: PMC9820533 DOI: 10.3390/ijms24010387] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/08/2022] [Accepted: 12/16/2022] [Indexed: 12/29/2022] Open
Abstract
Meat quality has a close relationship with fat and connective tissue; therefore, screening and identifying functional genes related to lipid metabolism is essential for the production of high-grade beef. The transcriptomes of the Longissimus dorsi muscle in Wagyu and Chinese Red Steppe cattle, breeds with significant differences in meat quality and intramuscular fat deposition, were analyzed using RNA-seq to screen for candidate genes associated with beef quality traits. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that the 388 differentially expressed genes (DEGs) were involved in biological processes such as short-chain fatty acid metabolism, regulation of fatty acid transport and the peroxisome proliferator-activated receptor (PPAR) signaling pathway. In addition, crystallin alpha B (CRYAB), ankyrin repeat domain 2 (ANKRD2), aldehyde dehydrogenase 9 family member A1 (ALDH9A1) and enoyl-CoA hydratase and 3-hydroxyacyl CoA dehydrogenase (EHHADH) were investigated for their effects on intracellular triglyceride and fatty acid content and their regulatory effects on genes in lipogenesis and fatty acid metabolism pathways. This study generated a dataset from transcriptome profiling of two cattle breeds, with differing capacities for fat-deposition in the muscle, and revealed molecular evidence that CRYAB, ANKRD2, ALDH9A1 and EHHADH are related to fat metabolism in bovine fetal fibroblasts (BFFs). The results provide potential functional genes for maker-assisted selection and molecular breeding to improve meat quality traits in beef cattle.
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Gómez-Prado J, Pereira AMF, Wang D, Villanueva-García D, Domínguez-Oliva A, Mora-Medina P, Hernández-Avalos I, Martínez-Burnes J, Casas-Alvarado A, Olmos-Hernández A, Ramírez-Necoechea R, Verduzco-Mendoza A, Hernández A, Torres F, Mota-Rojas D. Thermoregulation mechanisms and perspectives for validating thermal windows in pigs with hypothermia and hyperthermia: An overview. Front Vet Sci 2022; 9:1023294. [PMID: 36532356 PMCID: PMC9751486 DOI: 10.3389/fvets.2022.1023294] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 11/17/2022] [Indexed: 12/05/2022] Open
Abstract
Specific anatomical characteristics make the porcine species especially sensitive to extreme temperature changes, predisposing them to pathologies and even death due to thermal stress. Interest in improving animal welfare and porcine productivity has led to the development of various lines of research that seek to understand the effect of certain environmental conditions on productivity and the impact of implementing strategies designed to mitigate adverse effects. The non-invasive infrared thermography technique is one of the tools most widely used to carry out these studies, based on detecting changes in microcirculation. However, evaluations using this tool require reliable thermal windows; this can be challenging because several factors can affect the sensitivity and specificity of the regions selected. This review discusses the thermal windows used with domestic pigs and the association of thermal changes in these regions with the thermoregulatory capacity of piglets and hogs.
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Affiliation(s)
- Jocelyn Gómez-Prado
- Neurophysiology, Behavior and Animal Welfare Assessment, DPAA, Xochimilco Campus, Universidad Autónoma Metropolitana, Mexico City, Mexico
| | - Alfredo M. F. Pereira
- Mediterranean Institute for Agriculture, Environment and Development (MED), Institute for Advanced Studies and Research, Universidade de Évora, Polo da Mitra, Évora, Portugal
| | - Dehua Wang
- School of Life Sciences, Shandong University, Qingdao, China
| | - Dina Villanueva-García
- Division of Neonatology, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Adriana Domínguez-Oliva
- Neurophysiology, Behavior and Animal Welfare Assessment, DPAA, Xochimilco Campus, Universidad Autónoma Metropolitana, Mexico City, Mexico
| | - Patricia Mora-Medina
- Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Ismael Hernández-Avalos
- Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Julio Martínez-Burnes
- Animal Health Group, Facultad de Medicina Veterinaria y Zootecnia, Universidad Autónoma de Tamaulipas, Ciudad Victoria, Mexico
| | - Alejandro Casas-Alvarado
- Neurophysiology, Behavior and Animal Welfare Assessment, DPAA, Xochimilco Campus, Universidad Autónoma Metropolitana, Mexico City, Mexico
| | - Adriana Olmos-Hernández
- Division of Biotechnology—Bioterio and Experimental Surgery, Instituto Nacional de Rehabilitación-Luis Guillermo Ibarra Ibarra, Mexico City, Mexico
| | - Ramiro Ramírez-Necoechea
- Neurophysiology, Behavior and Animal Welfare Assessment, DPAA, Xochimilco Campus, Universidad Autónoma Metropolitana, Mexico City, Mexico
| | - Antonio Verduzco-Mendoza
- Division of Biotechnology—Bioterio and Experimental Surgery, Instituto Nacional de Rehabilitación-Luis Guillermo Ibarra Ibarra, Mexico City, Mexico
| | - Astrid Hernández
- Neurophysiology, Behavior and Animal Welfare Assessment, DPAA, Xochimilco Campus, Universidad Autónoma Metropolitana, Mexico City, Mexico
| | - Fabiola Torres
- Neurophysiology, Behavior and Animal Welfare Assessment, DPAA, Xochimilco Campus, Universidad Autónoma Metropolitana, Mexico City, Mexico
| | - Daniel Mota-Rojas
- Neurophysiology, Behavior and Animal Welfare Assessment, DPAA, Xochimilco Campus, Universidad Autónoma Metropolitana, Mexico City, Mexico
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11
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Metzger K, Kalbe C, Siengdee P, Ponsuksili S. The effects of temperature and donor piglet age on the transcriptomic profile and energy metabolism of myoblasts. Front Physiol 2022; 13:979283. [PMID: 36213238 PMCID: PMC9532859 DOI: 10.3389/fphys.2022.979283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 08/30/2022] [Indexed: 11/13/2022] Open
Abstract
Rapid climate change is associated with frequent extreme heat events and the resulting thermal stress has consequences for the health, welfare, and growth of farm animals. The aim of this study was to characterize the transcriptional changes and the effects on energy metabolism in proliferating porcine myoblasts derived from piglets of different ages, representing differences in thermoregulatory abilities, and cultivated below (35°C) and above (39°C, 41°C) the standard cultivation temperature (37°C). Satellite cells originating from Musculus rhomboideus of piglets isolated on days 5 (P5, thermolabile) and 20 (P20, thermostable) of age were used. Our expression analyses highlighted differentially expressed genes in porcine myoblasts cultures under heat or cold induced stress. These gene sets showed enrichment for biological processes and pathways related to organelle fission, cell cycle, chromosome organization, and DNA replication. Culture at 35°C resulted in increased metabolic flux as well as a greater abundance of transcripts of the cold shock protein-encoding gene RBM3 and those of genes related to biological processes and signaling pathways, especially those involving the immune system (cytokine–cytokine receptor interaction, TNF and IL-17 signaling pathways). For cultivation at 39°C, differences in the expression of genes related to DNA replication and cell growth were identified. The highest glutathione index ratio was also found under 39°C. Meanwhile, cultivation at 41°C induced a heat stress response, including the upregulation of HSP70 expression and the downregulation of many biological processes and signaling pathways related to proliferative ability. Our analysis also identified differentially expressed genes between cells of donors with a not yet (P5) and already fully developed (P20) capacity for thermoregulation at different cultivation temperatures. When comparing P5 and P20, most of the changes in gene expression were detected at 37°C. At this optimal temperature, muscle cells can develop to their full capacity. Therefore, the most diverse molecular signaling pathways, including PI3K-Akt signaling, Wnt signaling, and EGFR tyrosine kinase inhibitor, were found and are more pronounced in muscle cells from 20-day-old piglets. These results contribute to a better understanding of the mechanisms underlying the adaptation of skeletal muscle cells to temperature stress in terms of their thermoregulatory ability.
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Affiliation(s)
- Katharina Metzger
- Research Institute for Farm Animal Biology (FBN), Institute of Muscle Biology and Growth, Dummerstorf, Germany
- Research Institute for Farm Animal Biology (FBN), Institute of Genome Biology, Dummerstorf, Germany
| | - Claudia Kalbe
- Research Institute for Farm Animal Biology (FBN), Institute of Muscle Biology and Growth, Dummerstorf, Germany
| | - Puntita Siengdee
- Research Institute for Farm Animal Biology (FBN), Institute of Genome Biology, Dummerstorf, Germany
| | - Siriluck Ponsuksili
- Research Institute for Farm Animal Biology (FBN), Institute of Genome Biology, Dummerstorf, Germany
- *Correspondence: Siriluck Ponsuksili,
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12
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Dou J, Luo H, Sammad A, Lou W, Wang D, Schenkel F, Yu Y, Fang L, Wang Y. Epigenomics of rats' liver and its cross-species functional annotation reveals key regulatory genes underlying short term heat-stress response. Genomics 2022; 114:110449. [PMID: 35985612 DOI: 10.1016/j.ygeno.2022.110449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 07/28/2022] [Accepted: 08/12/2022] [Indexed: 11/04/2022]
Abstract
Molecular responses to heat stress are multifaceted and under a complex cellular post-transcriptional control. This study explores the epigenetic and transcriptional alterations induced by heat stress (42 °C for 120 min) in the liver of rats, by integrating ATAC-seq, RNA-Seq, and WGBS information. Out of 2586 differential ATAC-seq peaks induced by heat stress, 36 up-regulated and 22 down-regulated transcript factors (TFs) are predicted, such as Cebpα, Foxa2, Foxo4, Nfya and Sp3. Furthermore, 150,189 differentially methylated regions represent 2571 differentially expressed genes (DEGs). By integrating all data, 45 DEGs are concluded as potential heat stress response markers in rats. To comprehensively annotate and narrow down predicted markers, they are integrated with GWAS results of heat stress parameters in cows, and PheWAS data in humans. Besides better understanding of heat stress responses in mammals, INSR, MAPK8, RHPN2 and BTBD7 are proposed as candidate markers for heat stress in mammals.
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Affiliation(s)
- Jinhuan Dou
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, National Engineering Laboratory of Animal Breeding, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; Animal Science and Technology College, Beijing University of Agriculture, Beijing 102206, China
| | - Hanpeng Luo
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, National Engineering Laboratory of Animal Breeding, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Abdul Sammad
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, National Engineering Laboratory of Animal Breeding, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Wenqi Lou
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, National Engineering Laboratory of Animal Breeding, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Di Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, National Engineering Laboratory of Animal Breeding, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Flavio Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, N1G 2W1 Guelph, Ontario, Canada
| | - Ying Yu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, National Engineering Laboratory of Animal Breeding, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Lingzhao Fang
- MRC Human Genetics Unit at the Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom.
| | - Yachun Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, National Engineering Laboratory of Animal Breeding, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
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13
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Masroor S, Aalam MT, Khan O, Tanuj GN, Gandham RK, Dhara SK, Gupta PK, Mishra BP, Dutt T, Singh G, Sajjanar BK. Effect of acute heat shock on stress gene expression and DNA methylation in zebu (Bos indicus) and crossbred (Bos indicus × Bos taurus) dairy cattle. INTERNATIONAL JOURNAL OF BIOMETEOROLOGY 2022; 66:1797-1809. [PMID: 35796826 DOI: 10.1007/s00484-022-02320-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 05/15/2022] [Accepted: 06/21/2022] [Indexed: 05/19/2023]
Abstract
Environmental temperature is one of the major factors to affect health and productivity of dairy cattle. Gene expression networks within the cells and tissues coordinate stress response, metabolism, and milk production in dairy cattle. Epigenetic DNA methylations were found to mediate the effect of environment by regulating gene expression patterns. In the present study, we compared three Indian native zebu cattle, Bos indicus (Sahiwal, Tharparkar, and Hariana) and one crossbred Bos indicus × Bos taurus (Vrindavani) for stress gene expression and differences in the DNA methylation patterns. The results indicated acute heat shock to cultured PBMC affected their proliferation, stress gene expression, and DNA methylation. Interestingly, expressions of HSP70, HSP90, and STIP1 were found more pronounced in zebu cattle than the crossbred cattle. However, no significant changes were observed in global DNA methylation due to acute heat shock, even though variations were observed in the expression patterns of DNA methyltransferases (DNMT1, DNMT3a) and demethylases (TET1, TET2, and TET3) genes. The treatment 5-AzaC (5-azacitidine) that inhibit DNA methylation in proliferating PBMC caused significant increase in heat shock-induced HSP70 and STIP1 expression indicating that hypomethylation facilitated stress gene expression. Further targeted analysis DNA methylation in the promoter regions revealed no significant differences for HSP70, HSP90, and STIP1. However, there was a significant hypomethylation for BDNF in both zebu and crossbred cattle. Similarly, NR3C1 promoter region showed hypomethylation alone in crossbred cattle. Overall, the results indicated that tropically adapted zebu cattle had comparatively higher expression of stress genes than the crossbred cattle. Furthermore, DNA methylation may play a role in regulating expression of certain genes involved in stress response pathways.
