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Panda S, Kumar A, Gaur GK, Ahmad SF, Chauhan A, Mehrotra A, Dutt T. Genome wide copy number variations using Porcine 60K SNP Beadchip in Landlly pigs. Anim Biotechnol 2023; 34:1891-1899. [PMID: 35369845 DOI: 10.1080/10495398.2022.2056047] [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] [Indexed: 11/01/2022]
Abstract
In the present study, Porcine 60K SNP genotype data from 69 Landlly pigs were used to explore Copy Number Variations (CNVs) across the autosomes. A total of 386 CNVs were identified using Hidden Markov Model (HMM) in PennCNV software, which were subsequently aggregated to 115 CNV regions (CNVRs). Among the total detected CNVRs, 58 gain, 49 were loss type while remaining 8 events were both gain and loss types. Identified CNVRs covered 12.5 Mb (0.55%) of Sus scrofa reference 11.1 genome. Comparison of our results with previous investigations on pigs revealed that approximately 75% CNVRs were novel, which may be due to differences in genetic background, environment and implementation of artificial selection in Landlly pigs. Functional annotation and pathway analysis showed the significant enrichment of 267 well-annotated Sus scrofa genes in CNVRs. These genes were involved in different biological functions like sensory perception, meat quality traits, back fat thickness and immunity. Additionally, KIT and FUT1 were two major genes detected on CNVR in our population. This investigation provided a comprehensive overview of CNV distribution in the Indian porcine genome for the first time, which may be useful for further investigating the association of important quantitative traits in Landlly pigs.Highlights115 CNVRs were identified in 69 Landlly pig population.Approximately 75% detected CNVRs were novel for Landlly population.Significant enrichment of 267 well-annotated Sus scrofa genes observed in these CNVRs.These genes were involved in different biological functions like sensory perception, meat quality traits, back fat thickness and immunity.Comprehensive CNV map in the Indian porcine genome developed for the first time.
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Affiliation(s)
- Snehasmita Panda
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, UP, India
| | - Amit Kumar
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, UP, India
| | - Gyanendra Kumar Gaur
- Livestock Production and Management Section, ICAR-Indian Veterinary Research Institute, Izatnagar, UP, India
| | - Sheikh Firdous Ahmad
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, UP, India
| | - Anuj Chauhan
- Livestock Production and Management Section, ICAR-Indian Veterinary Research Institute, Izatnagar, UP, India
| | - Arnav Mehrotra
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, UP, India
- Animal Genomics, ETH Zürich, Zürich, Switzerland
| | - Triveni Dutt
- Livestock Production and Management Section, ICAR-Indian Veterinary Research Institute, Izatnagar, UP, India
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Identification of miR-192 target genes in porcine endometrial epithelial cells based on miRNA pull-down. Mol Biol Rep 2023; 50:4273-4284. [PMID: 36914869 DOI: 10.1007/s11033-023-08349-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 02/21/2023] [Indexed: 03/16/2023]
Abstract
INTRODUCTION MicroRNAs (miRNAs)-a class of small endogenous non-coding RNAs-are widely involved in post-transcriptional gene regulation of numerous physiological processes. High-throughput sequencing revealed that the miR-192 expression level appeared to be significantly higher in the blood exosomes of sows at early gestation than that in non-pregnant sows. Furthermore, miR-192 was hypothesized to have a regulatory role in embryo implantation; however, the target genes involved in exerting the regulatory function of miR-192 required further elucidation. METHODS In the present study, potential target genes of miR-192 in porcine endometrial epithelial cells (PEECs) were identified through biotin-labeled miRNA pull-down; functional and pathway enrichment analysis was performed via gene ontology analysis and Kyoto Encyclopedia of Genes and Genomes pathway enrichment. Bioinformatic analyses were concurrently used to predict the potential target genes associated with sow embryo implantation. In addition, double luciferase reporter vectors, reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR), and Western blot were performed to verify the targeting and regulatory roles of the abovementioned target genes. RESULTS A total of 1688 differentially expressed mRNAs were identified via miRNA pull-down. Through RT-qPCR, the accuracy of the sequencing data was verified. In the bioinformatics analysis, potential target genes of miR-192 appeared to form a dense inter-regulatory network and regulated multiple signaling pathways, such as metabolic pathways and the PI3K-Akt, MAPKs, and mTOR signaling pathways, that are relevant to the mammalian embryo implantation process. In addition, CSK (C-terminal Src kinase) and YY1 (Yin-Yang-1) were predicted to be potential candidates, and we validated that miR-192 directly targets and suppresses the expression of the CSK and YY1 genes. CONCLUSION We screened 1688 potential target genes of miR-192 were screened, and CSK and YY1 were identified as miR-192 target genes. The outcomes of the present study provide novel insights into the regulatory mechanism of porcine embryo implantation and the identification of miRNA target genes.
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Salazar-Petres E, Pereira-Carvalho D, Lopez-Tello J, Sferruzzi-Perri AN. Placental structure, function, and mitochondrial phenotype relate to fetal size in each fetal sex in mice†. Biol Reprod 2022; 106:1292-1311. [PMID: 35293971 PMCID: PMC9327737 DOI: 10.1093/biolre/ioac056] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 01/28/2022] [Accepted: 03/08/2022] [Indexed: 11/25/2022] Open
Abstract
Fetal growth depends on placental function, which requires energy from mitochondria. Here we investigated whether mitochondrial function in the placenta relates to the growth of the lightest and heaviest fetuses of each sex within the litter of mice. Placentas from the lightest and heaviest fetuses were taken to evaluate placenta morphology (stereology), mitochondrial energetics (high-resolution respirometry), mitochondrial regulators, nutrient transporters, hormone handling, and signaling pathways (qPCR and Western blotting). We found that mitochondrial complex I and II oxygen consumption rate was greater for placentas supporting the lightest female fetuses, although placental complex I abundance of the lightest females and complexes III and V of the lightest males were decreased compared to their heaviest counterparts. Expression of mitochondrial biogenesis (Nrf1) and fission (Drp1 and Fis1) genes was lower in the placenta from the lightest females, whilst biogenesis-related gene Tfam was greater in the placenta of the lightest male fetuses. In addition, placental morphology and steroidogenic gene (Cyp17a1 and Cyp11a1) expression were aberrant for the lightest females, but glucose transporter (Slc2a1) expression was lower in only the lightest males versus their heaviest counterparts. Differences in intra-litter placental phenotype were related to changes in the expression of hormone-responsive (androgen receptor) and metabolic signaling (AMPK, AKT, and PPARγ) pathways. Thus, in normal mouse pregnancy, placental structure, function, and mitochondrial phenotype are differentially responsive to the growth of the female and male fetus. This study may inform the design of sex-specific therapies for placental insufficiency and fetal growth abnormalities with life-long benefits for the offspring.
