1
|
Zhang J, Wu X. The Whole Genome DNA Methylation Signatures of Hindlimb Muscles in Chinese Alligators during Hibernation and Active Periods. Animals (Basel) 2024; 14:1972. [PMID: 38998084 PMCID: PMC11240547 DOI: 10.3390/ani14131972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Revised: 06/12/2024] [Accepted: 07/02/2024] [Indexed: 07/14/2024] Open
Abstract
Many ectotherms hibernate to increase their chances of survival during harsh winter conditions. The role of DNA methylation in regulating gene expression related to hibernation in ectotherms remains unclear. Here, we employed whole-genome bisulfite sequencing (WGBS) technology to construct a comprehensive genome-wide DNA methylation landscape of the hindlimb muscles in the Chinese alligator during hibernation and active periods. The results indicated that methylation modifications were most abundant at CG sites, identifying 9447 differentially methylated regions (DMRs) and 2329 differentially methylated genes (DMGs). KEGG pathway enrichment analysis of the DMGs revealed significant enrichment in major pathways such as the neurotrophin signaling pathway, the MAPK signaling pathway, the GnRH signaling pathway, the biosynthesis of amino acids, and the regulation of the actin cytoskeleton, which are closely related to lipid metabolism, energy metabolism, and amino acid metabolism. Among these, 412 differentially methylated genes were located in promoter regions, including genes related to energy metabolism such as ATP5F1C, ATP5MD, PDK3, ANGPTL1, and ANGPTL2, and genes related to ubiquitin-proteasome degradation such as FBXO28, FBXO43, KLHL40, and PSMD5. These findings suggest that methylation in promoter regions may play a significant role in regulating the adaptive hibernation mechanisms in the Chinese alligator. This study contributes to a further understanding of the epigenetic mechanisms behind the hibernation of the Chinese alligator.
Collapse
Affiliation(s)
- Jihui Zhang
- School of Food Science and Biology Engineering, Wuhu Institute of Technology, Wuhu 241000, China
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Xiaobing Wu
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| |
Collapse
|
2
|
Cheng X, Li X, Liu Y, Ma Y, Zhang R, Zhang Y, Fan C, Qu L, Ning Z. DNA methylome and transcriptome identified Key genes and pathways involved in Speckled Eggshell formation in aged laying hens. BMC Genomics 2023; 24:31. [PMID: 36658492 PMCID: PMC9854222 DOI: 10.1186/s12864-022-09100-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 12/26/2022] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND The quality of poultry eggshells is closely related to the profitability of egg production. Eggshell speckles reflect an important quality trait that influences egg appearance and customer preference. However, the mechanism of speckle formation remains poorly understood. In this study, we systematically compared serum immune and antioxidant indices of hens laying speckled and normal eggs. Transcriptome and methylome analyses were used to elucidate the mechanism of eggshell speckle formation. RESULTS The results showed that seven differentially expressed genes (DEGs) were identified between the normal and speckle groups. Gene set enrichment analysis (GSEA) revealed that the expressed genes were mainly enriched in the calcium signaling pathway, focal adhesion, and MAPK signaling pathway. Additionally, 282 differentially methylated genes (DMGs) were detected, of which 15 genes were associated with aging, including ARNTL, CAV1, and GCLC. Pathway analysis showed that the DMGs were associated with T cell-mediated immunity, response to oxidative stress, and cellular response to DNA damage stimulus. Integrative analysis of transcriptome and DNA methylation data identified BFSP2 as the only overlapping gene, which was expressed at low levels and hypomethylated in the speckle group. CONCLUSIONS Overall, these results indicate that aging- and immune-related genes and pathways play a crucial role in the formation of speckled eggshells, providing useful information for improving eggshell quality.