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Affiliation(s)
- Sana Masroor
- Veterinary Biotechnology Division, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly-243122, Uttar Pradesh, India
| | - Mohd Tanzeel Aalam
- Veterinary Biotechnology Division, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly-243122, Uttar Pradesh, India
| | - Owais Khan
- Veterinary Biotechnology Division, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly-243122, Uttar Pradesh, India
| | - Gunturu Narasimha Tanuj
- Veterinary Biotechnology Division, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly-243122, Uttar Pradesh, India
| | - Ravi Kumar Gandham
- Veterinary Biotechnology Division, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly-243122, Uttar Pradesh, India
| | - Sujoy K Dhara
- Veterinary Biotechnology Division, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly-243122, Uttar Pradesh, India
| | - Praveen K Gupta
- Veterinary Biotechnology Division, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly-243122, Uttar Pradesh, India
| | - Bishnu Prasad Mishra
- ICAR-National Bureau of Animal Genetic Resources, Haryana, Karnal, 132001, India
| | - Triveni Dutt
- Veterinary Biotechnology Division, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly-243122, Uttar Pradesh, India
| | - Gynendra Singh
- Physiology and Climatology Division, ICAR-Indian Veterinary Research Institute, Izatnagar Bareilly, 243122, Uttar Pradesh, India
| | - Basavaraj K Sajjanar
- Veterinary Biotechnology Division, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly-243122, Uttar Pradesh, India.
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14
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Zhao W, Green MP, Marth CD, Liu F, Le HH, Lynch GS, Bell AW, Leury BJ, Dunshea FR, Cottrell JJ. Gestational heat stress alters skeletal muscle gene expression profiles and vascularity in fetal pigs in a sexually dimorphic manner. J Anim Sci Biotechnol 2022; 13:76. [PMID: 35836286 PMCID: PMC9284688 DOI: 10.1186/s40104-022-00730-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 05/08/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND There is evidence that sow heat stress (HS) during gestation affects fetal development with implications for impaired muscle growth. We have previously demonstrated that maternal HS during early to mid-gestation compromised muscle fibre hyperplasia in developing fetal pigs. Thus, we hypothesised these phenotypic changes are associated with a change in expression of genes regulating fetal skeletal muscle development and metabolism. To test this, at d 60 of gestation, RNA sequencing and immunohistochemistry were performed on fetal longissimus dorsi (LD) muscle biopsies collected from pregnant gilts that had experienced either thermoneutral control (CON, 20 °C, n = 7 gilts, 18 LD samples) or controlled HS (cyclic 28 to 33 °C, n = 8 gilts, 23 LD samples) conditions for 3 weeks. RESULTS A total of 282 genes were differentially expressed between the HS and CON groups in female LD muscles (false discovery rate (FDR) ≤ 0.05), whereas no differentially expressed genes were detected in male LD muscles between the two groups (FDR > 0.05). Gestational HS increased the expression of genes associated with transcription corepressor activity, adipogenesis cascades, negative regulation of angiogenesis and pro-inflammatory signalling in female LD muscles. Immunohistochemical analyses revealed a decreased muscle vascularity density in fetuses from HS group for both sexes compared to those from the CON group (P = 0.004). CONCLUSIONS These results reveal gilt HS during early to mid-gestation altered gene expression profiles in fetal LD muscles in a sexually dimorphic manner. The molecular responses, including transcription and angiogenesis repressions and enhanced adipogenesis cascades, were exclusively observed in females. However, the associated reductions in muscle vascularity were observed independently of sexes. Collectively this may indicate female fetal pigs are more adaptive to gestational HS in terms of gene expression changes, and/or there may be sexually dimorphic differences with respect to the timing of muscle molecular responses to gestational HS.
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Affiliation(s)
- Weicheng Zhao
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia.
| | - Mark P Green
- School of BioSciences, Faculty of Science, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Christina D Marth
- Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Werribee, VIC, 3030, Australia
| | - Fan Liu
- Rivalea Australia Pty Ltd, Corowa, NSW, 2646, Australia
| | - Hieu H Le
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Gordon S Lynch
- Centre for Muscle Research, Department of Anatomy and Physiology, The University of Melbourne, Parkville, 3010, Australia
| | - Alan W Bell
- Department of Animal Science, Cornell University, Ithaca, NY, 14853-4801, USA
| | - Brian J Leury
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Frank R Dunshea
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia.,Faculty of Biological Sciences, The University of Leeds, Leeds, LS2 9JT, UK
| | - Jeremy J Cottrell
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia
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Chen Y, Zhang T, Xian M, Zhang R, Yang W, Su B, Yang G, Sun L, Xu W, Xu S, Gao H, Xu L, Gao X, Li J. A draft genome of Drung cattle reveals clues to its chromosomal fusion and environmental adaptation. Commun Biol 2022; 5:353. [PMID: 35418663 PMCID: PMC9008013 DOI: 10.1038/s42003-022-03298-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 03/21/2022] [Indexed: 12/02/2022] Open
Abstract
Drung cattle (Bos frontalis) have 58 chromosomes, differing from the Bos taurus 2n = 60 karyotype. To date, its origin and evolution history have not been proven conclusively, and the mechanisms of chromosome fusion and environmental adaptation have not been clearly elucidated. Here, we assembled a high integrity and good contiguity genome of Drung cattle with 13.7-fold contig N50 and 4.1-fold scaffold N50 improvements over the recently published Indian mithun assembly, respectively. Speciation time estimation and phylogenetic analysis showed that Drung cattle diverged from Bos taurus into an independent evolutionary clade. Sequence evidence of centromere regions provides clues to the breakpoints in BTA2 and BTA28 centromere satellites. We furthermore integrated a circulation and contraction-related biological process involving 43 evolutionary genes that participated in pathways associated with the evolution of the cardiovascular system. These findings may have important implications for understanding the molecular mechanisms of chromosome fusion, alpine valleys adaptability and cardiovascular function.
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Affiliation(s)
- Yan Chen
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 100193, Beijing, P.R. China
| | - Tianliu Zhang
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 100193, Beijing, P.R. China
| | - Ming Xian
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 100193, Beijing, P.R. China
| | - Rui Zhang
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 100193, Beijing, P.R. China
| | - Weifei Yang
- 1 Gene Co., Ltd, 310051, Hangzhou, P.R. China
- Annoroad Gene Technology (Beijing) Co., Ltd, 100176, Beijing, P.R. China
| | - Baqi Su
- Drung Cattle Conservation Farm in Jiudang Wood, Drung and Nu Minority Autonomous County, Gongshan, 673500, Kunming, Yunnan, P.R. China
| | - Guoqiang Yang
- Livestock and Poultry Breed Improvement Center, Nujiang Lisu Minority Autonomous Prefecture, 673199, Kunming, Yunnan, P.R. China
| | - Limin Sun
- Yunnan Animal Husbandry Service, 650224, Kunming, Yunnan, P.R. China
| | - Wenkun Xu
- Yunnan Animal Husbandry Service, 650224, Kunming, Yunnan, P.R. China
| | - Shangzhong Xu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 100193, Beijing, P.R. China
| | - Huijiang Gao
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 100193, Beijing, P.R. China
| | - Lingyang Xu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 100193, Beijing, P.R. China
| | - Xue Gao
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 100193, Beijing, P.R. China.
| | - Junya Li
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 100193, Beijing, P.R. China.
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Gu Z, Yang J, Yang M, Jiao Y. Exploring crucial molecular events in pearl oyster after pre-grafting conditioning by genome-wide bisulfite sequencing for DNA methylation analysis. FISH & SHELLFISH IMMUNOLOGY 2022; 123:10-19. [PMID: 35182724 DOI: 10.1016/j.fsi.2022.02.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 02/13/2022] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Abstract
Pre-grafting condition is an important method to promote recovery from transplant surgery during pearl production. In the present study, we constructed two DNA methylomes from pearl oysters with and without conditioning to investigate the molecular mechanism of the pearl oyster Pinctada fucata martensii underlying the pre-grafting condition. A total of 4,594,997 and 4,930,813 methyl CG in the control (Con) and pre-grafting group (PT) were detected, resulting in the whole genome methylation profile and methylation pattern in P. f. martensii. Results reveal that the promoter, especially the CpG island-rich region, was more infrequently methylated than the gene function elements in P. f. martensii. A total of 51,957 differently methylated regions (DMRs) between Con and PT were obtained, including 3789 DMR in the promoter and 16,021 in the gene body. Based on gene ontology and pathway enrichment analyses, these DMRs were mainly related to "cellular process", "metabolic process", "Epstein-Barr virus infection", and "Fanconi anemia pathway". The methylation site in the promoter region may be associated with the promoter activity and transcription factor binding. These results help our understanding of the mechanism of pre-grafting condition, thereby providing key information in guiding to improve the conditioning methods for enhanced pearl oyster survival rate after transplantation.
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Affiliation(s)
- Zefeng Gu
- Fishery College, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Jingmiao Yang
- Fishery College, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Min Yang
- Fishery College, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Yu Jiao
- Fishery College, Guangdong Ocean University, Zhanjiang, 524088, China; Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang, 524088, China; Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang, 524088, China; Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Zhanjiang, 524088, China.
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17
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Robaire B, Delbes G, Head JA, Marlatt VL, Martyniuk CJ, Reynaud S, Trudeau VL, Mennigen JA. A cross-species comparative approach to assessing multi- and transgenerational effects of endocrine disrupting chemicals. ENVIRONMENTAL RESEARCH 2022; 204:112063. [PMID: 34562476 DOI: 10.1016/j.envres.2021.112063] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 09/09/2021] [Accepted: 09/10/2021] [Indexed: 06/13/2023]
Abstract
A wide range of chemicals have been identified as endocrine disrupting chemicals (EDCs) in vertebrate species. Most studies of EDCs have focused on exposure of both male and female adults to these chemicals; however, there is clear evidence that EDCs have dramatic effects when mature or developing gametes are exposed, and consequently are associated with in multigenerational and transgenerational effects. Several publications have reviewed such actions of EDCs in subgroups of species, e.g., fish or rodents. In this review, we take a holistic approach synthesizing knowledge of the effects of EDCs across vertebrate species, including fish, anurans, birds, and mammals, and discuss the potential mechanism(s) mediating such multi- and transgenerational effects. We also propose a series of recommendations aimed at moving the field forward in a structured and coherent manner.
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Affiliation(s)
- Bernard Robaire
- Department of Pharmacology and Therapeutics and of Obstetrics and Gynecology, McGill University, Montreal, Canada.
| | - Geraldine Delbes
- Centre Armand Frappier Santé Biotechnologie, Institut National de La Recherche Scientifique (INRS), Laval, QC, Canada
| | - Jessica A Head
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Canada
| | - Vicki L Marlatt
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Christopher J Martyniuk
- Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - Stéphane Reynaud
- Univ. Grenoble-Alpes, Université. Savoie Mont Blanc, CNRS, LECA, Grenoble, 38000, France
| | - Vance L Trudeau
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Jan A Mennigen
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
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18
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Meevassana J, Nacharoenkul P, Wititsuwannakul J, Kitkumthorn N, Hamill K, Angspatt A, Mutirangura A. B1 repetitive sequence methylation enhances wound healing of second‑degree burns in rats. Biomed Rep 2022; 16:20. [PMID: 35251607 PMCID: PMC8850962 DOI: 10.3892/br.2022.1503] [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: 09/10/2021] [Accepted: 12/22/2021] [Indexed: 11/24/2022] Open
Abstract
The accumulation of DNA damage in burn wounds delays wound healing. DNA methylation by short interspersed nuclear element (SINE) small interfering (si)RNA prevents DNA damage and promotes cell proliferation. Therefore, SINE siRNA may be able to promote burn wound healing. Here, a SINE B1 siRNA was used to treat burn wounds in rats. Second-degree burn wounds were introduced on the backs of rats. The rats were then divided into three groups: a B1 siRNA-treated, saline-treated control, and saline + calcium phosphate-nanoparticle-treated control group (n=15/group). The wounds were imaged on days 0, 7, 14, 21 and 28 post-injury. The tissue sections were processed for methylation, histological and immunohistochemical examination, and scored based on the overall expression of histone H2AX phosphorylated on serine 139 (γH2AX) and 8-hydroxy-2'-deoxyguanosine (8-OHdG). Burn wound closure improved in the B1 siRNA-treated group compared with that in the control group, especially from days 14-28 post-injury (P<0.001). The overall pathological score and degree of B1 methylation in the B1 siRNA-treated group improved significantly at days 14-28 post-injury, with the maximum improvement observed on day 14 (P<0.01) compared with the NSS and Ca-P nanoparticle groups. Immunohistochemical staining revealed lower expression of γH2AX and 8-OHdG in the B1 siRNA-treated group than in the control groups at days 14-28 post-injury; the maximum improvement was observed on days 14 and 21. These data imply that administering SINE siRNA is a promising therapeutic option for managing second-degree burns.