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Affiliation(s)
- Esteban Salazar-Petres
- Department of Physiology, Development and Neuroscience, Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
| | - Daniela Pereira-Carvalho
- Department of Physiology, Development and Neuroscience, Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
| | - Jorge Lopez-Tello
- Department of Physiology, Development and Neuroscience, Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
| | - Amanda Nancy Sferruzzi-Perri
- Department of Physiology, Development and Neuroscience, Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
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Xing P, Hong L, Yan G, Tan B, Qiao J, Wang S, Li Z, JieYang, Zheng E, Cai G, Wu Z, Gu T. Neuronatin gene expression levels affect foetal growth and development by regulating glucose transport in porcine placenta. Gene 2021; 809:146051. [PMID: 34756962 DOI: 10.1016/j.gene.2021.146051] [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: 05/31/2021] [Revised: 10/18/2021] [Accepted: 10/26/2021] [Indexed: 11/04/2022]
Abstract
Imprinted genes play important regulatory roles in the growth and development of placentas and foetuses during pregnancy. In a previous study, we found that the imprinted gene Neuronatin (NNAT) is involved in foetal development; NNAT expression was significantly lower in the placentas of piglets that died neonatally compared to the placentas of surviving piglets. However, the function and mechanism of NNAT in regulating porcine placental development is still unknown. In this study, we collected the placentas of high- and low-weight foetuses at gestational day (GD 65, 90), (n = 4-5 litters/GD) to investigate the role of NNAT in regulating foetal growth and development. We found that the mRNA and protein levels of NNAT were significantly higher in the placentas of high-weight than low-weight foetuses. We then overexpressed NNAT in porcine placental trophoblast cell lines (pTr2) and demonstrated that NNAT activated the PI3K-AKT pathway, and further promoted the expression of glucose transporter 1 (GLUT1) and increased cellular calcium ion levels, which improved glucose transport in placental trophoblast cells in vitro. To conclude, our study suggests that NNAT expression impacts porcine foetal development by regulating placental glucose transport.
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Affiliation(s)
- Pingping Xing
- National Engineering Research Center for Breeding Swine Industry, Guangzhou, China & College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Linjun Hong
- National Engineering Research Center for Breeding Swine Industry, Guangzhou, China & College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Guanhao Yan
- National Engineering Research Center for Breeding Swine Industry, Guangzhou, China & College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Baohua Tan
- National Engineering Research Center for Breeding Swine Industry, Guangzhou, China & College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Jiaxin Qiao
- National Engineering Research Center for Breeding Swine Industry, Guangzhou, China & College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Shanshan Wang
- National Engineering Research Center for Breeding Swine Industry, Guangzhou, China & College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Zicong Li
- National Engineering Research Center for Breeding Swine Industry, Guangzhou, China & College of Animal Science, South China Agricultural University, Guangzhou, China; State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangzhou, China; Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, Guangzhou, China; Guangdong Wens Breeding Swine Technology Co., Ltd, Yunfu, China
| | - JieYang
- National Engineering Research Center for Breeding Swine Industry, Guangzhou, China & College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Enqin Zheng
- National Engineering Research Center for Breeding Swine Industry, Guangzhou, China & College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Gengyuan Cai
- National Engineering Research Center for Breeding Swine Industry, Guangzhou, China & College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Zhenfang Wu
- National Engineering Research Center for Breeding Swine Industry, Guangzhou, China & College of Animal Science, South China Agricultural University, Guangzhou, China; State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangzhou, China; Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, Guangzhou, China; Guangdong Wens Breeding Swine Technology Co., Ltd, Yunfu, China
| | - Ting Gu
- National Engineering Research Center for Breeding Swine Industry, Guangzhou, China & College of Animal Science, South China Agricultural University, Guangzhou, China.
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Denoyelle L, de Villemereuil P, Boyer F, Khelifi M, Gaffet C, Alberto F, Benjelloun B, Pompanon F. Genetic Variations and Differential DNA Methylation to Face Contrasted Climates in Small Ruminants: An Analysis on Traditionally-Managed Sheep and Goats. Front Genet 2021; 12:745284. [PMID: 34650601 PMCID: PMC8508783 DOI: 10.3389/fgene.2021.745284] [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: 07/21/2021] [Accepted: 09/02/2021] [Indexed: 12/13/2022] Open
Abstract
The way in which living organisms mobilize a combination of long-term adaptive mechanisms and short-term phenotypic plasticity to face environmental variations is still largely unknown. In the context of climate change, understanding the genetic and epigenetic bases for adaptation and plasticity is a major stake for preserving genomic resources and the resilience capacity of livestock populations. We characterized both epigenetic and genetic variations by contrasting 22 sheep and 21 goats from both sides of a climate gradient, focusing on free-ranging populations from Morocco. We produced for each individual Whole-Genome Sequence at 12X coverage and MeDIP-Seq data, to identify regions under selection and those differentially methylated. For both species, the analysis of genetic differences (FST) along the genome between animals from localities with high vs. low temperature annual variations detected candidate genes under selection in relation to environmental perception (5 genes), immunity (4 genes), reproduction (8 genes) and production (11 genes). Moreover, we found for each species one differentially methylated gene, namely AGPTA4 in goat and SLIT3 in sheep, which were both related, among other functions, to milk production and muscle development. In both sheep and goats, the comparison between genomic regions impacted by genetic and epigenetic variations suggests that climatic variations impacted similar biological pathways but different genes.