Collapse
Affiliation(s)
- Xue Cheng
- grid.22935.3f0000 0004 0530 8290National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Xinghua Li
- grid.22935.3f0000 0004 0530 8290National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Yuchen Liu
- grid.22935.3f0000 0004 0530 8290National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Ying Ma
- grid.22935.3f0000 0004 0530 8290National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Ruiqi Zhang
- grid.22935.3f0000 0004 0530 8290National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Yalan Zhang
- grid.22935.3f0000 0004 0530 8290National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Cuidie Fan
- Rongde Breeding Company Limited, Hebei, 053000 China
| | - Lujiang Qu
- grid.22935.3f0000 0004 0530 8290National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Zhonghua Ning
- grid.22935.3f0000 0004 0530 8290National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| |
Collapse
|
3
|
Podgorniak T, Dhanasiri A, Chen X, Ren X, Kuan PF, Fernandes J. Early fish domestication affects methylation of key genes involved in the rapid onset of the farmed phenotype. Epigenetics 2022; 17:1281-1298. [PMID: 35006036 PMCID: PMC9542679 DOI: 10.1080/15592294.2021.2017554] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 11/02/2021] [Accepted: 12/07/2021] [Indexed: 12/18/2022] Open
Abstract
Animal domestication is a process of environmental modulation and artificial selection leading to permanent phenotypic modifications. Recent studies showed that phenotypic changes occur very early in domestication, i.e., within the first generation in captivity, which raises the hypothesis that epigenetic mechanisms may play a critical role on the early onset of the domestic phenotype. In this context, we applied reduced representation bisulphite sequencing to compare methylation profiles between wild Nile tilapia females and their offspring reared under farmed conditions. Approximately 700 differentially methylated CpG sites were found, many of them associated not only with genes involved in muscle growth, immunity, autophagy and diet response but also related to epigenetic mechanisms, such as RNA methylation and histone modifications. This bottom-up approach showed that the phenotypic traits often related to domestic animals (e.g., higher growth rate and different immune status) may be regulated epigenetically and prior to artificial selection on gene sequences. Moreover, it revealed the importance of diet in this process, as reflected by differential methylation patterns in genes critical to fat metabolism. Finally, our study highlighted that the TGF-β1 signalling pathway may regulate and be regulated by several differentially methylated CpG-associated genes. This could be an important and multifunctional component in promoting adaptation of fish to a domestic environment while modulating growth and immunity-related traits.
Collapse
Affiliation(s)
- Tomasz Podgorniak
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Anusha Dhanasiri
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Xianquan Chen
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Xu Ren
- Department of Applied Mathematics and Statistics, Stony Brook University, New York, NY, USA
| | - Pei-Fen Kuan
- Department of Applied Mathematics and Statistics, Stony Brook University, New York, NY, USA
| | - Jorge Fernandes
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Fu Y, Fan P, Wang L, Shu Z, Zhu S, Feng S, Li X, Qiu X, Zhao S, Liu X. Improvement, identification, and target prediction for miRNAs in the porcine genome by using massive, public high-throughput sequencing data. J Anim Sci 2021; 99:skab018. [PMID: 33493272 PMCID: PMC7885162 DOI: 10.1093/jas/skab018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 01/21/2021] [Indexed: 12/27/2022] Open
Abstract
Despite the broad variety of available microRNA (miRNA) research tools and methods, their application to the identification, annotation, and target prediction of miRNAs in nonmodel organisms is still limited. In this study, we collected nearly all public sRNA-seq data to improve the annotation for known miRNAs and identify novel miRNAs that have not been annotated in pigs (Sus scrofa). We newly annotated 210 mature sequences in known miRNAs and found that 43 of the known miRNA precursors were problematic due to redundant/missing annotations or incorrect sequences. We also predicted 811 novel miRNAs with high confidence, which was twice the current number of known miRNAs for pigs in miRBase. In addition, we proposed a correlation-based strategy to predict target genes for miRNAs by using a large amount of sRNA-seq and RNA-seq data. We found that the correlation-based strategy provided additional evidence of expression compared with traditional target prediction methods. The correlation-based strategy also identified the regulatory pairs that were controlled by nonbinding sites with a particular pattern, which provided abundant complementarity for studying the mechanism of miRNAs that regulate gene expression. In summary, our study improved the annotation of known miRNAs, identified a large number of novel miRNAs, and predicted target genes for all pig miRNAs by using massive public data. This large data-based strategy is also applicable for other nonmodel organisms with incomplete annotation information.