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Affiliation(s)
- Jiraroch Meevassana
- Department of Anatomy, Center of Excellence in Molecular Genetics of Cancer and Human Disease, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Panupong Nacharoenkul
- Department of Surgery, Division of Plastic and Reconstructive Surgery, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Jade Wititsuwannakul
- Department of Medicine, Division of Dermatology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Nakarin Kitkumthorn
- Department of Oral Biology, Faculty of Dentistry, Mahidol University, Bangkok 10400, Thailand
| | - Kevin Hamill
- Institute of Life Course and Medical Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZX, United Kingdom
| | - Apichai Angspatt
- Department of Surgery, Division of Plastic and Reconstructive Surgery, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Apiwat Mutirangura
- Department of Anatomy, Center of Excellence in Molecular Genetics of Cancer and Human Disease, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
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Exposure of pigs to glyphosate affects gene-specific DNA methylation and gene expression. Toxicol Rep 2022; 9:298-310. [PMID: 35284244 PMCID: PMC8908043 DOI: 10.1016/j.toxrep.2022.02.007] [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: 09/19/2021] [Revised: 02/09/2022] [Accepted: 02/14/2022] [Indexed: 12/24/2022] Open
Abstract
Glyphosate (N-(phosphonomethyl)glycine) is a broad-spectrum systemic herbicide and crop desiccant. Glyphosate has long been suspected of leading to the development of cancer and of compromising fertility. Herbicides have been increasingly recognized as epigenetic modifiers, and the impact of glyphosate on human and animal health might be mediated by epigenetic modifications. This article presents the results from an animal study where pigs were exposed to glyphosate while feeding. The experimental setup included a control group with no glyphosate added to the feed and two groups of pigs with 20 ppm and 200 ppm of glyphosate added to the feed, respectively. After exposure, the pigs were dissected, and tissues of the small intestine, liver, and kidney were used for DNA methylation and gene expression analyses. No significant change in global DNA methylation was found in the small intestine, kidney, or liver. Methylation status was determined for selected genes involved in various functions such as DNA repair and immune defense. In a CpG island of the promoter for IL18, we observed significantly reduced DNA methylation for certain individual CpG positions. However, this change in DNA methylation had no influence on IL18 mRNA expression. The expression of the DNA methylation enzymes DNMT1, DNMT3A, and DNMT3B was measured in the small intestine, kidney, and liver of pigs exposed to glyphosate. No significant changes in relative gene expression were found for these enzymes following dietary exposure to 20 and 200 ppm glyphosate. In contrast, a significant increase in expression of the enzyme TET3, responsible for demethylation, was observed in kidneys exposed to 200 ppm glyphosate. A large animal study with exposure of pigs to glyphosate is presented here. Pigs were exposed to 20 ppm and 200 ppm in the diet. No significant changes in global DNA methylation was observed. A significantly reduced DNA methylation was found in the porcine IL18 promoter. A significant increase in TET3 expression was seen in porcine kidneys exposed to 200 ppm glyphosate.
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20
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How Epigenetics Can Enhance Pig Welfare? Animals (Basel) 2021; 12:ani12010032. [PMID: 35011138 PMCID: PMC8749669 DOI: 10.3390/ani12010032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/15/2021] [Accepted: 12/21/2021] [Indexed: 12/12/2022] Open
Abstract
Epigenetics works as an interface between the individual and its environment to provide phenotypic plasticity to increase individual adaptation capabilities. Recently, a wide variety of epi-genetic findings have indicated evidence for its application in the development of putative epi-biomarkers of stress in farm animals. The purpose of this study was to evaluate previously reported stress epi-biomarkers in swine and encourage researchers to investigate potential paths for the development of a robust molecular tool for animal welfare certification. In this literature review, we report on the scientific concerns in the swine production chain, the management carried out on the farms, and the potential implications of these practices for the animals' welfare and their epigenome. To assess reported epi-biomarkers, we identified, from previous studies, potentially stress-related genes surrounding epi-biomarkers. With those genes, we carried out a functional enrichment analysis of differentially methylated regions (DMRs) of the DNA of swine subjected to different stress-related conditions (e.g., heat stress, intrauterine insult, and sanitary challenges). We identified potential epi-biomarkers for target analysis, which could be added to the current guidelines and certification schemes to guarantee and certify animal welfare on farms. We believe that this technology may have the power to increase consumers' trust in animal welfare.
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21
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Pacht E, Murdoch B, McKay S. Examining the extent of environmental contributions toward DNA methylation and phenotypic variation. Anim Front 2021; 11:83-89. [PMID: 34934533 PMCID: PMC8683128 DOI: 10.1093/af/vfab056] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Emory Pacht
- Department of Animal and Veterinary Sciences, University of Vermont, Burlington, VT, USA
| | - Brenda Murdoch
- Department of Animal, Veterinary and Food Sciences, University of Idaho, Moscow, ID, USA
| | - Stephanie McKay
- Department of Animal and Veterinary Sciences, University of Vermont, Burlington, VT, USA
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22
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Zhang J, Han B, Zheng W, Lin S, Li H, Gao Y, Sun D. Genome-Wide DNA Methylation Profile in Jejunum Reveals the Potential Genes Associated With Paratuberculosis in Dairy Cattle. Front Genet 2021; 12:735147. [PMID: 34721525 PMCID: PMC8554095 DOI: 10.3389/fgene.2021.735147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/23/2021] [Indexed: 12/04/2022] Open
Abstract
Paratuberculosis in cattle causes substantial economic losses to the dairy industry. Exploring functional genes and corresponding regulatory pathways related to resistance or susceptibility to paratuberculosis is essential to the breeding of disease resistance in cattle. Co-analysis of genome-wide DNA methylation and transcriptome profiles is a critically important approach to understand potential regulatory mechanism underlying the development of diseases. In this study, we characterized the profiles of DNA methylation of jejunum from nine Holstein cows in clinical, subclinical, and healthy groups using whole-genome bisulfite sequencing (WGBS). The average methylation level in functional regions was 29.95% in the promoter, 29.65% in the 5’ untranslated region (UTR), 68.24% in exons, 71.55% in introns, and 72.81% in the 3’ UTR. A total of 3,911, 4,336, and 4,094 differentially methylated genes (DMGs) were detected in clinical vs. subclinical, clinical vs. healthy, and subclinical vs. healthy comparative group, respectively. Gene ontology (GO) and analysis based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) showed that these DMGs were significantly enriched in specific biological processes related to immune response, such as Th1 and Th2 cell differentiation, wnt, TNF, MAPK, ECM-receptor interaction, cellular senescence, calcium, and chemokine signaling pathways (q value <0.05). The integration of information about DMGs, differentially expressed genes (DEGs), and biological functions suggested nine genes CALCRL, TNC, GATA4, CD44, TGM3, CXCL9, CXCL10, PPARG, and NFATC1 as promising candidates related to resistance/susceptibility to Mycobacterium avium subspecies paratuberculosis (MAP). This study reports on the high-resolution DNA methylation landscapes of the jejunum methylome across three conditions (clinical, subclinical, and healthy) in dairy cows. Our investigations integrated different sources of information about DMGs, DEGs, and pathways, enabling us to find nine functional genes that might have potential application in resisting paratuberculosis in dairy cattle.
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Affiliation(s)
- Junnan Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Bo Han
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Weijie Zheng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shan Lin
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Houcheng Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yahui Gao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Dongxiao Sun
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, China Agricultural University, Beijing, China
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23
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Wang M, Bissonnette N, Dudemaine PL, Zhao X, Ibeagha-Awemu EM. Whole Genome DNA Methylation Variations in Mammary Gland Tissues from Holstein Cattle Producing Milk with Various Fat and Protein Contents. Genes (Basel) 2021; 12:1727. [PMID: 34828333 PMCID: PMC8618717 DOI: 10.3390/genes12111727] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 10/22/2021] [Accepted: 10/22/2021] [Indexed: 12/20/2022] Open
Abstract
Milk fat and protein contents are among key elements of milk quality, and they are attracting more attention in response to consumers' demand for high-quality dairy products. To investigate the potential regulatory roles of DNA methylation underlying milk component yield, whole genome bisulfite sequencing was employed to profile the global DNA methylation patterns of mammary gland tissues from 17 Canada Holstein cows with various milk fat and protein contents. A total of 706, 2420 and 1645 differentially methylated CpG sites (DMCs) were found between high vs. low milk fat (HMF vs. LMF), high vs. low milk protein (HMP vs. LMP), and high vs. low milk fat and protein (HMFP vs. LMFP) groups, respectively (q value < 0.1). Twenty-seven, 56 and 67 genes harboring DMCs in gene regions (denoted DMC genes) were identified for HMF vs. LMF, HMP vs. LMP and HMFP vs. LMFP, respectively. DMC genes from HMP vs. LMP and HMFP vs. LMFP comparisons were significantly overrepresented in GO terms related to aerobic electron transport chain and/or mitochondrial ATP (adenosine triphosphate) synthesis coupled electron transport. A total of 83 (HMF vs. LMF), 708 (HMP vs. LMP) and 408 (HMFP vs. LMFP) DMCs were co-located with 87, 147 and 158 quantitative trait loci (QTL) for milk component and yield traits, respectively. In conclusion, the identified methylation changes are potentially involved in the regulation of milk fat and protein yields, as well as the variation in reported co-located QTLs.
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Affiliation(s)
- Mengqi Wang
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC J1M 0C8, Canada; (M.W.); (N.B.); (P.-L.D.)
| | - Nathalie Bissonnette
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC J1M 0C8, Canada; (M.W.); (N.B.); (P.-L.D.)
| | - Pier-Luc Dudemaine
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC J1M 0C8, Canada; (M.W.); (N.B.); (P.-L.D.)
| | - Xin Zhao
- Department of Animal Science, McGill University, Ste-Anne-De-Bellevue, QC H9X 3V9, Canada;
| | - Eveline M. Ibeagha-Awemu
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC J1M 0C8, Canada; (M.W.); (N.B.); (P.-L.D.)
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24
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Petrelli S, Buglione M, Maselli V, Troiano C, Larson G, Frantz L, Manin A, Ricca E, Baccigalupi L, Wright D, Pietri C, Fulgione D. Population genomic, olfactory, dietary, and gut microbiota analyses demonstrate the unique evolutionary trajectory of feral pigs. Mol Ecol 2021; 31:220-237. [PMID: 34676935 DOI: 10.1111/mec.16238] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 08/31/2021] [Accepted: 10/12/2021] [Indexed: 10/20/2022]
Abstract
Domestication is an intriguing evolutionary process. Many domestic populations are subjected to strong human-mediated selection, and when some individuals return to the wild, they are again subjected to selective forces associated with new environments. Generally, these feral populations evolve into something different from their wild predecessors and their members typically possess a combination of both wild and human selected traits. Feralisation can manifest in different forms on a spectrum from a wild to a domestic phenotype. This depends on how the rewilded domesticated populations can readapt to natural environments based on how much potential and flexibility the ancestral genome retains after its domestication signature. Whether feralisation leads to the evolution of new traits that do not exist in the wild or to convergence with wild forms, however, remains unclear. To address this question, we performed population genomic, olfactory, dietary, and gut microbiota analyses on different populations of Sus scrofa (wild boar, hybrid, feral and several domestic pig breeds). Porcine single nucleotide polymorphisms (SNPs) analysis shows that the feral population represents a cluster distinctly separate from all others. Its members display signatures of past artificial selection, as demonstrated by values of FST in specific regions of the genome and bottleneck signature, such as the number and length of runs of homozygosity. Generalised FST values, reacquired olfactory abilities, diet, and gut microbiota variation show current responses to natural selection. Our results suggest that feral pigs are an independent evolutionary unit which can persist so long as levels of human intervention remain unchanged.