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Affiliation(s)
- Laure Denoyelle
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, Grenoble, France.,GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, France
| | - Pierre de Villemereuil
- Institut de Systématique, Évolution, Biodiversité (ISYEB), École Pratique des Hautes Études
- PSL, MNHN, CNRS, SU, UA, Paris, France
| | - Frédéric Boyer
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Meidhi Khelifi
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Clément Gaffet
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Florian Alberto
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Badr Benjelloun
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, Grenoble, France.,Institut National de la Recherche Agronomique Maroc (INRA-Maroc), Centre Régional de Beni Mellal, Beni Mellal, Morocco
| | - François Pompanon
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, Grenoble, France
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Tao L, He X, Jiang Y, Liu Y, Ouyang Y, Shen Y, Hong Q, Chu M. Genome-Wide Analyses Reveal Genetic Convergence of Prolificacy between Goats and Sheep. Genes (Basel) 2021; 12:480. [PMID: 33810234 PMCID: PMC8065816 DOI: 10.3390/genes12040480] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/16/2021] [Accepted: 03/23/2021] [Indexed: 12/20/2022] Open
Abstract
The litter size of domestic goats and sheep is an economically important trait that shows variation within breeds. Strenuous efforts have been made to understand the genetic mechanisms underlying prolificacy in goats and sheep. However, there has been a paucity of research on the genetic convergence of prolificacy between goats and sheep, which likely arose because of similar natural and artificial selection forces. Here, we performed comparative genomic and transcriptomic analyses to identify the genetic convergence of prolificacy between goats and sheep. By combining genomic and transcriptomic data for the first time, we identified this genetic convergence in (1) positively selected genes (CHST11 and SDCCAG8), (2) differentially expressed genes (SERPINA14, RSAD2, and PPIG at follicular phase, and IGF1, GPRIN3, LIPG, SLC7A11, and CHST15 at luteal phase), and (3) biological pathways (genomic level: osteoclast differentiation, ErbB signaling pathway, and relaxin signaling pathway; transcriptomic level: the regulation of viral genome replication at follicular phase, and protein kinase B signaling and antigen processing and presentation at luteal phase). These results indicated the potential physiological convergence and enhanced our understanding of the overlapping genetic makeup underlying litter size in goats and sheep.
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Affiliation(s)
- Lin Tao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (L.T.); (X.H.); (Y.L.)
| | - Xiaoyun He
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (L.T.); (X.H.); (Y.L.)
| | - Yanting Jiang
- Yunnan Animal Science and Veterinary Institute, Kunming 650224, China; (Y.J.); (Y.O.)
| | - Yufang Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (L.T.); (X.H.); (Y.L.)
- College of Life Science and Food Engineering, Hebei University of Engineering, Handan 056038, China
| | - Yina Ouyang
- Yunnan Animal Science and Veterinary Institute, Kunming 650224, China; (Y.J.); (Y.O.)
| | - Yezhen Shen
- Annoroad Gene Technology Co., Ltd., Beijing 100176, China;
| | - Qionghua Hong
- Yunnan Animal Science and Veterinary Institute, Kunming 650224, China; (Y.J.); (Y.O.)
| | - Mingxing Chu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (L.T.); (X.H.); (Y.L.)
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Gao H, Zhang L, Wang L, Liu X, Hou X, Zhao F, Yan H, Wang L. Liver transcriptome profiling and functional analysis of intrauterine growth restriction (IUGR) piglets reveals a genetic correction and sexual-dimorphic gene expression during postnatal development. BMC Genomics 2020; 21:701. [PMID: 33032518 PMCID: PMC7545842 DOI: 10.1186/s12864-020-07094-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 09/23/2020] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Intrauterine growth restriction (IUGR) remains a major problem associated with swine production. Thus, understanding the physiological changes of postnatal IUGR piglets would aid in improving growth performance. Moreover, liver metabolism plays an important role in the growth and survival of neonatal piglets. RESULTS By profiling the transcriptome of liver samples on postnatal Days 1, 7, and 28, our study focused on characterizing the growth, function, and metabolism in the liver of IUGR neonatal piglets. Our study demonstrates that the livers of IUGR piglets were associated with a series of complications, including inflammatory stress and immune dysregulation; cytoskeleton and membrane structure disorganization; dysregulated transcription events; and abnormal glucocorticoid metabolism. In addition, the abnormal liver function index in the serum [alanine aminotransferase (ALT), aspartate aminotransferase (AST), and total protein (TP)], coupled with hepatic pathological and ultrastructural morphological changes are indicative of liver damage and dysfunction in IUGR piglets. Moreover, these results reveal the sex-biased developmental dynamics between male and female IUGR piglets, and that male IUGR piglets may be more sensitive to disrupted metabolic homeostasis. CONCLUSIONS These observations provide a detailed reference for understanding the mechanisms and characterizations of IUGR liver functions, and suggest that the potential strategies for improving the survival and growth performance of IUGR offspring should consider the balance between postnatal catch-up growth and adverse metabolic consequences. In particular, sex-specific intervention strategies should be considered for both female and male IUGR piglets.
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Affiliation(s)
- Hongmei Gao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, P. R. China
| | - Longchao Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, P. R. China
| | - Ligang Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, P. R. China
| | - Xin Liu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, P. R. China
| | - Xinhua Hou
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, P. R. China
| | - Fuping Zhao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, P. R. China
| | - Hua Yan
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, P. R. China
| | - Lixian Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, P. R. China.
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RNA-seq reveals downregulated osteochondral genes potentially related to tibia bacterial chondronecrosis with osteomyelitis in broilers. BMC Genet 2020; 21:58. [PMID: 32493207 PMCID: PMC7271470 DOI: 10.1186/s12863-020-00862-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 05/18/2020] [Indexed: 12/14/2022] Open
Abstract
Background Bacterial chondronecrosis with osteomyelitis (BCO) develops in the growth plate (GP) of the proximal femur and tibia and is initiated by damage to the less mineralized chondrocytes followed by colonization of opportunistic bacteria. This condition affects approximately 1% of all birds housed, being considered one of the major causes of lameness in fast growing broilers. Although several studies have been previously performed aiming to understand its pathogenesis, the molecular mechanisms involved with BCO remains to be elucidated. Therefore, this study aimed to generate a profile of global differential gene expression involved with BCO in the tibia of commercial broilers, through RNA sequencing analysis to identity genes and molecular pathways involved with BCO in chickens. Results Our data showed 192 differentially expressed (DE) genes: 63 upregulated and 129 downregulated in the GP of the tibia proximal epiphysis of BCO-affected broilers. Using all DE genes, six Biological Processes (BP) were associated with bone development (connective tissue development, cartilage development, skeletal system development, organ morphogenesis, system development and skeletal system morphogenesis). The analyses of the upregulated genes did not indicate any significant BP (FDR < 0.05). However, with the downregulated genes, the same BP were identified when using all DE genes in the analysis, with a total of 26 coding genes explaining BCO in the tibia: ACAN, ALDH1A2, CDH7, CHAD, CHADL, COL11A1, COMP, CSGALNACT1, CYR61, FRZB, GAL3ST1, HAPLN1, IHH, KIF26B, LECT1, LPPR1, PDE6B, RBP4A, SERINC5, SFRP1, SOX8, SOX9, TENM2, THBS1, UCHL1 and WFIKKN2. In addition, seven transcription factors were also associated to BCO: NFATC2, MAFB, HIF1A-ARNT, EWSR1-FLI1, NFIC, TCF3 and NF-KAPPAB. Conclusions Our data show that osteochondral downregulated genes are potential molecular causes of BCO in broilers, and the bacterial process seems to be, in fact, a secondary condition. Sixteen genes responsible for bone and cartilage formation were downregulated in BCO-affected broilers being strong candidate genes to trigger this disorder.