Collapse
Affiliation(s)
- Yuhua Fu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education; Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, PR China
- School of Computer Science and Technology, Wuhan University of Technology, Wuhan, Hubei, PR China
| | - Pengyu Fan
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education; Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, PR China
| | - Lu Wang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education; Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, PR China
| | - Ziqiang Shu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education; Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, PR China
| | - Shilin Zhu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education; Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, PR China
| | - Siyuan Feng
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, USA
| | - Xinyun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education; Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, PR China
| | - Xiaotian Qiu
- National Animal Husbandry Service, Beijing, PR China
| | - Shuhong Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education; Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, PR China
| | - Xiaolei Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education; Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, PR China
| |
Collapse
|
6
|
Tan X, Liu R, Zhang Y, Wang X, Wang J, Wang H, Zhao G, Zheng M, Wen J. Integrated analysis of the methylome and transcriptome of chickens with fatty liver hemorrhagic syndrome. BMC Genomics 2021; 22:8. [PMID: 33407101 PMCID: PMC7789526 DOI: 10.1186/s12864-020-07305-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 12/06/2020] [Indexed: 12/22/2022] Open
Abstract
Background DNA methylation, a biochemical modification of cytosine, has an important role in lipid metabolism. Fatty liver hemorrhagic syndrome (FLHS) is a serious disease and is tightly linked to lipid homeostasis. Herein, we compared the methylome and transcriptome of chickens with and without FLHS. Results We found genome-wide dysregulated DNA methylation pattern in which regions up- and down-stream of gene body were hypo-methylated in chickens with FLHS. A total of 4155 differentially methylated genes and 1389 differentially expressed genes were identified. Genes were focused when a negative relationship between mRNA expression and DNA methylation in promoter and gene body were detected. Based on pathway enrichment analysis, we found expression of genes related to lipogenesis and oxygenolysis (e.g., PPAR signaling pathway, fatty acid biosynthesis, and fatty acid elongation) to be up-regulated with associated down-regulated DNA methylation. In contrast, genes related to cellular junction and communication pathways (e.g., vascular smooth muscle contraction, phosphatidylinositol signaling system, and gap junction) were inhibited and with associated up-regulation of DNA methylation. Conclusions In the current study, we provide a genome-wide scale landscape of DNA methylation and gene expression. The hepatic hypo-methylation feature has been identified with FLHS chickens. By integrated analysis, the results strongly suggest that increased lipid accumulation and hepatocyte rupture are central pathways that are regulated by DNA methylation in chickens with FLHS. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07305-3.
Collapse
Affiliation(s)
- Xiaodong Tan
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Ranran Liu
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yonghong Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.,College of Animal Science, Jilin University, Changchun, 130062, China
| | - Xicai Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Jie Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Hailong Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Guiping Zhao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Maiqing Zheng
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Jie Wen
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| |
Collapse
|
7
|
Wang X, Li X, Wu S, Shi K, He Y. DNA methylation and transcriptome comparative analysis for Lvliang Black goats in distinct feeding pattern reveals epigenetic basis for environment adaptation. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2021.1914164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- Xi Wang
- Department of Animal Breeding and Genetics, College of animal science, Shanxi Agricultural University, Taigu, Shanxi, P.R. China
| | - Xi Li
- Department of Animal Breeding and Genetics, College of animal science, Shanxi Agricultural University, Taigu, Shanxi, P.R. China
| | - Sujun Wu
- Department of Animal Breeding and Genetics, College of animal science, Shanxi Agricultural University, Taigu, Shanxi, P.R. China
| | - Kerong Shi
- Department of Animal Breeding and Genetics, College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong, P.R. China
| | - Yanghua He
- Department of Human Nutrition, Food and Animal Sciences, College of Tropical Agriculture and Human Resources, University of Hawaii at Manoa, Honolulu, HI, USA
| |
Collapse
|
8
|
Fu Y, Xu J, Tang Z, Wang L, Yin D, Fan Y, Zhang D, Deng F, Zhang Y, Zhang H, Wang H, Xing W, Yin L, Zhu S, Zhu M, Yu M, Li X, Liu X, Yuan X, Zhao S. A gene prioritization method based on a swine multi-omics knowledgebase and a deep learning model. Commun Biol 2020; 3:502. [PMID: 32913254 PMCID: PMC7483748 DOI: 10.1038/s42003-020-01233-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 08/07/2020] [Indexed: 12/27/2022] Open
Abstract
The analyses of multi-omics data have revealed candidate genes for objective traits. However, they are integrated poorly, especially in non-model organisms, and they pose a great challenge for prioritizing candidate genes for follow-up experimental verification. Here, we present a general convolutional neural network model that integrates multi-omics information to prioritize the candidate genes of objective traits. By applying this model to Sus scrofa, which is a non-model organism, but one of the most important livestock animals, the model precision was 72.9%, recall 73.5%, and F1-Measure 73.4%, demonstrating a good prediction performance compared with previous studies in Arabidopsis thaliana and Oryza sativa. Additionally, to facilitate the use of the model, we present ISwine (http://iswine.iomics.pro/), which is an online comprehensive knowledgebase in which we incorporated almost all the published swine multi-omics data. Overall, the results suggest that the deep learning strategy will greatly facilitate analyses of multi-omics integration in the future. Yuhua Fu et al. develop a CNN model that integrates multi-omics information to prioritize candidate genes of objective traits. Their model performs well when applied to important livestock non-model animals like Sus scrofa. Finally, the authors present ISwine, an online comprehensive knowledgebase which includes all published swine omics data to facilitate the integration of heterogeneous data.