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Affiliation(s)
- Simona Petrelli
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Maria Buglione
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Valeria Maselli
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Claudia Troiano
- Department of Humanities, University of Naples Federico II, Naples, Italy
| | - Greger Larson
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Laurent Frantz
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Aurelie Manin
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Ezio Ricca
- Department of Biology, University of Naples Federico II, Naples, Italy.,Task Force on Microbiome Studies, University of Naples Federico II, Napoli, Italy
| | - Loredana Baccigalupi
- Task Force on Microbiome Studies, University of Naples Federico II, Napoli, Italy.,Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Dominic Wright
- IFM Biology, AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden
| | - Christian Pietri
- Fédération Départementale des Chasseurs de Haute-Corse (FDCHC), Résidence Nouvelle-Corniche, St Joseph, Bastia, France
| | - Domenico Fulgione
- Department of Biology, University of Naples Federico II, Naples, Italy.,Task Force on Microbiome Studies, University of Naples Federico II, Napoli, Italy
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25
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Genome-wide DNA methylation profiles provide insight into epigenetic regulation of red and white muscle development in Chinese perch Siniperca chuatsi. Comp Biochem Physiol B Biochem Mol Biol 2021; 256:110647. [PMID: 34271193 DOI: 10.1016/j.cbpb.2021.110647] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 06/04/2021] [Accepted: 07/09/2021] [Indexed: 12/19/2022]
Abstract
Fish skeletal muscles are composed of spatially well-separated fiber types, namely, red and white muscles with different physiological functions and metabolism. To compare the DNA methylation profiles of the two types of muscle tissues and identify potential candidate genes for the muscle growth and development under epigenetic regulation, genome-wide DNA methylation of the red and white muscle in Chinese perch Siniperca chuatsi were comparatively analyzed using bisulfate sequencing methods. An average of 0.9 billion 150-bp paired-end reads were obtained, of which 86% were uniquely mapped to the genome. Methylation mostly occurred at CG sites at a ratio of 94.43% in the red muscle and 93.16% in the white muscle. The mean methylation levels at C-sites were 5.95% in red muscle and 5.83% in white muscle, whereas the mean methylation levels of CG, CHG, and CHH were 73.23%, 0.62%, and 0.67% in red muscle, and 71.01%, 0.62%, and 0.67% in white muscle, respectively. A total of 4192 differentially methylated genes (DMGs) were identified significantly enriched in cell signaling pathways related to skeletal muscle differentiation and growth. Various muscle-related genes, including myosin gene isoforms and regulatory factors, are differentially methylated in the promoter region between the red and white muscles. Further analysis of the transcriptional expression of these genes showed that the muscle regulatory factors (myf5, myog, pax3, pax7, and twitst2) and myosin genes (myh10, myh16, myo18a, myo7a, myo9a, and myl3) were differentially expressed between the two kinds of muscles, consistent with the DNA methylation analysis results. ELISA assays confirmed that the level of 5mC in red muscle was significantly higher than in white muscle (P < 0.05). The RT-qPCR assays revealed that the expression levels of the three DNA methylation transferase (dnmt) subtypes, dnmt1, dnmt3ab, and dnmt3bb1, were significantly higher in red muscle than in white muscle. The higher DNA methylation levels in the red muscle may result from higher DNA methylation transferase expression in the red muscles. Thus, this study might provide a theoretical foundation to better understand epigenetic regulation in the growth and development of red and white muscles in animals, at least in Chinese perch fish.
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26
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Kang B, Wang J, Zhang H, Shen W, El-Mahdy Othman O, Zhao Y, Min L. Genome-wide profile in DNA methylation in goat ovaries of two different litter size populations. J Anim Physiol Anim Nutr (Berl) 2021; 106:239-249. [PMID: 34212445 DOI: 10.1111/jpn.13600] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 05/18/2021] [Accepted: 06/13/2021] [Indexed: 12/14/2022]
Abstract
Although some studies have investigated the DNA methylation modification in goat ovaries, it is not understood DNA methylation related to goat litter size. This investigation was designed to explore the DNA methylation status in the ovaries of high litter size and low litter size groups using whole-genome bisulfite sequencing (WGBS). We found that there was global difference on DNA methylation in high litter size and low litter size goat ovaries. Many differentially methylated region-related genes (DMGs) were found in the ovaries of these two different goat populations. Moreover, enrichment analysis discovered that many DMGs were involved in gamete development, reproductive system development, wingless-type MMTV integration site family (WNT) signalling pathways and mitogen-activated protein kinase 1 (MAPK) signalling pathways. The data indicated that DNA methylation in goat ovaries may play important roles in the folliculogenesis, the oocyte ovulation rate and finally the litter size. This study provides a comprehensive analysis of genome-wide DNA methylation patterns in ovaries of high and low litter size goat which helps the understanding of ovarian DNA methylation in relation to goat fertility capability.
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Affiliation(s)
- Beining Kang
- College of Animal Sciences and Technology, Qingdao Agricultural University, Qingdao, China
| | - Junjie Wang
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Hongfu Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wei Shen
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | | | - Yong Zhao
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China.,State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lingjiang Min
- College of Animal Sciences and Technology, Qingdao Agricultural University, Qingdao, China
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27
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Verma N, Alyethodi RR, Kathuria A, Alex R, Hussain S, Singh U, Tyagi S, Sirohi AS, Kumar S, Sengar GS, Raja TV, Prakash B. Comparative CpG methylation kinetic patterns of cis-regulatory regions of heat stress-related genes in Sahiwal and Frieswal cattle upon persistent heat stress. INTERNATIONAL JOURNAL OF BIOMETEOROLOGY 2021; 65:1025-1032. [PMID: 33683454 DOI: 10.1007/s00484-021-02084-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 11/24/2020] [Accepted: 01/18/2021] [Indexed: 06/12/2023]
Abstract
The kinetic patterns of CpG methylation of the cis-regulatory region of heat stress-related genes on exposed to heat stress (at 42 °C) between the Sahiwal and Frieswal cattle was compared in the present study. Using an in vitro whole blood culture model, cells were continuously exposed to heat stress (at 42 °C) for 6 h. Methylation levels of five genes, viz., GPX1, HSP70, HSP90, c-FOS, and JUN were estimated by SyberGreen-based quantitative methylation-specific PCR (qMSP) assay. CpG methylation kinetics at different time points of heat stress (0.5, 1, 2, 4, 6 h) were analyzed using mixed ANOVA. The initial methylation level, estimated at 37 °C, of HSP70 was significantly high in the Sahiwal breed. A significant (p<0.001) time-dependent hypomethylation of an antioxidant gene (GPX1) CpG islands was detected at the acute phase of the stress. Heat shock protein gene (HSP70) showed a similar CpG methylation kinetics where the hypomethylation was prominent from 1 h and persisted up to 4 h. The heat stress responses of both Sahiwal and Frieswal cattle were identical as there was no distinctiveness in the methylation kinetics of CpG islands of studied genes. The acclimatization of Frieswal cattle-a breed developed in India over the years to the tropical climatic conditions, maybe one of the reasons for this similarity. Thus, the present study results could pave a path to understand the molecular mechanism of heat stress and adaptation of indigenous and crossbred cattle populations to the changing scenario in tropical climate conditions.
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Affiliation(s)
- Nitika Verma
- Department of Biotechnology and Microbiology, MIET, Meerut, India
| | - Rafeeque R Alyethodi
- ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India.
| | - Ashima Kathuria
- Department of Biotechnology and Microbiology, MIET, Meerut, India
| | - Rani Alex
- ICAR-National Dairy Research Institute, Karnal, India
| | - Shaziya Hussain
- Department of Biotechnology and Microbiology, MIET, Meerut, India
| | - Umesh Singh
- ICAR-Central Institute for Research on Cattle, Meerut, UP, India
| | - S Tyagi
- ICAR-Central Institute for Research on Cattle, Meerut, UP, India
| | | | - Sushil Kumar
- ICAR-Central Institute for Research on Cattle, Meerut, UP, India
| | | | - T V Raja
- ICAR-Central Institute for Research on Cattle, Meerut, UP, India
| | - B Prakash
- ICAR-Central Institute for Research on Cattle, Meerut, UP, India
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28
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Metzger K, Dannenberger D, Tuchscherer A, Ponsuksili S, Kalbe C. Effects of temperature on proliferation of myoblasts from donor piglets with different thermoregulatory maturities. BMC Mol Cell Biol 2021; 22:36. [PMID: 34174812 PMCID: PMC8236195 DOI: 10.1186/s12860-021-00376-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 06/10/2021] [Indexed: 12/13/2022] Open
Abstract
Background Climate change and the associated risk for the occurrence of extreme temperature events or permanent changes in ambient temperature are important in the husbandry of farm animals. The aim of our study was to investigate the effects of permanent cultivation temperatures below (35 °C) and above (39 °C, 41 °C) the standard cultivation temperature (37 °C) on porcine muscle development. Therefore, we used our porcine primary muscle cell culture derived from satellite cells as an in vitro model. Neonatal piglets have limited thermoregulatory stability, and several days after birth are required to maintain their body temperature. To consider this developmental step, we used myoblasts originating from thermolabile (five days of age) and thermostable piglets (twenty days of age). Results The efficiency of myoblast proliferation using real-time monitoring via electrical impedance was comparable at all temperatures with no difference in the cell index, slope or doubling time. Both temperatures of 37 °C and 39 °C led to similar biochemical growth properties and cell viability. Only differences in the mRNA expression of myogenesis-associated genes were found at 39 °C compared to 37 °C with less MYF5, MYOD and MSTN and more MYH3 mRNA. Myoblasts grown at 35 °C are smaller, exhibit higher DNA synthesis and express higher amounts of the satellite cell marker PAX7, muscle growth inhibitor MSTN and metabolic coactivator PPARGC1A. Only permanent cultivation at 41 °C resulted in higher HSP expression at the mRNA and protein levels. Interactions between the temperature and donor age showed that MYOD, MYOG, MYH3 and SMPX mRNAs were temperature-dependently expressed in myoblasts of thermolabile but not thermostable piglets. Conclusions We conclude that 37 °C to 39 °C is the best physiological temperature range for adequate porcine myoblast development. Corresponding to the body temperatures of piglets, it is therefore possible to culture primary muscle cells at 39 °C. Only the highest temperature of 41 °C acts as a thermal stressor for myoblasts with increased HSP expression, but it also accelerates myogenic development. Cultivation at 35 °C, however, leads to less differentiated myoblasts with distinct thermogenetic activity. The adaptive behavior of derived primary muscle cells to different cultivation temperatures seems to be determined by the thermoregulatory stability of the donor piglets. Supplementary Information The online version contains supplementary material available at 10.1186/s12860-021-00376-4.
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Affiliation(s)
- Katharina Metzger
- Institute of Muscle Biology and Growth, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany.,Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Dirk Dannenberger
- Institute of Muscle Biology and Growth, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Armin Tuchscherer
- Institute of Genetics and Biometry, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Siriluck Ponsuksili
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Claudia Kalbe
- Institute of Muscle Biology and Growth, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany.
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29
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Yang Z, Zhao J, Li J, Wang J, Wang W. Genome-wide DNA methylation profiling of high-fat emulsion-induced hyperlipidemia mice intervened by a polysaccharide from Cyclocarya paliurus (Batal) Iljinskaja. Food Chem Toxicol 2021. [DOI: https://doi.org/10.1016/j.fct.2021.112230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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30
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Yang Z, Zhao J, Li J, Wang J, Wang W. Genome-wide DNA methylation profiling of high-fat emulsion-induced hyperlipidemia mice intervened by a polysaccharide from Cyclocarya paliurus (Batal) Iljinskaja. Food Chem Toxicol 2021; 152:112230. [PMID: 33878369 DOI: 10.1016/j.fct.2021.112230] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 04/09/2021] [Accepted: 04/14/2021] [Indexed: 02/07/2023]
Abstract
Genome-wide DNA methylation was used to study the lipid-lowering effect of Cyclocarya paliurus (Batal) Iljinskaja polysaccharide (CPP). The objective of this study was to investigate the hypolipidemic effects and the potential underlying mechanisms of action of CPP-2 in high-fat emulsion (HFE)-induced mice. The results showed that CPP-2 reduced the level of genome-wide DNA methylation in the liver of HFE-induced mice, which had a lipid-lowering effect by regulating the AMP-activated protein kinase (AMPK) signaling-, fatty acid metabolism-, fatty acid biosynthesis- and adipocytokine signaling pathways. A series of lipid metabolism genes were screened out by conjoint analysis of the Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Hereafter, fatty acid synthase (FAS) and peroxisome proliferators-activated receptor α (PPARα) as target genes were selected to validate the accuracy of the results. The findings demonstrated that CPP-2 might be effective in lowering the lipid content, thereby protecting against HFE-induced hyperlipidemia.