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N 6-methyladenosine modification of circNSUN2 facilitates cytoplasmic export and stabilizes HMGA2 to promote colorectal liver metastasis. Nat Commun 2019; 10:4695. [PMID: 31619685 PMCID: PMC6795808 DOI: 10.1038/s41467-019-12651-2] [Citation(s) in RCA: 420] [Impact Index Per Article: 84.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 09/22/2019] [Indexed: 02/07/2023] Open
Abstract
Circular RNAs (circRNAs) have been implicated in cancer progression through largely unknown mechanisms. Herein, we identify an N6-methyladenosine (m6A) modified circRNA, circNSUN2, frequently upregulated in tumor tissues and serum samples from colorectal carcinoma (CRC) patients with liver metastasis (LM) and predicts poorer patient survival. The upregulated expression of circNSUN2 promotes LM in PDX metastasis models in vivo and accelerates cancer cells invasion in vitro. Importantly, N6-methyladenosine modification of circNSUN2 increases export to the cytoplasm. By forming a circNSUN2/IGF2BP2/HMGA2 RNA-protein ternary complex in the cytoplasm, circNSUN2 enhances the stability of HMGA2 mRNA to promote CRC metastasis progression. Clinically, the upregulated expressions of circNSUN2 and HMGA2 are more prevalent in LM tissues than in primary CRC tissues. These findings elucidate that N6-methyladenosine modification of circNSUN2 modulates cytoplasmic export and stabilizes HMGA2 to promote CRC LM, and suggest that circNSUN2 could represent a critical prognostic marker and/or therapeutic target for the disease.
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Srikanth K, Park W, Lim D, Lee KT, Jang GW, Choi BH, Ka H, Park JE, Kim JM. Serial gene co-expression network approach to mine biological meanings from integrated transcriptomes of the porcine endometrium during estrous cycle. Funct Integr Genomics 2019; 20:117-131. [PMID: 31396752 DOI: 10.1007/s10142-019-00703-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 07/03/2019] [Accepted: 07/22/2019] [Indexed: 01/22/2023]
Abstract
The estrous cycle is a complex process regulated by several hormones. To understand the dynamic changes in gene expression that takes place in the swine endometrium during the estrous cycle relative to the day of estrus onset, we performed RNA-sequencing analysis on days 0, 3, 6, 9, 12, 15, and 18, resulting in the identification of 4495 differentially expressed genes (DEGs; Q ≤ 0.05 and |log2FC| ≥ 1) at various phases in the estrous cycle. These DEGs were integrated into multiple gene co-expression networks based on different fold changes and correlation coefficient (R2) thresholds and a suitable network, which included 899 genes (|log2FC| ≥ 2 and R2 ≥ 0.99), was identified for downstream analyses based on the biological relevance of the Gene Ontology (GO) terms enriched. The genes in this network were partitioned into 6 clusters based on the expression pattern. Several GO terms including cell cycle, apoptosis, hormone signaling, and lipid biosynthetic process were found to be enriched. Furthermore, we found 15 significant KEGG pathways, including cell adhesion molecules, cytokine-cytokine receptor signaling, steroid biosynthesis, and estrogen signaling pathways. We identified several genes and GO terms to be stage-specific. Moreover, the identified genes and pathways extend our understanding of porcine endometrial regulation during estrous cycle and will serve as a good resource for future studies.
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Affiliation(s)
- Krishnamoorthy Srikanth
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, 55365, Republic of Korea
| | - WonCheoul Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, 55365, Republic of Korea
| | - Dajeong Lim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, 55365, Republic of Korea
| | - Kyung Tai Lee
- Animal Genetics and Breeding Division, National Institute of Animal Science, RDA, Wanju, 55365, Republic of Korea
| | - Gul Won Jang
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, 55365, Republic of Korea
| | - Bong Hwan Choi
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, 55365, Republic of Korea
| | - Hakhyun Ka
- Division of Biological Science and Technology, Yonsei University, Wonju, 26493, Republic of Korea.
| | - Jong-Eun Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, 55365, Republic of Korea.
| | - Jun-Mo Kim
- Department of Animal Science and Technology, Chung-Ang University, Anseong, Gyeonggi-do, 17546, Republic of Korea.
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Ando A, Imaeda N, Matsubara T, Takasu M, Miyamoto A, Oshima S, Nishii N, Kametani Y, Shiina T, Kulski JK, Kitagawa H. Genetic Association between Swine Leukocyte Antigen Class II Haplotypes and Reproduction Traits in Microminipigs. Cells 2019; 8:cells8080783. [PMID: 31357541 PMCID: PMC6721486 DOI: 10.3390/cells8080783] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 07/16/2019] [Accepted: 07/22/2019] [Indexed: 02/06/2023] Open
Abstract
The effects of swine leukocyte antigen (SLA) molecules on numerous production and reproduction performance traits have been mainly reported as associations with specific SLA haplotypes that were assigned using serological typing methods. In this study, we intended to clarify the association between SLA class II genes and reproductive traits in a highly inbred population of 187 Microminipigs (MMP), that have eight different types of SLA class II haplotypes. In doing so, we compared the reproductive performances, such as fertility index, gestation period, litter size, and number of stillbirth among SLA class II low resolution haplotypes (Lrs) that were assigned by a polymerase chain reaction-sequence specific primers (PCR-SSP) typing method. Only low resolution haplotypes were used in this study because the eight SLA class II high-resolution haplotypes had been assigned to the 14 parents or the progenitors of the highly inbred MMP herd in a previous publication. The fertility index of dams with Lr-0.13 was significantly lower than that of dams with Lr-0.16, Lr-0.17, Lr-0.18, or Lr-0.37. Dams with Lr-0.23 had significantly smaller litter size at birth than those with Lr-0.17, Lr-0.18, or Lr-0.37. Furthermore, litter size at weaning of dams with Lr-0.23 was also significantly smaller than those dams with Lr-0.16, Lr-0.17, Lr-0.18, or Lr-0.37. The small litter size of dams with Lr-0.23 correlated with the smaller body sizes of these MMPs. These results suggest that SLA class II haplotypes are useful differential genetic markers for further haplotypic and epistatic studies of reproductive traits, selective breeding programs, and improvements in the production and reproduction performances of MMPs.