Collapse
Affiliation(s)
- Yuhua Fu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, 430070, Wuhan, Hubei, P.R. China.,School of Computer Science and Technology, Wuhan University of Technology, 430070, Wuhan, Hubei, P.R. China
| | - Jingya Xu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, 430070, Wuhan, Hubei, P.R. China
| | - Zhenshuang Tang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, 430070, Wuhan, Hubei, P.R. China
| | - Lu Wang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, 430070, Wuhan, Hubei, P.R. China
| | - Dong Yin
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, 430070, Wuhan, Hubei, P.R. China
| | - Yu Fan
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, 430070, Wuhan, Hubei, P.R. China
| | - Dongdong Zhang
- School of Computer Science and Technology, Wuhan University of Technology, 430070, Wuhan, Hubei, P.R. China
| | - Fei Deng
- School of Computer Science and Technology, Wuhan University of Technology, 430070, Wuhan, Hubei, P.R. China
| | - Yanping Zhang
- School of Computer Science and Technology, Wuhan University of Technology, 430070, Wuhan, Hubei, P.R. China
| | - Haohao Zhang
- School of Computer Science and Technology, Wuhan University of Technology, 430070, Wuhan, Hubei, P.R. China
| | - Haiyan Wang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, 430070, Wuhan, Hubei, P.R. China
| | - Wenhui Xing
- School of Computer Science and Technology, Wuhan University of Technology, 430070, Wuhan, Hubei, P.R. China
| | - Lilin Yin
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, 430070, Wuhan, Hubei, P.R. China
| | - Shilin Zhu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, 430070, Wuhan, Hubei, P.R. China
| | - Mengjin Zhu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, 430070, Wuhan, Hubei, P.R. China
| | - Mei Yu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, 430070, Wuhan, Hubei, P.R. China
| | - Xinyun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, 430070, Wuhan, Hubei, P.R. China
| | - Xiaolei Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, 430070, Wuhan, Hubei, P.R. China.
| | - Xiaohui Yuan
- School of Computer Science and Technology, Wuhan University of Technology, 430070, Wuhan, Hubei, P.R. China.
| | - Shuhong Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, 430070, Wuhan, Hubei, P.R. China.
| |
Collapse
|
9
|
Fu Y, Wang L, Tang Z, Yin D, Xu J, Fan Y, Li X, Zhao S, Liu X. An integration analysis based on genomic, transcriptomic and QTX information reveals credible candidate genes for fat-related traits in pigs. Anim Genet 2020; 51:683-693. [PMID: 32557818 DOI: 10.1111/age.12971] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 05/15/2020] [Accepted: 05/23/2020] [Indexed: 12/27/2022]
Abstract
Meat quality improvement is of great interest to researchers in pig breeding and many researchers have identified abundant associated quantitative trait loci, genes and polymorphisms (QTXs) for fat-related traits. However, it is challenging to determine credible candidate genes from a mass of associations. The efficiency of identification of credible candidate genes in these QTXs is restricted by limited integration analyses of data from multiple omics. In this study, we constructed a 'candidate gene map' of fat-related traits in pigs based on published literature and the latest genome. In total, 6,861 QTXs, which covered 9,323 genes on the pig genome, were used. Combining the QTX hotspots and pathway analysis, we identified 180 candidate genes that may regulate the fat-related traits, and choose PNPLA2, PPARG, SREBF1, ACACA, PPARD and PPARA as credible candidate genes. In addition, we discussed the importance of incorporating transcriptome data and genomic data in causal gene identification, and the multi-omics information can effectively improve the credibility of identified candidate genes.