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Affiliation(s)
- Zhanwei Yang
- Key Lab for Agro-product Processing and Quality Control of Nanchang City, College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang 330045, China; School of Food Sciences and Engineering, South China University of Technology, Guangzhou, 510640, China
| | - Jing Zhao
- Guang' an Vocation &Technical College, Guang' an 638000, China
| | - Jing'en Li
- Key Lab for Agro-product Processing and Quality Control of Nanchang City, College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang 330045, China
| | - Jin Wang
- The State Centre of Quality Supervision and Inspection for Camellia Products (Jiangxi), Ganzhou 341000, China
| | - Wenjun Wang
- Key Lab for Agro-product Processing and Quality Control of Nanchang City, College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang 330045, China.
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31
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An X, Zhang S, Li T, Chen N, Wang X, Zhang B, Ma Y. Transcriptomics analysis reveals the effect of Broussonetia papyrifera L. fermented feed on meat quality traits in fattening lamb. PeerJ 2021; 9:e11295. [PMID: 33987003 PMCID: PMC8086582 DOI: 10.7717/peerj.11295] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 03/27/2021] [Indexed: 11/20/2022] Open
Abstract
To date, utilization of feed grains is increasing, which competes for human food. It is imperative to develop and utilize unconventional feed materials. Broussonetia papyrifera L. (B. papyrifera) is a good feeding material with high crude protein, crude fat, and low crude fiber, which is widely distributed in China. In this study, 12 Dorper ♂×Hu ♀ crossbred weaned male lambs were seleted into four groups based on the feed that ratio of the B. papyrifera fermented feed in the total mixed diet (0%, 6%, 18%, and 100%), to character the lambs' longissimus dorsi (LD) fatty acids, morphology and transcriptome. Results showed that the muscle fiber's diameter and area were the smallest in the 100% group. The highest content of beneficial fatty acids and the lowest content of harmful fatty acids in group 18%. RNA-seq identified 443 differentially expressed genes (DEGs) in the LD of lambs from 4 groups. Among these genes, 169 (38.1%) were up-regulated and 274 (61.9%) were down-regulated. The DEGs were mostly enriched in in fatty acid metabolism, arginine and proline metabolism, and PPAR signaling pathways. Our results provide knowledge to understand effect of different ratios of B. papyrifera fermented feed on sheep meat quality traits, also a basis for understanding of the molecular regulation mechanism of B. papyrifera fermented feed affecting on sheep meat quality.
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Affiliation(s)
- Xuejiao An
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Shengwei Zhang
- Gansu Provincial Farmer Education and Training Station, Lanzhou, China
| | - Taotao Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Nana Chen
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Xia Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Baojun Zhang
- Gansu Provincial Farmer Education and Training Station, Lanzhou, China
| | - Youji Ma
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
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32
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Huang Y, Shen Y, Zou H, Jiang Q. Analysis of long non-coding RNAs in skeletal muscle of Bama Xiang pigs in response to heat stress. Trop Anim Health Prod 2021; 53:259. [PMID: 33852074 DOI: 10.1007/s11250-021-02701-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 04/03/2021] [Indexed: 02/06/2023]
Abstract
The aim of this study was to identify differentially expressed long non-coding RNAs (lncRNAs) molecules and predict their target genes related to muscle development and lipid metabolism in longissimus dorsi (LD) muscles of Bama Xiang pigs under constant heat stress. Ten male Bama Xiang pigs with an average initial body weight of 14 kg were randomly divided into control group (22°C) and heat stress (35 °C) group. The experiment lasted for 28 days. All the pigs were slaughtered at the end of the experiment, and LD muscles were collected for muscle quality analysis and transcriptome sequencing. Heat stress reduced meat quality of Bama Xiang pigs. lncRNAs in LD were identified systematically by deep RNA sequencing between the two groups. The results showed that 365 lncRNAs from the LD were identified, including 128 intergenic lncRNAs, 82 intronic lncRNAs, and 155 anti-sense lncRNAs. The differences lie in transcript of length, number of exons and wider size distribution, and expression level per KB fragment in three subtypes of lncRNAs. The three types of transposable elements coverage, including Line/L1, SINE/tRNA, and LTR/ERVL-MaLR, are the highest in mRNA and the three subtypes of lncRNAs in pigs. lncRNAs and mRNAs were different in comparison of features. The results predicted the target genes of the significant differentially expressed lncRNAs related to muscle development and lipid metabolism. This is the first study to expand the knowledge about muscle-related lncRNAs biology in Bama Xiang pigs under heat stress and will contribute to the development of alleviating the adverse effects of heat stress on pork quality targeting lncRNAs.
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Affiliation(s)
- Yanna Huang
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi, China
| | - Yujian Shen
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi, China
| | - Hui Zou
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi, China
| | - Qinyang Jiang
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi, China.
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33
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Dong W, Yang J, Zhang Y, Liu S, Ning C, Ding X, Wang W, Zhang Y, Zhang Q, Jiang L. Integrative analysis of genome-wide DNA methylation and gene expression profiles reveals important epigenetic genes related to milk production traits in dairy cattle. J Anim Breed Genet 2021; 138:562-573. [PMID: 33620112 DOI: 10.1111/jbg.12530] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 11/17/2020] [Accepted: 12/04/2020] [Indexed: 02/03/2023]
Abstract
Epigenetic modification plays a critical role in establishing and maintaining cell differentiation, embryo development, tumorigenesis and many complex diseases. However, little is known about the epigenetic regulatory mechanisms for milk production in dairy cattle. Here, we conducted an epigenome-wide study, together with gene expression profiles to identify important epigenetic candidate genes related to the milk production traits in dairy cattle. Whole-genome bisulphite sequencing and RNA sequencing were employed to detect differentially methylated genes (DMG) and differentially expressed genes (DEG) in blood samples in dry period and lactation period between two groups of cows with extremely high and low milk production performance. A total of 10,877 and 6,617 differentially methylated regions were identified between the two groups in the two periods, which corresponded to 3,601 and 2,802 DMGs, respectively. Furthermore, 156 DEGs overlap with DMGs in comparison of the two groups, and 131 DEGs overlap with DMGs in comparison of the two periods. By integrating methylome, transcriptome and GWAS data, some potential candidate genes for milk production traits in dairy cattle were suggested, such as DOCK1, PTK2 and PIK3R1. Our studies may contribute to a better understanding of epigenetic modification on milk production traits of dairy cattle.
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Affiliation(s)
- Wanting Dong
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jie Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yu Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shuli Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Chao Ning
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an, China
| | - Xiangdong Ding
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Wenwen Wang
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an, China
| | - Yi Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Qin Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China.,College of Animal Science and Technology, Shandong Agricultural University, Tai'an, China
| | - Li Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
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34
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Wang M, Ibeagha-Awemu EM. Impacts of Epigenetic Processes on the Health and Productivity of Livestock. Front Genet 2021; 11:613636. [PMID: 33708235 PMCID: PMC7942785 DOI: 10.3389/fgene.2020.613636] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 12/21/2020] [Indexed: 12/23/2022] Open
Abstract
The dynamic changes in the epigenome resulting from the intricate interactions of genetic and environmental factors play crucial roles in individual growth and development. Numerous studies in plants, rodents, and humans have provided evidence of the regulatory roles of epigenetic processes in health and disease. There is increasing pressure to increase livestock production in light of increasing food needs of an expanding human population and environment challenges, but there is limited related epigenetic data on livestock to complement genomic information and support advances in improvement breeding and health management. This review examines the recent discoveries on epigenetic processes due to DNA methylation, histone modification, and chromatin remodeling and their impacts on health and production traits in farm animals, including bovine, swine, sheep, goat, and poultry species. Most of the reports focused on epigenome profiling at the genome-wide or specific genic regions in response to developmental processes, environmental stressors, nutrition, and disease pathogens. The bulk of available data mainly characterized the epigenetic markers in tissues/organs or in relation to traits and detection of epigenetic regulatory mechanisms underlying livestock phenotype diversity. However, available data is inadequate to support gainful exploitation of epigenetic processes for improved animal health and productivity management. Increased research effort, which is vital to elucidate how epigenetic mechanisms affect the health and productivity of livestock, is currently limited due to several factors including lack of adequate analytical tools. In this review, we (1) summarize available evidence of the impacts of epigenetic processes on livestock production and health traits, (2) discuss the application of epigenetics data in livestock production, and (3) present gaps in livestock epigenetics research. Knowledge of the epigenetic factors influencing livestock health and productivity is vital for the management and improvement of livestock productivity.
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Affiliation(s)
- Mengqi Wang
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC, Canada
- Department of Animal Science, Laval University, Quebec, QC, Canada
| | - Eveline M. Ibeagha-Awemu
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC, Canada
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35
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Corbett RJ, Luttman AM, Wurtz KE, Siegford JM, Raney NE, Ford LM, Ernst CW. Weaning Induces Stress-Dependent DNA Methylation and Transcriptional Changes in Piglet PBMCs. Front Genet 2021; 12:633564. [PMID: 33613645 PMCID: PMC7893110 DOI: 10.3389/fgene.2021.633564] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 01/14/2021] [Indexed: 11/19/2022] Open
Abstract
Changes to the epigenome, including those to DNA methylation, have been proposed as mechanisms by which stress can induce long-term physiological changes in livestock species. Pig weaning is associated with dietary and social stress, both of which elicit an immune response and changes to the hypothalamic–pituitary–adrenal (HPA) axis. While differential methylation following stress has been assessed in model organisms, it remains poorly understood how the pig methylome is altered by stressors in production settings. We quantified changes in CpG methylation and transcript abundance in piglet peripheral blood mononuclear cells (PBMCs) following weaning and also assessed differential patterns in pigs exhibiting high and low stress response as measured by cortisol concentration and lesion scores. Blood was collected from nine gilt piglets 24 h before and after weaning, and whole-genome bisulfite sequencing (WGBS) and RNA-sequencing were performed on six and nine animals, respectively, at both time points. We identified 2,674 differentially methylated regions (DMRs) that were enriched within promoters of genes associated with lymphocyte stimulation and transcriptional regulation. Stress groups displayed unique differential methylation and expression patterns associated with activation and suppression of T cell immunity in low and high stress animals, respectively. Differential methylation was strongly associated with differential expression; specifically, upregulated genes were enriched among hypomethylated genes. We observed post-weaning hypermethylation of the glucocorticoid receptor (NR3C1) promoter and a significant decrease in NR3C1 expression (n = 9, p = 6.1 × 10–3). Our results indicate that weaning-associated stress elicits genome-wide methylation changes associated with differential gene expression, reduced T cell activation, and an altered HPA axis response.
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Affiliation(s)
- Ryan J Corbett
- Genetics and Genome Sciences Graduate Program, Michigan State University, East Lansing, MI, United States
| | - Andrea M Luttman
- Genetics and Genome Sciences Graduate Program, Michigan State University, East Lansing, MI, United States
| | - Kaitlin E Wurtz
- Department of Animal Science, Michigan State University, East Lansing, MI, United States
| | - Janice M Siegford
- Department of Animal Science, Michigan State University, East Lansing, MI, United States
| | - Nancy E Raney
- Department of Animal Science, Michigan State University, East Lansing, MI, United States
| | - Laura M Ford
- Department of Animal Science, Michigan State University, East Lansing, MI, United States
| | - Catherine W Ernst
- Department of Animal Science, Michigan State University, East Lansing, MI, United States
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36
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Chen Y, Hu S, Liu M, Zhao B, Yang N, Li J, Chen Q, Zhou J, Bao G, Wu X. Analysis of Genome DNA Methylation at Inherited Coat Color Dilutions of Rex Rabbits. Front Genet 2021; 11:603528. [PMID: 33552123 PMCID: PMC7859435 DOI: 10.3389/fgene.2020.603528] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 12/15/2020] [Indexed: 12/02/2022] Open
Abstract
Background: The dilution of color in rabbits is associated with many different genetic mechanisms that form different color groups. A number of previous studies have revealed potential regulatory mechanisms by which epigenetics regulate pigmentation. However, the genome-wide DNA methylation involved in animal coat color dilution remains unknown. Results: We compared genome-wide DNA methylation profiles in Rex rabbit hair follicles in a Chinchilla group (Ch) and a diluted Chinchilla group (DCh) through whole-genome bisulfite sequencing (WGBS). Approximately 3.5% of the cytosine sites were methylated in both groups, of which the CG methylation type was in greatest abundance. In total, we identified 126,405 differentially methylated regions (DMRs) between the two groups, corresponding to 11,459 DMR-associated genes (DMGs). Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed that these DMGs were principally involved in developmental pigmentation and Wnt signaling pathways. In addition, two DMRs were randomly selected to verify that the WGBS data were reliable using bisulfite sequencing PCR, and seven DMGs were analyzed to establish the relationship between the level of DNA methylation and mRNA expression using qRT-PCR. Due to the limitation of small sample size, replication of the results with a larger sample size would be important in future studies. Conclusion: These findings provide evidence that there is an association between inherited color dilution and DNA methylation alterations in hair follicles, greatly contributing to our understanding of the epigenetic regulation of rabbit pigmentation.