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Affiliation(s)
- Asako Ando
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara 259-1193, Japan
| | - Noriaki Imaeda
- Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan
| | - Tatsuya Matsubara
- Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan
| | - Masaki Takasu
- Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan
| | - Asuka Miyamoto
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara 259-1193, Japan
| | - Shino Oshima
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara 259-1193, Japan
| | - Naohito Nishii
- Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan
| | - Yoshie Kametani
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara 259-1193, Japan
| | - Takashi Shiina
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara 259-1193, Japan
| | - Jerzy K Kulski
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara 259-1193, Japan
- Faculty of Health and Medical Sciences, UWA Medical School, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Hitoshi Kitagawa
- Laboratory of Veterinary Internal Medicine, Faculty of Veterinary Medicine, Okayama University of Science, 1-3 Ikoino-oka, Imabari, Ehime 794-8555, Japan.
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Abstract
BACKGROUND Management of tumors has become more complex owing to tumor heterogeneity. Fewer studies have been performed on intra-tumor heterogeneity of endometrial cancer (EC) until now. Therefore, it is of great clinical value to explore the intra-tumor heterogeneity of EC based on clinical features and gene expression profiles. METHODS A total of 1688 patients with EC were screened and 114 patients were finally selected, including specimens from 84 patients with primary EC without relapse (PE) and the paired metastases (P-M) specimens, as well as specimens from 30 patients with primary EC with relapse (RPE) and the paired relapsed EC (P-RE) specimens. Microarray and RNA-seq were used to detect gene expression of EC samples. Clinicopathological characteristics and molecular data were compared between PE and P-M groups and between RPE and P-RE groups to explore the intra-tumor heterogeneity of EC. RESULTS The clinical intra-tumor spatial heterogeneity of pathological type, grade, ER status, and PR status between PE and P-M were 17.9%, 13.1%, 28.6%, and 28.6%, respectively. The clinical intra-tumor spatiotemporal heterogeneity of pathological type, grade, ER status, and PR status between RPE and P-RE were 16.7%, 33.3%, 25.0%, and 37.5%, respectively. Cluster analysis sorts EC samples based on progression type of lesion and their pathological type. There were differentially expressed genes between PE and P-M and between RPE and P-RE, of which gene ontology and Kyoto Encyclopedia of Genes and Genomes analysis were mainly enriched in cell proliferation, the p53 signaling pathway, etc. CONCLUSIONS:: Clinical and molecular data showed that there was spatiotemporal heterogeneity in intra-tumor of EC, which may add to the complexity of diagnosis and therapeutics for EC. Considering the intra-tumor heterogeneity, sequential chemotherapy and precision medicine may be a more suitable treatment plan for EC.
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13
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Yin F, Shao X, Zhao L, Li X, Zhou J, Cheng Y, He X, Lei S, Li J, Wang J. Predicting prognosis of endometrioid endometrial adenocarcinoma on the basis of gene expression and clinical features using Random Forest. Oncol Lett 2019; 18:1597-1606. [PMID: 31423227 PMCID: PMC6607378 DOI: 10.3892/ol.2019.10504] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 04/03/2019] [Indexed: 12/29/2022] Open
Abstract
Traditional clinical features are not sufficient to accurately judge the prognosis of endometrioid endometrial adenocarcinoma (EEA). Molecular biological characteristics and traditional clinical features are particularly important in the prognosis of EEA. The aim of the present study was to establish a predictive model that considers genes and clinical features for the prognosis of EEA. The clinical and RNA sequencing expression data of EEA were derived from samples from The Cancer Genome Atlas (TCGA) and Peking University People's Hospital (PKUPH; Beijing, China). Samples from TCGA were used as the training set, and samples from the PKUPH were used as the testing set. Variable selection using Random Forests (VSURF) was used to select the genes and clinical features on the basis of TCGA samples. The RF classification method was used to establish the prediction model. Kaplan-Meier curves were tested with the log-rank test. The results from this study demonstrated that on the basis of TCGA samples, 11 genes and the grade were selected as the input features. In the training set, the out-of-bag (OOB) error of RF model-1, which was established using the '11 genes', was 0.15; the OOB error of RF model-2, which was established using the 'grade', was 0.39; and the OOB error of RF model-3, established using the '11 genes and grade', was 0.15. In the testing set, the classification accuracy of RF model-1, model-2 and model-3 was 71.43, 66.67 and 80.95%, respectively. In conclusion, to the best of our knowledge, the VSURF was used to select features relevant to EEA prognosis, and an EEA predictive model combining genes and traditional features was established for the first time in the present study. The prediction accuracy of the RF model on the basis of the 11 genes and grade was markedly higher than that of the RF models established by either the 11 genes or grade alone.
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Affiliation(s)
- Fufen Yin
- Department of Obstetrics and Gynecology, Peking University People's Hospital, Beijing 100044, P.R. China
| | - Xingyang Shao
- College of Automation, Faculty of Information Technology, Beijing University of Technology, Beijing 100124, P.R. China.,Beijing Key Laboratory of Computational Intelligence and Intelligent System, Beijing 100124, P.R. China
| | - Lijun Zhao
- Department of Obstetrics and Gynecology, Peking University People's Hospital, Beijing 100044, P.R. China
| | - Xiaoping Li
- Department of Obstetrics and Gynecology, Peking University People's Hospital, Beijing 100044, P.R. China
| | - Jingyi Zhou
- Department of Obstetrics and Gynecology, Peking University People's Hospital, Beijing 100044, P.R. China
| | - Yuan Cheng
- Department of Obstetrics and Gynecology, Peking University People's Hospital, Beijing 100044, P.R. China
| | - Xiangjun He
- Department of Obstetrics and Gynecology, Peking University People's Hospital, Beijing 100044, P.R. China
| | - Shu Lei
- Department of Obstetrics and Gynecology, Peking University People's Hospital, Beijing 100044, P.R. China
| | - Jiangeng Li
- College of Automation, Faculty of Information Technology, Beijing University of Technology, Beijing 100124, P.R. China.,Beijing Key Laboratory of Computational Intelligence and Intelligent System, Beijing 100124, P.R. China
| | - Jianliu Wang
- Department of Obstetrics and Gynecology, Peking University People's Hospital, Beijing 100044, P.R. China
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14
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Choi J, Kwon K, Lee Y, Ko E, Kim Y, Choi Y. Characteristics of Pig Carcass and Primal Cuts Measured by the Autofom Ⅲ Depend on Seasonal Classification. Food Sci Anim Resour 2019; 39:332-344. [PMID: 31149674 PMCID: PMC6533396 DOI: 10.5851/kosfa.2019.e30] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 04/04/2019] [Accepted: 04/04/2019] [Indexed: 11/23/2022] Open
Abstract
The objective of this study was to investigate slaughtering performance, carcass
grade, and quantitative traits of cuts according to seasonal influence by each
month in pigs slaughtered in livestock processing complex (LPC) slaughterhouse
in Korea, 2017. A total of 267,990 LYD (Landrace×Yorkshire×Duroc)
pig data were used in this study. Results of slaughter heads, sex distribution,
carcass weight, backfat thickness, grading class, total weight, and fat and lean
meat percentages of each cut predicted by Autofom Ⅲ were obtained each
month. The number of slaughtered pigs was the highest in early and late fall but
the lowest in midsummer. Only in midsummer that the number of females was higher
than that of castrates. During 2017, carcass weight was the lowest in late
summer. Backfat thickness was in the range of 21–22 mm. In mid and late
spring, pigs showed high 1+ grade ratio (37.05% and 36.15%,
respectively). For traits of 11 cuts predicted by Autofom Ⅲ, porkbelly
showed lower total weight, lean weight, and fat weight in midsummer to early
fall but higher lean meat percentage compared to other seasons. Weights of
deboned neck, loin, and lean meat were the highest in midfall compared to other
seasons (p<0.05). In conclusion, characteristics of slaughtering,
grading, and economic traits of pigs seemed to be highly seasonal. They were
influenced by seasons. Results of this study could be used as basic data to
develop seasonal specified management ways to improve pork production.