Collapse
Affiliation(s)
- Y Fu
- School of Computer Science and Technology, Wuhan University of Technology, Wuhan, Hubei, 430070, China.,Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture and College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - L Wang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture and College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Z Tang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture and College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - D Yin
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture and College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - J Xu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture and College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Y Fan
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture and College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - X Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture and College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - S Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture and College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - X Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture and College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| |
Collapse
|
10
|
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.
Collapse
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.
| |
Collapse
|
11
|
Sun L, Guo L, Wang J, Li M, Appiah MO, Liu H, Zhao J, Yang L, Lu W. Photoperiodic effect on the testicular transcriptome in broiler roosters. J Anim Physiol Anim Nutr (Berl) 2020; 104:918-927. [PMID: 32100373 DOI: 10.1111/jpn.13336] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 01/03/2020] [Accepted: 01/30/2020] [Indexed: 01/01/2023]
Abstract
Information about the effects of photoperiod on the testicular transcriptome of broiler roosters is limited. The aim of the present study was to explore the effect of different photoperiodic regimes on gene expression in the testes of broiler breeder roosters. One hundred and twenty Arbor Acres broiler breeder roosters aged 20 weeks were assigned to one of three groups (n = 40) and subjected to different photoperiodic regimes: control (CTR; 12.5 L:11.5 D), short day (SD; 8 L:16 D) and long day (LD; 16 L:8 D). After 4 weeks, the testes of 10 randomly selected birds from each group were dissected, sliced and haematoxylin-eosin stained. The testicular transcriptome of roosters from the SD and LD groups was determined by RNA sequencing (RNA-Seq), and the results were confirmed using quantitative real-time PCR. The seminiferous tubule area and sperm count increased significantly with the prolongation of photoperiod (p < .01). Additionally, the RNA-Seq results indicated that 387 genes were upregulated and 1,052 genes were downregulated in the LD group compared with those in the SD group. Several crucial genes involved in rooster testicular development and reproduction were also screened, including heat shock proteins 90, extracellular regulated protein kinases 1, phosphatidylinositol 3-kinase, adenosine 5'-monophosphate -activated protein kinase, BCL-6 and Smad3. The differentially expressed genes were enriched in the mammalian targets of rapamycin (mTOR), forkhead box (FoxO), transforming growth factor beta (TGF-β) and insulin signalling pathway. In conclusion, a 16 hr photoperiod for 4 weeks increased the seminiferous tubule duct area and promoted spermatogenesis in the rooster's testicles, and the mTOR, FoxO, TGF-β and insulin signalling pathways may be involved.
Collapse
Affiliation(s)
- Lei Sun
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China.,College of Animal Husbandry and Veterinary Medicine, Jinzhou Medical University, Jinzhou, China
| | - Lewei Guo
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Jun Wang
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Meng Li
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Michael Osei Appiah
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Hongyu Liu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Jing Zhao
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Lianyu Yang
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Wenfa Lu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| |
Collapse
|
12
|
Thompson RP, Nilsson E, Skinner MK. Environmental epigenetics and epigenetic inheritance in domestic farm animals. Anim Reprod Sci 2020; 220:106316. [PMID: 32094003 DOI: 10.1016/j.anireprosci.2020.106316] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 02/13/2020] [Accepted: 02/17/2020] [Indexed: 01/26/2023]
Abstract
Epigenetics refers to molecular factors and processes around DNA that can affect genome activity and gene expression independent of DNA sequence. Epigenetic mechanisms drive developmental processes and have also been shown to be tied to disease development. Many epigenetic studies have been done using plants, rodent, and human models, but fewer have focused on domestic livestock species. The goal of this review is to present current epigenetic findings in livestock species (cattle, pigs, sheep and poultry). Much of this research examined epigenetic effects following exposure to toxicants, nutritional changes or infectious disease in those animals directly exposed, or in the offspring they produced. A limited number of studies in domestic animals have examined epigenetic transgenerational inheritance in the absence of continued exposures. One example used a porcine model to investigate the effect that feeding males a diet supplemented with micronutrients had on liver DNA methylation and muscle mass in grand-offspring (the transgenerational F2 generation). Further research into how epigenetic mechanisms affect the health and production traits of domestic livestock and their offspring is important to elucidate.
Collapse
Affiliation(s)
- Ryan P Thompson
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Eric Nilsson
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Michael K Skinner
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, USA.
| |
Collapse
|