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Affiliation(s)
- Yang Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou, China
| | - Shuaishuai Hu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Ming Liu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Bohao Zhao
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Naisu Yang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Jiali Li
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Qiuran Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Juan Zhou
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Guolian Bao
- Animal Husbandry and Veterinary Research Institute Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xinsheng Wu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou, China
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37
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Chen P, Xiao WF, Pan MH, Xiao JS, Feng YJ, Dong ZQ, Zou BX, Zhou L, Zhang YH, Lu C. Comparative genome-wide DNA methylation analysis reveals epigenomic differences in response to heat-humidity stress in Bombyx mori. Int J Biol Macromol 2020; 164:3771-3779. [PMID: 32891645 DOI: 10.1016/j.ijbiomac.2020.08.251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/30/2020] [Accepted: 08/31/2020] [Indexed: 11/26/2022]
Abstract
DNA methylation is an important epigenetic modification and has been shown to be involved in the response to abiotic stress. However, there are few studies on DNA methylation in insect response to environmental signals. In this study, we conducted a comprehensive comparative analysis of DNA methylation profiles between two silkworm strains with significantly different resistance to heat and humidity by whole-genome bisulfite sequencing (WGBS). We identified, in total, 2934 differentially methylated regions (DMRs) between RT_48h (resistant strain with high-temperature/humidity treatment for 48 h) and ST_48h (sensitive strain with high-temperature/humidity treatment for 48 h) under cytosine context (CG), which corresponded to 1230 DMR-related genes (DMGs), and the DMRs were primarily located in the gene body (exon and intron) region. Gene ontology (GO) and KEGG analysis showed that these DMGs were most significantly enriched in binding, cellular metabolic process, and RNA transport pathways. Moreover, 10 DMGs have been revealed to be involved in the heat-humidity stress response in the silkworm. The results of this study indicated that DNA methylation plays crucial roles in silkworm response to environmental stressors and provides important clues to identify key resistance genes in silkworm under high-temperature/humidity stress response.
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Affiliation(s)
- Peng Chen
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Beibei 400715, China
| | - Wen-Fu Xiao
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Beibei 400715, China; Sericultural Research Institute Sichuan Academy of Agricultural Sciences, Nanchong 637000, China
| | - Min-Hui Pan
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Beibei 400715, China
| | - Jin-Shu Xiao
- Sericultural Research Institute Sichuan Academy of Agricultural Sciences, Nanchong 637000, China
| | - Yu-Jie Feng
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Beibei 400715, China
| | - Zhan-Qi Dong
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Beibei 400715, China
| | - Bang-Xing Zou
- Sericultural Research Institute Sichuan Academy of Agricultural Sciences, Nanchong 637000, China
| | - Li Zhou
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Beibei 400715, China
| | - You-Hong Zhang
- Sericultural Research Institute Sichuan Academy of Agricultural Sciences, Nanchong 637000, China.
| | - Cheng Lu
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Beibei 400715, China.
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38
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Corbett RJ, Te Pas MFW, van den Brand H, Groenen MAM, Crooijmans RPMA, Ernst CW, Madsen O. Genome-Wide Assessment of DNA Methylation in Chicken Cardiac Tissue Exposed to Different Incubation Temperatures and CO 2 Levels. Front Genet 2020; 11:558189. [PMID: 33193638 PMCID: PMC7655987 DOI: 10.3389/fgene.2020.558189] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 09/30/2020] [Indexed: 12/26/2022] Open
Abstract
Temperature and CO2 concentration during incubation have profound effects on broiler chick development, and numerous studies have identified significant effects on hatch heart weight (HW) as a result of differences in these parameters. Early life environment has also been shown to affect broiler performance later in life; it has thus been suggested that epigenetic mechanisms may mediate long-term physiological changes induced by environmental stimuli. DNA methylation is an epigenetic modification that can confer heritable changes in gene expression. Using reduced-representation bisulfite sequencing (RRBS), we assessed DNA methylation patterns in cardiac tissue of 84 broiler hatchlings incubated at two egg shell temperatures (EST; 37.8°C and 38.9°C) and three CO2 concentrations (0.1%, 0.4%, and 0.8%) from day 8 of incubation onward. We assessed differential methylation between EST treatments and identified 2,175 differentially methylated (DM) CpGs (1,121 hypermethylated, 1,054 hypomethylated at 38.9° vs. 37.8°) in 269 gene promoters and 949 intragenic regions. DM genes (DMGs) were associated with heart developmental processes, including cardiomyocyte proliferation and differentiation. We identified enriched binding motifs among DM loci, including those for transcription factors associated with cell proliferation and heart development among hypomethylated CpGs that suggest increased binding ability at higher EST. We identified 9,823 DM CpGs between at least two CO2 treatments, with the greatest difference observed between 0.8 and 0.1% CO2 that disproportionately impacted genes involved in cardiac muscle development and response to low oxygen levels. Using HW measurements from the same chicks, we performed an epigenome-wide association study (EWAS) for HW, and identified 23 significantly associated CpGs, nine of which were also DM between ESTs. We found corresponding differences in transcript abundance between ESTs in three DMGs (ABLIM2, PITX2, and THRSP). Hypomethylation of an exonic CpG in PITX2 at 38.9°C was associated with increased expression, and suggests increased cell proliferation in broiler hatchlings incubated at higher temperatures. Overall, these results identified numerous epigenetic associations between chick incubation factors and heart development that may manifest in long-term differences in animal performance.
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Affiliation(s)
- Ryan J Corbett
- Genetics and Genome Sciences Graduate Program, Michigan State University, East Lansing, MI, United States
| | - Marinus F W Te Pas
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, Netherlands
| | - Henry van den Brand
- Adaptation Physiology Group, Wageningen University & Research, Wageningen, Netherlands
| | - Martien A M Groenen
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, Netherlands
| | | | - Catherine W Ernst
- Department of Animal Science, Michigan State University, East Lansing, MI, United States
| | - Ole Madsen
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, Netherlands
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39
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Yang Y, Zheng Y, Sun L, Chen M. Genome-Wide DNA Methylation Signatures of Sea Cucumber Apostichopus japonicus during Environmental Induced Aestivation. Genes (Basel) 2020; 11:genes11091020. [PMID: 32877994 PMCID: PMC7565549 DOI: 10.3390/genes11091020] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 08/21/2020] [Accepted: 08/28/2020] [Indexed: 02/07/2023] Open
Abstract
Organisms respond to severe environmental changes by entering into hypometabolic states, minimizing their metabolic rates, suspending development and reproduction, and surviving critical ecological changes. They come back to an active lifestyle once the environmental conditions are conducive. Marine invertebrates live in the aquatic environment and adapt to environmental changes in their whole life. Sea cucumbers and sponges are only two recently known types of marine organisms that aestivate in response to temperature change. Sea cucumber has become an excellent model organism for studies of environmentally-induced aestivation by marine invertebrates. DNA methylation, the most widely considered epigenetic marks, has been reported to contribute to phenotypic plasticity in response to environmental stress in aquatic organisms. Most of methylation-related enzymes, including DNA methyltransferases, Methyl-CpG binding domain proteins, and DNA demethylases, were up-regulated during aestivation. We conducted high-resolution whole-genome bisulfite sequencing of the intestine from sea cucumber at non-aestivation and deep-aestivation stages. Further DNA methylation profile analysis was also conducted across the distinct genomic features and entire transcriptional units. A different elevation in methylation level at internal exons was observed with clear demarcation of intron/exon boundaries during transcriptional unit scanning. The lowest methylation level occurs in the first exons, followed by the last exons and the internal exons. A significant increase in non-CpG methylation (CHG and CHH) was observed within the intron and mRNA regions in aestivation groups. A total of 1393 genes were annotated within hypermethylated DMRs (differentially methylated regions), and 749 genes were annotated within hypomethylated DMRs. Differentially methylated genes were enriched in the mRNA surveillance pathway, metabolic pathway, and RNA transport. Then, 24 hypermethylated genes and 15 hypomethylated genes were Retrovirus-related Pol polyprotein from transposon (RPPT) genes. This study provides further understanding of epigenetic control on environmental induced hypometabolism in aquatic organisms.
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Affiliation(s)
- Yujia Yang
- Laboratory for Evolution and Development, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China;
| | - Yingqiu Zheng
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266071, China;
| | - Lina Sun
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences (CAS), Qingdao 266003, China
- Correspondence: (L.S.); (M.C.)
| | - Muyan Chen
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266071, China;
- Correspondence: (L.S.); (M.C.)
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Godyń D, Herbut P, Angrecka S, Corrêa Vieira FM. Use of Different Cooling Methods in Pig Facilities to Alleviate the Effects of Heat Stress-A Review. Animals (Basel) 2020; 10:ani10091459. [PMID: 32825297 PMCID: PMC7552673 DOI: 10.3390/ani10091459] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 08/17/2020] [Accepted: 08/19/2020] [Indexed: 12/20/2022] Open
Abstract
An increase in the frequency of hot periods, which has been observed over the past decades, determines the novel approach to livestock facilities improvement. The effects of heat stress are revealed in disorders in physiological processes, impaired immunity, changes in behaviour and decreases in animal production, thus implementation of cooling technologies is a key factor for alleviating these negative consequences. In pig facilities, various cooling methods have been implemented. Air temperature may be decreased by using adiabatic cooling technology such as a high-pressure fogging system or evaporative pads. In modern-type buildings large-surface evaporative pads may support a tunnel ventilation system. Currently a lot of attention has also been paid to developing energy- and water-saving cooling methods, using for example an earth-air or earth-to-water heat exchanger. The pigs' skin surface may be cooled by using sprinkling nozzles, high-velocity air stream or conductive cooling pads. The effectiveness of these technologies is discussed in this article, taking into consideration the indicators of animal welfare such as respiratory rate, skin surface and body core temperature, performance parameters and behavioural changes.