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Affiliation(s)
- Jungseok Choi
- Department of Physiology, Maastricht University, Maastricht, 6229 ER, The Netherlands
| | - Kimun Kwon
- Korea Institute for Animal Products Quality Evaluation, Sejong 30100, Korea
| | - Youngkyu Lee
- Dodram Pig Farmers Cooperative, Icheon 17405, Korea
| | - Eunyoung Ko
- Dodram Pig Farmers Cooperative, Icheon 17405, Korea
| | - Yongsun Kim
- Dodram Pig Farmers Cooperative, Icheon 17405, Korea
| | - Yangil Choi
- Department of Animal Science, Chungbuk National University, Cheongju 28644, Korea
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15
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Wang X, Kadarmideen HN. An Epigenome-Wide DNA Methylation Map of Testis in Pigs for Study of Complex Traits. Front Genet 2019; 10:405. [PMID: 31114612 PMCID: PMC6502962 DOI: 10.3389/fgene.2019.00405] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 04/12/2019] [Indexed: 12/17/2022] Open
Abstract
Epigenetic changes are important for understanding complex trait variation and inheritance in pigs that are also a valuable biomedical model for human health research. Testis is the main organ for reproduction and boar taint in pigs; however, there have been no studies to-date on adult pig testis epigenome. The main objective of this study was to establish a genome-wide DNA methylation map of pig testis that would help identify candidate epigenetic biomarkers and methylated genes for complex traits such as male reproduction, fertility or boar taint. Reduced Representation Bisulfite Sequencing (RRBS) was used to study methylation levels of cytosine in nine pig testis samples. The results showed that genome-wide methylation status of nine samples overlapped greatly and their variation among pigs were low. The methylation levels of promoter, exon, intron, cytosine and guanine dinucleotide (CpG) islands and CpG island shores regions were 0.15, 0.47, 0.55, 0.39, and 0.53, respectively. Cytosines binding to CpG islands showed different methylation levels between exon and intron regions. All methylation levels of CpG islands were lower than CpG island shores in different genic features. The distribution of 12,738 differentially methylated cytosines (DMCs) within CpG islands, CpG island shores and other regions was 36.86, 21.65, and 41.49%, respectively, and was 0.33, 1.71, 5.95, and 92.01% in promoter, exon, intron and intergenic regions, respectively. Methylation levels of DMCs in promoter, exon and intron regions were significantly different between CpG islands and CpG island shores (P < 0.05). A total of 898 genes with 2089 DMCs were enriched in 112 Gene Ontology (GO) terms. Fifteen methylated genes from our study were associated with fertility or boar taint traits. Our analysis revealed the methylation patterns in different genic features and CpG island regions of testis in pigs, and summarized several candidate genes associated with DMCs and the involved GO terms. These findings are helpful to understand the relationship between DNA methylation and genic CpG islands, to provide candidate epigenetic regions or biomarkers for pig production and welfare and for translational epigenomic studies that use pigs as an animal model for human research.
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Affiliation(s)
- Xiao Wang
- Quantitative Genomics, Bioinformatics and Computational Biology Group, Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Haja N Kadarmideen
- Quantitative Genomics, Bioinformatics and Computational Biology Group, Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, Denmark
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16
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Analysis of differential gene expression of the transgenic pig with overexpression of PGC1α in muscle. Mol Biol Rep 2019; 46:3427-3435. [PMID: 30980266 DOI: 10.1007/s11033-019-04805-8] [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: 11/22/2018] [Accepted: 04/09/2019] [Indexed: 10/27/2022]
Abstract
In order to better understand the key regulatory mechanisms of PGC1α in muscle fiber type transition, the RNA-seq was used to compare the change of gene expression in gastrocnemius muscles between wild type pigs and transgenic pigs with overexpression of PGC1α gene in muscle. 371 differentially expressed genes (P ≤ 0.05 and Ratio ≥ 2), including 184 up-regulated genes and 187 down-regulated genes, were identified. Five main signaling pathways including metabolic pathways, ECM-receptor interaction, PPAR signaling pathway, adipocytokine signaling pathway and insulin signaling pathway, were authenticated using KEGG pathway analysis. Our results indicate that the fat metabolism pathway plays an important role in the transformation of muscle fiber types regulated by PGC1α.
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17
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Krombeen SK, Shankar V, Noorai RE, Saski CA, Sharp JL, Wilson ME, Wilmoth TA. The identification of differentially expressed genes between extremes of placental efficiency in maternal line gilts on day 95 of gestation. BMC Genomics 2019; 20:254. [PMID: 30925895 PMCID: PMC6441153 DOI: 10.1186/s12864-019-5626-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 03/20/2019] [Indexed: 12/11/2022] Open
Abstract
Background Placental efficiency (PE) describes the relationship between placental and fetal weights (fetal wt/placental wt). Within litters, PE can vary drastically, resulting in similarly sized pigs associated with differently sized placentas, up to a 25% weight difference. However, the mechanisms enabling the smaller placenta to grow a comparable littermate are unknown. To elucidate potential mechanisms, morphological measurements and gene expression profiles in placental and associated endometrial tissues of high PE and low PE feto-placental units were compared. Tissue samples were obtained from eight maternal line gilts during gestational day 95 ovario-hysterectomies. RNA was extracted from tissues of feto-placental units with the highest and lowest PE in each litter and sequenced. Results Morphological measurements, except placental weight, were not different (P > 0.05) between high and low PE. No DEG were identified in the endometrium and 214 DEG were identified in the placenta (FDR < 0.1), of which 48% were upregulated and 52% were downregulated. Gene ontology (GO) analysis revealed that a large percentage of DEG were involved in catalytic activity, binding, transporter activity, metabolism, biological regulation, and localization. Four GO terms were enriched in the upregulated genes and no terms were enriched in the downregulated genes (FDR < 0.05). Eight statistically significant correlations (P < 0.05) were identified between the morphological measurements and DEG. Conclusion Morphological measures between high and low PE verified comparisons were of similarly sized pigs grown on different sized placentas, and indicated that any negative effects of a reduced placental size on fetal growth were not evident by day 95. The identification of DEG in the placenta, but absence of DEG in the endometrium confirmed that the placenta responds to the fetus. The GO analyses provided evidence that extremes of PE are differentially regulated, affecting components of placental transport capacity like nutrient transport and blood flow. However, alternative GO terms were identified, indicating the complexity of the relationship between placental and fetal weights. These findings support the use of PE as a marker of placental function and provide novel insight into the genetic control of PE, but further research is required to make PE production applicable.