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Affiliation(s)
- Dorota Godyń
- Department of Cattle Breeding, National Research Institute of Animal Production, Balice n Kraków, 31-047 Kraków, Poland
- Correspondence:
| | - Piotr Herbut
- Department of Rural Building, Faculty of Environmental Engineering and Land Surveying, University of Agriculture in Krakow, 31-120 Kraków, Poland; (P.H.); (S.A.)
| | - Sabina Angrecka
- Department of Rural Building, Faculty of Environmental Engineering and Land Surveying, University of Agriculture in Krakow, 31-120 Kraków, Poland; (P.H.); (S.A.)
| | - Frederico Márcio Corrêa Vieira
- Biometeorology Study Group (GEBIOMET), Universida de Tecnológica Federal do Paraná (UTFPR), Estrada para Boa Esperança, km 04, Comunidade São Cristóvão, Dois Vizinhos PR 85660-000, Brazil;
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Halli K, Brügemann K, Bohlouli M, König S. Time-lagged and acute impact of heat stress on production and fertility traits in the local dual-purpose cattle breed "Rotes Höhenvieh" under pasture-based conditions. Transl Anim Sci 2020; 4:txaa148. [PMID: 33033792 PMCID: PMC7528550 DOI: 10.1093/tas/txaa148] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 07/30/2020] [Indexed: 12/21/2022] Open
Abstract
Climate change causes rising temperatures and extreme weather events worldwide, with possible detrimental time-lagged and acute impact on production and functional traits of cattle kept in outdoor production systems. The aim of the present study was to infer the influence of mean daily temperature humidity index (mTHI) and number of heat stress days (nHS) from different recording periods on birth weight (BWT), 200 d- and 365 d-weight gain (200 dg, 365 dg) of calves, and on the probability of stillbirth (SB), and calving interval (CINT) of their dams. Data recording included 4,362 observations for BWT, 3,136 observations for 200 dg, 2,502 observations for 365 dg, 9,293 observations for the birth status, and 2,811 observations for CINT of the local dual-purpose cattle breed "Rotes Höhenvieh" (RHV). Trait responses on mTHI and nHS were studied via generalized linear mixed model applications with identity link functions for Gaussian traits (BWT, 200 dg, 365 dg, CINT) and logit link functions for binary SB. High mTHI and high nHS before autumn births had strongest detrimental impact on BWT across all antepartum- (a.p.) periods (34.4 ± 0.79 kg maximum). Prolonged CINT was observed when cows suffered heat stress (HS) before or after spring calvings, with maximum length of 391.6 ± 3.82 d (56 d a.p.-period). High mTHI and high nHS during the 42 d- and 56 d a.p.-period implied increased probabilities for SB. We found a significant (P < 0.05) seasonal effect on SB in model 3 across all a.p.-periods, with the highest probability in autumn (maximum of 5.4 ± 0.82% in the 7 d a.p.-period). Weight gains of calves (200 dg and 365 dg) showed strongest HS response for mTHI and nHS measurements from the long-term postnatal periods (42 d- and 56 d-periods), with minimum 200 dg of 194.2 ± 4.15 kg (nHS of 31 to 42 d in the 42 d-period) or minimum 365 dg of 323.8 ± 3.82 kg (mTHI ≥ 60 in the 42 d-period). Calves born in summer, combined with high mTHI or high nHS pre- or postnatal, had lower weight gains, compared with calves born in other calving seasons or under cooler conditions. Highest BWT, weight gains, and shortest CINT mostly were detected under cool to moderate climate conditions for mTHI, and small to moderate nHS. Results indicate acute and time-lagged HS effects and address possible HS-induced epigenetic modifications of the bovine genome across generations and limited acclimatization processes to heat, especially when heat occurs during the cooler spring and autumn months.
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Affiliation(s)
- Kathrin Halli
- Institute of Animal Breeding and Genetics, Group Animal Breeding, Justus-Liebig-University, Giessen, Germany
| | - Kerstin Brügemann
- Institute of Animal Breeding and Genetics, Group Animal Breeding, Justus-Liebig-University, Giessen, Germany
| | - Mehdi Bohlouli
- Institute of Animal Breeding and Genetics, Group Animal Breeding, Justus-Liebig-University, Giessen, Germany
| | - Sven König
- Institute of Animal Breeding and Genetics, Group Animal Breeding, Justus-Liebig-University, Giessen, Germany
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Del Corvo M, Bongiorni S, Stefanon B, Sgorlon S, Valentini A, Ajmone Marsan P, Chillemi G. Genome-Wide DNA Methylation and Gene Expression Profiles in Cows Subjected to Different Stress Level as Assessed by Cortisol in Milk. Genes (Basel) 2020; 11:genes11080850. [PMID: 32722461 PMCID: PMC7464205 DOI: 10.3390/genes11080850] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/10/2020] [Accepted: 07/22/2020] [Indexed: 12/20/2022] Open
Abstract
Dairy cattle health, wellbeing and productivity are deeply affected by stress. Its influence on metabolism and immune response is well known, but the underlying epigenetic mechanisms require further investigation. In this study, we compared DNA methylation and gene expression signatures between two dairy cattle populations falling in the high- and low-variant tails of the distribution of milk cortisol concentration (MC), a neuroendocrine marker of stress in dairy cows. Reduced Representation Bisulfite Sequencing was used to obtain a methylation map from blood samples of these animals. The high and low groups exhibited similar amounts of methylated CpGs, while we found differences among non-CpG sites. Significant methylation changes were detected in 248 genes. We also identified significant fold differences in the expression of 324 genes. KEGG and Gene Ontology (GO) analysis showed that genes of both groups act together in several pathways, such as nervous system activity, immune regulatory functions and glucocorticoid metabolism. These preliminary results suggest that, in livestock, cortisol secretion could act as a trigger for epigenetic regulation and that peripheral changes in methylation can provide an insight into central nervous system functions.
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Affiliation(s)
- Marcello Del Corvo
- Department of Animal Science Food and Nutrition—DIANA, Nutrigenomics and Proteomics Research Centre—PRONUTRIGEN, and Biodiversity and Ancient DNA Research Centre, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy;
- Istituto di Biologia e BiotecnologiaAgraria, Consiglio Nazionale delle Ricerche, 20133 Milan, Italy
- Correspondence:
| | - Silvia Bongiorni
- Department of Ecological and Biological sciences DEB, University of Tuscia, 01100 Viterbo, Italy;
| | - Bruno Stefanon
- Department of Agrifood, Environmental and Animal Science–University of Udine, 33100 Udine, Italy; (B.S.); (S.S.)
| | - Sandy Sgorlon
- Department of Agrifood, Environmental and Animal Science–University of Udine, 33100 Udine, Italy; (B.S.); (S.S.)
| | - Alessio Valentini
- Department for Innovation in Biological, Agro-food and Forest systems DIBAF, University of Tuscia, 01100 Viterbo, Italy; (A.V.); (G.C.)
| | - Paolo Ajmone Marsan
- Department of Animal Science Food and Nutrition—DIANA, Nutrigenomics and Proteomics Research Centre—PRONUTRIGEN, and Biodiversity and Ancient DNA Research Centre, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy;
| | - Giovanni Chillemi
- Department for Innovation in Biological, Agro-food and Forest systems DIBAF, University of Tuscia, 01100 Viterbo, Italy; (A.V.); (G.C.)
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, IBIOM, CNR, 70126 Bari, Italy
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Xu C, Wang X, Zhuang Z, Wu J, Zhou S, Quan J, Ding R, Ye Y, Peng L, Wu Z, Zheng E, Yang J. A Transcriptome Analysis Reveals that Hepatic Glycolysis and Lipid Synthesis Are Negatively Associated with Feed Efficiency in DLY Pigs. Sci Rep 2020; 10:9874. [PMID: 32555275 PMCID: PMC7303214 DOI: 10.1038/s41598-020-66988-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 06/01/2020] [Indexed: 12/25/2022] Open
Abstract
Feed efficiency (FE) is an important trait in the porcine industry. Therefore, understanding the molecular mechanisms of FE is vital for the improvement of this trait. In this study, 6 extreme high-FE and 6 low-FE pigs were selected from 225 Duroc × (Landrace × Yorkshire) (DLY) pigs for transcriptomic analysis. RNA-seq analysis was performed to determine differentially expressed genes (DEGs) in the liver tissues of the 12 individuals, and 507 DEGs were identified between high-FE pigs (HE- group) and low-FE pigs (LE- group). A gene ontology (GO) enrichment and pathway enrichment analysis were performed and revealed that glycolytic metabolism and lipid synthesis-related pathways were significantly enriched within DEGs; all of these DEGs were downregulated in the HE- group. Moreover, Weighted gene co-expression analysis (WGCNA) revealed that oxidative phosphorylation, thermogenesis, and energy metabolism-related pathways were negatively related to HE- group, which might result in lower energy consumption in higher efficiency pigs. These results implied that the higher FE in the HE- group may be attributed to a lower glycolytic, energy consumption and lipid synthesizing potential in the liver. Furthermore, our findings suggested that the inhibition of lipid synthesis and glucose metabolic activity in the liver may be strategies for improving the FE of DLY pigs.
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Affiliation(s)
- Cineng Xu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, P.R. China
| | - Xingwang Wang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, P.R. China
| | - Zhanwei Zhuang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, P.R. China
| | - Jie Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, P.R. China
| | - Shenping Zhou
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, P.R. China
| | - Jianping Quan
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, P.R. China
| | - Rongrong Ding
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, P.R. China
| | - Yong Ye
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, P.R. China
| | - Longlong Peng
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, P.R. China
| | - Zhenfang Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, P.R. China
| | - Enqin Zheng
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, P.R. China.
| | - Jie Yang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, P.R. China.
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Srikanth K, Park JE, Ji SY, Kim KH, Lee YK, Kumar H, Kim M, Baek YC, Kim H, Jang GW, Choi BH, Lee SD. Genome-Wide Transcriptome and Metabolome Analyses Provide Novel Insights and Suggest a Sex-Specific Response to Heat Stress in Pigs. Genes (Basel) 2020; 11:genes11050540. [PMID: 32403423 PMCID: PMC7291089 DOI: 10.3390/genes11050540] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 05/06/2020] [Accepted: 05/06/2020] [Indexed: 12/16/2022] Open
Abstract
Heat stress (HS) negatively impacts pig production and swine health. Therefore, to understand the genetic and metabolic responses of pigs to HS, we used RNA-Seq and high resolution magic angle spinning (HR-MAS) NMR analyses to compare the transcriptomes and metabolomes of Duroc pigs (n = 6, 3 barrows and 3 gilts) exposed to heat stress (33 °C and 60% RH) with a control group (25 °C and 60% RH). HS resulted in the differential expression of 552 (236 up, 316 down) and 879 (540 up, 339 down) genes and significant enrichment of 30 and 31 plasma metabolites in female and male pigs, respectively. Apoptosis, response to heat, Toll-like receptor signaling and oxidative stress were enriched among the up-regulated genes, while negative regulation of the immune response, ATP synthesis and the ribosomal pathway were enriched among down-regulated genes. Twelve and ten metabolic pathways were found to be enriched (among them, four metabolic pathways, including arginine and proline metabolism, and three metabolic pathways, including pantothenate and CoA biosynthesis), overlapping between the transcriptome and metabolome analyses in the female and male group respectively. The limited overlap between pathways enriched with differentially expressed genes and enriched plasma metabolites between the sexes suggests a sex-specific response to HS in pigs.
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Affiliation(s)
- Krishnamoorthy Srikanth
- Amimal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Korea; (K.S.); (J.-E.P.); (H.K.); (H.K.); (G.-W.J.); (B.-H.C.)
| | - Jong-Eun Park
- Amimal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Korea; (K.S.); (J.-E.P.); (H.K.); (H.K.); (G.-W.J.); (B.-H.C.)
| | - Sang Yun Ji
- Animal Nutrition and Physiology Team, National Institute of Animal Science, RDA, Wanju 55365, Korea; (S.Y.J.); (K.H.K.); (Y.K.L.); (M.K.); (Y.C.B.)
| | - Ki Hyun Kim
- Animal Nutrition and Physiology Team, National Institute of Animal Science, RDA, Wanju 55365, Korea; (S.Y.J.); (K.H.K.); (Y.K.L.); (M.K.); (Y.C.B.)
| | - Yoo Kyung Lee
- Animal Nutrition and Physiology Team, National Institute of Animal Science, RDA, Wanju 55365, Korea; (S.Y.J.); (K.H.K.); (Y.K.L.); (M.K.); (Y.C.B.)
| | - Himansu Kumar
- Amimal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Korea; (K.S.); (J.-E.P.); (H.K.); (H.K.); (G.-W.J.); (B.-H.C.)
| | - Minji Kim
- Animal Nutrition and Physiology Team, National Institute of Animal Science, RDA, Wanju 55365, Korea; (S.Y.J.); (K.H.K.); (Y.K.L.); (M.K.); (Y.C.B.)
| | - Youl Chang Baek
- Animal Nutrition and Physiology Team, National Institute of Animal Science, RDA, Wanju 55365, Korea; (S.Y.J.); (K.H.K.); (Y.K.L.); (M.K.); (Y.C.B.)
| | - Hana Kim
- Amimal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Korea; (K.S.); (J.-E.P.); (H.K.); (H.K.); (G.-W.J.); (B.-H.C.)
| | - Gul-Won Jang
- Amimal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Korea; (K.S.); (J.-E.P.); (H.K.); (H.K.); (G.-W.J.); (B.-H.C.)
| | - Bong-Hwan Choi
- Amimal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Korea; (K.S.); (J.-E.P.); (H.K.); (H.K.); (G.-W.J.); (B.-H.C.)
| | - Sung Dae Lee
- Animal Nutrition and Physiology Team, National Institute of Animal Science, RDA, Wanju 55365, Korea; (S.Y.J.); (K.H.K.); (Y.K.L.); (M.K.); (Y.C.B.)
- Correspondence: ; Tel.: +82-63-238-7454; Fax: +82-63-238-7497
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Sajjanar B, Siengdee P, Trakooljul N, Liu X, Kalbe C, Wimmers K, Ponsuksili S. Cross-talk between energy metabolism and epigenetics during temperature stress response in C2C12 myoblasts. Int J Hyperthermia 2020; 36:776-784. [PMID: 31431083 DOI: 10.1080/02656736.2019.1639834] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Objective: Environmental stress induces disturbances in cell energy metabolism and may cause epigenetic modifications. This study aimed to understand the possible impact of temperature stress (35 °C, 39 °C and 41 °C, compared to control 37 °C) on energy metabolism and epigenetic modifications, such as DNA methylation and histone H4 acetylation, as well as its effects on the expression of genes responsible for epigenetic changes, in mouse skeletal myoblasts (C2C12 cells). Methods: The results showed significantly reduced maximal respiration and spare respiratory capacity under heat stress (39 °C and 41 °C), suggesting that mitochondrial functions were compromised under these conditions. The glycolytic capacity and glycolysis markedly increased following low-temperature stress (35 °C). The results suggested that, under cold stress, cells prefer glycolysis as a rapid compensatory mechanism to meet energy requirements for adaptive thermogenic response. Results: Epigenetic changes (histone H4 acetylation and global DNA methylation) were observed under both heat and cold stress. Among the genes coding for DNA methyltransferases, the Dnmt3a was significantly increased under high-temperature conditions (39 °C and 41 °C), while Dnmt1 expression was significantly increased at low temperature (35 °C), indicating that under these conditions the cells preferred maintenance of methylation to de novo methylation activity. An expression pattern similar to Dnmt3a was observed for Gcn5, encoding for a histone acetyltransferase. The study revealed that temperature stress induced changes in the metabolic profiles, as well as epigenetic modifications, including the dynamics of the key enzymes. Conclusion: The results indicated the existence of crosstalk mechanisms between energy metabolism and epigenetics during cell stress response.
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Affiliation(s)
- Basavaraj Sajjanar
- Functional Genome Analysis Research Unit, Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN) , Dummerstorf , Germany
| | - Puntita Siengdee
- Functional Genome Analysis Research Unit, Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN) , Dummerstorf , Germany
| | - Nares Trakooljul
- Functional Genome Analysis Research Unit, Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN) , Dummerstorf , Germany
| | - Xuan Liu
- Functional Genome Analysis Research Unit, Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN) , Dummerstorf , Germany
| | - Claudia Kalbe
- Institute of Muscle Biology and Growth, Leibniz Institute for Farm Animal Biology (FBN) , Dummerstorf , Germany
| | - Klaus Wimmers
- Functional Genome Analysis Research Unit, Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN) , Dummerstorf , Germany.,Faculty of Agricultural and Environmental Sciences, University Rostock , Rostock , Germany
| | - Siriluck Ponsuksili
- Functional Genome Analysis Research Unit, Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN) , Dummerstorf , Germany
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Expression and localization of MYH11 in mouse tissues, oocytes and preimplantation embryos. Biologia (Bratisl) 2019. [DOI: 10.2478/s11756-019-00353-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Podgorniak T, Brockmann S, Konstantinidis I, Fernandes JMO. Differences in the fast muscle methylome provide insight into sex-specific epigenetic regulation of growth in Nile tilapia during early stages of domestication. Epigenetics 2019; 14:818-836. [PMID: 31131688 PMCID: PMC6597363 DOI: 10.1080/15592294.2019.1618164] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 05/02/2019] [Accepted: 05/04/2019] [Indexed: 01/14/2023] Open
Abstract
Growth is a complex trait whose variability within a population cannot be explained solely by genetic variation. Epigenetic regulation is often suggested as an important factor shaping the phenotype, but its association with growth can be highly context- and species-dependent. Nevertheless, the mechanisms involved in epigenetic regulation of growth in fish are poorly understood. We have used reduced representation bisulphite sequencing to determine the genome-wide CpG methylation patterns in male and female Nile tilapia of different sizes but at the same early stage of domestication. The average CpG methylation level in the reduced genome representation was 63% across groups but many sites displayed group-specific methylation patterns. The number of differentially methylated (DM) CpGs was much higher when the interaction between sex and weight was included rather than when these factors were considered separately. There were 1128 DM CpGs between large and small females and 970 DM CpGs between large and small males. We have found many growth-related genes associated with DM CpGs, namely map3k5 and akt3 in females and gadd45g and ppargc1a in males. Only 5% of CpG locations associated with growth were common to both sexes. In particular, the autophagy-related gene atg14 displayed a high association of methylation with growth exclusively in males. The sexually dimorphic association between atg14 methylation and growth may uncover novel metabolic mechanisms at play during mouth brooding in Nile tilapia females. Taken together, our data suggest that epigenetic regulation of growth in Nile tilapia involves different gene networks in males and females.
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Affiliation(s)
- Tomasz Podgorniak
- Genomics Division, Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Sven Brockmann
- Genomics Division, Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Ioannis Konstantinidis
- Genomics Division, Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Jorge M. O. Fernandes
- Genomics Division, Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
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Fang W, Wen X, Meng Q, Wu W, Everaert N, Xie J, Zhang H. Alteration in bile acids profile in Large White pigs during chronic heat exposure. J Therm Biol 2019; 84:375-383. [PMID: 31466777 DOI: 10.1016/j.jtherbio.2019.07.027] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 07/01/2019] [Accepted: 07/25/2019] [Indexed: 12/25/2022]
Abstract
Bile acids (BAs) are critical for cholesterol homeostasis and new roles in metabolism and endocrinology have been demonstrated recently. It remains unknown whether BA metabolism can be affected by heat stress (HS). The objective of this study was to describe the shifts in serum, hepatic and intestinal BA profiles induced by chronic HS. Twenty-seven Large White pigs weighing 40.8 ± 2.7 kg were assigned to one of the three treatments: a control group (CON, 23 °C), a HS group (33 °C), or a pair-fed group (PF, 23 °C and fed the same amount as HS group) for 21 d. The concentrations of taurine-conjugated BAs (TUDCA and THDCA in serum and TCDCA, TUDCA, THDCA and THCA in liver) were decreased in HS and PF pigs. However, in HS pigs, a reduction in taurine-conjugated BAs (TCBA) correlated with decreased liver genes expression of BA synthesis, conjugation and uptake transport. BA regulated-genes (FXR, TGR5 and FGFR4) in HS pigs and TGR5, FGFR4 and KLβ in PF pigs were down-regulated in liver. In ileum, total BAs and glycoursodeoxycholic acid concentrations were higher in HS pigs than other groups and PF group, respectively (P < 0.05). TCBA (P = 0.01) and tauroursodeoxycholic acid (P < 0.01) were decreased in PF group. BA transporters (OSTα and MRP3) were up-regulated in HS pigs compared with CON and PF pigs, respectively (P < 0.01). In cecum, ursodeoxycholic acid was higher in HS (P = 0.02) group than CON group. The expression of apical sodium-coupled bile acid transporter (P = 0.04) was lower in HS pigs than CON pigs, while OSTβ (P < 0.01) was greater in HS group than PF group. These results suggest that chronic HS suppressed liver activity of synthesis and uptake of TCBA, at least in part, which was independent of reduced feed intake.
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Affiliation(s)
- Wei Fang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, China; Precision Livestock and Nutrition Unit, Gembloux Agro-Bio Tech, TERRA Teaching and Research Unit, Liège University, Passage des Déportés 2, Gembloux, Belgium
| | - Xiaobin Wen
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, China
| | - Qingshi Meng
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, China
| | - Weida Wu
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, China
| | - Nadia Everaert
- Precision Livestock and Nutrition Unit, Gembloux Agro-Bio Tech, TERRA Teaching and Research Unit, Liège University, Passage des Déportés 2, Gembloux, Belgium
| | - Jingjing Xie
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, China.
| | - Hongfu Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, China.
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Lu Z, Ma Y, Li Q, Liu E, Jin M, Zhang L, Wei C. The role of N 6-methyladenosine RNA methylation in the heat stress response of sheep (Ovis aries). Cell Stress Chaperones 2019; 24:333-342. [PMID: 30701478 PMCID: PMC6439051 DOI: 10.1007/s12192-018-00965-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 12/14/2018] [Accepted: 12/17/2018] [Indexed: 11/30/2022] Open
Abstract
With the intensive development of the sheep industry and increasing global temperatures, heat stress in sheep has become an increasingly severe and important issue in recent years. The level of N6-methyladenosine (m6A) RNA methylation changes in response to stress plays important roles in stress responses. However, the role of m6A in the heat stress response of sheep remains unclear. To explore this issue, we measured heat stress protein (HSP) expression, liver function indexes, m6A on RNA, m6A-related enzyme expression, and tissue damage in sheep that had been subjected to heat stress. At the transcriptome level, our results showed significant increases in m6A on RNA and increased mRNA levels of HSPs (HSP70, HSP90, and HSP110) and m6A-related enzymes [METTL3 (methyltransferase-like 3), METTL14 (methyltransferase-like 14), WTAP (wilms tumor 1-associated protein), FTO (fat mass and obesity-associated protein), ALKBH5 (alkB homologue 5), YTHDF1-3 (YTH domain family proteins), and YTHDC1-2 (YTH domain-containing proteins)] following heat stress. At the protein level, the expression of METTL3, YTHDF1-2, and YTHDC2 showed no significant differences following heat stress. However, in contrast to its mRNA level after heat stress, the protein expression of YTHDF3 was reduced, while the expression of HSPs (HSP70, HSP90, and HSP110), METTL14, WTAP, FTO, ALKBH5, YTHDF3, and YTHDC1 increased in line with their measured mRNA levels. Histological experiments revealed that heat stress caused varying degrees of damage to sheep liver tissue. Moreover, immunohistochemical staining indicated that the m6A-related enzymes were expressed in sheep hepatocytes, and differences in expression patterns were observed between the control and heat stress groups. In summary, differences in the level of m6A and the expression of m6A-related enzymes in the liver of sheep were observed after heat stress. This indicates that m6A is involved in the regulation of heat stress in sheep. Our findings provide a new avenue for studying the responses to heat stress in sheep.
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Affiliation(s)
- Zengkui Lu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Youji Ma
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Qing Li
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Enmin Liu
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Meilin Jin
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Liping Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China.
| | - Caihong Wei
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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50
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An SM, Kwon S, Hwang JH, Yu GE, Kang DG, Park DH, Kim TW, Park HC, Ha J, Kim CW. Hypomethylation in the promoter region of ZPBP as a potential litter size indicator in Berkshire pigs. Arch Anim Breed 2019; 62:69-76. [PMID: 31807615 PMCID: PMC6852858 DOI: 10.5194/aab-62-69-2019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 03/01/2019] [Indexed: 01/09/2023] Open
Abstract
In pigs, litter size is typically defined as the total number of piglets born (TNB) or the number of piglets born alive (NBA). Increasing pig litter size is of great economic interest as a means to increase productivity. The capacity of the uterus is a critical component of litter size and may play a central role in prolificacy. In this study, we investigated litter-size-related epigenetic markers in uterine tissue from Berkshire pigs with smaller litter size groups (SLGs) and larger litter size groups (LLGs) using genome-wide bisulfite sequencing (GWBS). A total of 3269 differentially methylated regions (DMRs) were identified: 1566 were hypermethylated and 1703 hypomethylated in LLG compared to SLG. The zona pellucida binding protein (ZPBP) gene was significantly hypomethylated in the LLG promoter region, and its expression was significantly upregulated in uterine tissue. Thus, the methylation status of ZPBP gene was identified as a potential indicator of litter size. Furthermore, we verified its negative correlation with litter size traits (TNB and NBA) in whole blood samples from 172 Berkshire sows as a blood-based biomarker by a porcine methylation-specific restriction enzyme polymerase chain reaction (PMP) assay. The results suggest that the methylation status of the ZPBP gene can serve as a valuable epigenetic biomarker for hyperprolific sows.
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Affiliation(s)
- Sang Mi An
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju, 52725, South Korea
| | - Seulgi Kwon
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju, 52725, South Korea
| | - Jung Hye Hwang
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju, 52725, South Korea
| | - Go Eun Yu
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju, 52725, South Korea
| | - Deok Gyeong Kang
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju, 52725, South Korea
| | - Da Hye Park
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju, 52725, South Korea
| | - Tae Wan Kim
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju, 52725, South Korea
| | | | - Jeongim Ha
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju, 52725, South Korea
| | - Chul Wook Kim
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju, 52725, South Korea
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