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Affiliation(s)
- Shanice K Krombeen
- Department of Animal and Veterinary Science, Clemson University, Clemson, SC, 29634, USA
| | - Vijay Shankar
- Center for Human Genetics, Clemson University, Greenwood, SC, 29646, USA
| | - Rooksana E Noorai
- Genomics and Bioinformatics Facility, Clemson University, Clemson, SC, 29634, USA
| | - Christopher A Saski
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, 29634, USA
| | - Julia L Sharp
- Department of Statistics, Colorado State University, Fort Collins, CO, 80523, USA
| | - Matthew E Wilson
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV, 26506, USA
| | - Tiffany A Wilmoth
- Department of Animal and Veterinary Science, Clemson University, Clemson, SC, 29634, USA.
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18
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Krombeen SK, Bridges WC, Wilson ME, Wilmoth TA. Factors contributing to the variation in placental efficiency on days 70, 90, and 110 of gestation in gilts. J Anim Sci 2019; 97:359-373. [PMID: 30329058 PMCID: PMC6313123 DOI: 10.1093/jas/sky409] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 10/13/2018] [Indexed: 12/18/2022] Open
Abstract
Variations in placental efficiency (PE), a measure of grams of fetus produced per gram of placenta, were initially researched between swine breeds, where increased PE was associated with larger litters. Placental efficiency was also found to vary greatly within production herds and individual litters; however, the use of PE as a selection tool has been debated. Nonetheless, PE is an index of feto-placental adaptation and may help identify compensatory mechanisms that maintain fetal growth when placental size is reduced, potentially providing an opportunity to address production concerns like low birth weights and preweaning survival. Since the nutrient transport capacity of the placenta largely depends on vasculature and nutrient transporter abundance, the objectives of this experiment were to 1) determine the mRNA expression of genes encoding nutrient transporters in the placenta and adjacent endometrium, and 2) evaluate if a relationship existed between PE and vascular density and/or nutrient transporters. Gilts (n = 19) were ovario-hysterectomized on day 70, 90, or 110 of gestation to collect placental and adjacent endometrial samples. The mean litter size was 11.1. Placental efficiency increased (P < 0.0001) throughout the end of gestation, while the range of PE increased from day 70 to 90 and was reduced on day 110 (P < 0.0001). Placental efficiency and placental weight were negatively correlated throughout gestation (70 d, r = -0.83, P < 0.0001; 90 d, r = -0.81, P < 0.0001; 110 d, r = -0.44, P < 0.0007), but the negative correlation between PE and fetal weight was not maintained as gestation progressed (70 d, r = -0.58, P < 0.0001; 90 d, r = -0.36, P < 0.0005; 110 d, r = 0.09, P = 0.51). Based on conditional effects plots, variations in PE were associated with alterations in amino acid transporter expression in the placenta (SLC7A7, SLC3A1) and endometrium (SLC7A1) on day 70. On day 90, PE had a positive relationship with placental expression of a glucose transporter (SLC2A3), and on day 110 PE was positively related to placental vascular density. The results suggest utero-placental adaptations occur as a compensation for reduced placental size to meet the increasing nutrient demands of the growing fetus during late gestation in swine. Furthermore, nutrient requirements differ for individual feto-placental units on a given day; therefore, optimizing nutrient availability during late gestation may improve fetal growth and survival.
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Affiliation(s)
- Shanice K Krombeen
- Department of Animal and Veterinary Sciences, Clemson University, Clemson, SC
| | - William C Bridges
- Department of Mathematical Sciences, Clemson University, Clemson, SC
| | - Matthew E Wilson
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV
| | - Tiffany A Wilmoth
- Department of Animal and Veterinary Sciences, Clemson University, Clemson, SC
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19
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Yang S, Zhou X, Pei Y, Wang H, He K, Zhao A. Identification of Differentially Expressed Genes in Porcine Ovaries at Proestrus and Estrus Stages Using RNA-Seq Technique. BIOMED RESEARCH INTERNATIONAL 2018; 2018:9150723. [PMID: 29662904 PMCID: PMC5832140 DOI: 10.1155/2018/9150723] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 12/29/2017] [Accepted: 01/18/2018] [Indexed: 12/11/2022]
Abstract
Estrus is an important factor for the fecundity of sows, and it is involved in ovulation and hormone secretion in ovaries. To better understand the molecular mechanisms of porcine estrus, the expression patterns of ovarian mRNA at proestrus and estrus stages were analyzed using RNA sequencing technology. A total of 2,167 differentially expressed genes (DEGs) were identified (P ≤ 0.05, |log2 Ratio| ≥ 1), of which 784 were upregulated and 1,383 were downregulated in the estrus compared with the proestrus group. Gene Ontology (GO) enrichment indicated that these DEGs were mainly involved in the cellular process, single-organism process, cell and cell part, and binding and metabolic process. In addition, a pathway analysis showed that these DEGs were significantly enriched in 33 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, including cell adhesion molecules, ECM-receptor interaction, and cytokine-cytokine receptor interaction. Quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) confirmed the differential expression of 10 selected DEGs. Many of the novel candidate genes identified in this study will be valuable for understanding the molecular mechanisms of the sow estrous cycle.
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Affiliation(s)
- Songbai Yang
- College of Animal Science and Technology, Zhejiang A&F University, Lin'an, Zhejiang 311300, China
| | - Xiaolong Zhou
- College of Animal Science and Technology, Zhejiang A&F University, Lin'an, Zhejiang 311300, China
| | - Yue Pei
- College of Animal Science and Technology, Zhejiang A&F University, Lin'an, Zhejiang 311300, China
| | - Han Wang
- College of Animal Science and Technology, Zhejiang A&F University, Lin'an, Zhejiang 311300, China
| | - Ke He
- College of Animal Science and Technology, Zhejiang A&F University, Lin'an, Zhejiang 311300, China
| | - Ayong Zhao
- College of Animal Science and Technology, Zhejiang A&F University, Lin'an, Zhejiang 311300, China
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20
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Xu Q, Qu C, Wan J, Cheng G, Yang W, Gong C, He J, Du Y. Effect of dietary chitosan oligosaccharide supplementation on the pig ovary transcriptome. RSC Adv 2018; 8:13266-13273. [PMID: 35542534 PMCID: PMC9079672 DOI: 10.1039/c7ra10172d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 03/27/2018] [Indexed: 11/21/2022] Open
Abstract
Fecundity improvement is one of the most important economic traits for the swine industry. In this study, we identified 486 differentially expressed genes associated with sow prolificacy from COS administrated sow ovaries by RNA-seq.
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Affiliation(s)
- Qingsong Xu
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control
- Dalian Ocean University
- Dalian 116023
- China
| | - Chen Qu
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control
- Dalian Ocean University
- Dalian 116023
- China
| | - Jin Wan
- Institute of Animal Nutrition
- Sichuan Agricultural University
- Chengdu 611130
- China
| | - Gong Cheng
- Institute of Process Engineering
- Chinese Academy of Sciences
- Beijing 100190
- China
- Zhongke Runxin (Suzhou) Biological Technology Co., Ltd
| | - Wen Yang
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control
- Dalian Ocean University
- Dalian 116023
- China
| | - Changhao Gong
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control
- Dalian Ocean University
- Dalian 116023
- China
| | - Jun He
- Institute of Animal Nutrition
- Sichuan Agricultural University
- Chengdu 611130
- China
| | - Yuguang Du
- Institute of Process Engineering
- Chinese Academy of Sciences
- Beijing 100190
- China
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21
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Hwang JH, An SM, Kwon S, Park DH, Kim TW, Kang DG, Yu GE, Kim IS, Park HC, Ha J, Kim CW. DNA methylation patterns and gene expression associated with litter size in Berkshire pig placenta. PLoS One 2017; 12:e0184539. [PMID: 28880934 PMCID: PMC5589248 DOI: 10.1371/journal.pone.0184539] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 08/26/2017] [Indexed: 11/18/2022] Open
Abstract
Increasing litter size is of great interest to the pig industry. DNA methylation is an important epigenetic modification that regulates gene expression, resulting in livestock phenotypes such as disease resistance, milk production, and reproduction. We classified Berkshire pigs into two groups according to litter size and estimated breeding value: smaller (SLG) and larger (LLG) litter size groups. Genome-wide DNA methylation and gene expression were analyzed using placenta genomic DNA and RNA to identify differentially methylated regions (DMRs) and differentially expressed genes (DEGs) associated with litter size. The methylation levels of CpG dinucleotides in different genomic regions were noticeably different between the groups, while global methylation pattern was similar, and excluding intergenic regions they were found the most frequently in gene body regions. Next, we analyzed RNA-Seq data to identify DEGs between the SLG and LLG groups. A total of 1591 DEGs were identified: 567 were downregulated and 1024 were upregulated in LLG compared to SLG. To identify genes that simultaneously exhibited changes in DNA methylation and mRNA expression, we integrated and analyzed the data from bisulfite-Seq and RNA-Seq. Nine DEGs positioned in DMRs were found. The expression of only three of these genes (PRKG2, CLCA4, and PCK1) was verified by RT-qPCR. Furthermore, we observed the same methylation patterns in blood samples as in the placental tissues by PCR-based methylation analysis. Together, these results provide useful data regarding potential epigenetic markers for selecting hyperprolific sows.
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Affiliation(s)
- Jung Hye Hwang
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju, South Korea
| | - Sang Mi An
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju, South Korea
| | - Seulgi Kwon
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju, South Korea
| | - Da Hye Park
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju, South Korea
| | - Tae Wan Kim
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju, South Korea
| | - Deok Gyeong Kang
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju, South Korea
| | - Go Eun Yu
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju, South Korea
| | - Il-Suk Kim
- Department of Animal Resource Technology, Gyeongnam National University of Science & Technology, Jinju, South Korea
| | | | - Jeongim Ha
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju, South Korea
- * E-mail: (JH); (CWK)
| | - Chul Wook Kim
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju, South Korea
- * E-mail: (JH); (CWK)
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22
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Wijesena HR, Lents CA, Riethoven JJ, Trenhaile-Grannemann MD, Thorson JF, Keel BN, Miller PS, Spangler ML, Kachman SD, Ciobanu DC. GENOMICS SYMPOSIUM: Using genomic approaches to uncover sources of variation in age at puberty and reproductive longevity in sows1,2. J Anim Sci 2017. [DOI: 10.2527/jas.2016.1334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- H. R. Wijesena
- Department of Animal Science, University of Nebraska, Lincoln 68583
| | - C. A. Lents
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, 68933
| | - J.-J. Riethoven
- Center for Biotechnology, University of Nebraska, Lincoln 68583
| | | | - J. F. Thorson
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, 68933
| | - B. N. Keel
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, 68933
| | - P. S. Miller
- Department of Animal Science, University of Nebraska, Lincoln 68583
| | - M. L. Spangler
- Department of Animal Science, University of Nebraska, Lincoln 68583
| | - S. D. Kachman
- Department of Statistics, University of Nebraska, Lincoln 68583
| | - D. C. Ciobanu
- Department of Animal Science, University of Nebraska, Lincoln 68583
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23
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Liu L, Zhao H, Peng S, Wang T, Su J, Liang Y, Li H, Wang H. Transcriptomic Analysis of Oenococcus oeni SD-2a Response to Acid Shock by RNA-Seq. Front Microbiol 2017; 8:1586. [PMID: 28878748 PMCID: PMC5572241 DOI: 10.3389/fmicb.2017.01586] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 08/04/2017] [Indexed: 12/18/2022] Open
Abstract
Oenococcus oeni can be applied to conduct malolactic fermentation (MLF), but also is the main species growing naturally in wine. Due to the high stress tolerance, it is an interesting model for investigating acid response mechanisms. In this study, the changes in the transcriptome of O.oeni SD-2a during the adaptation period have been studied. RNA-seq was introduced for the transcriptomic analysis of O. oeni samples treated with pH 4.8 and pH 3.0 at 0 and 1 h, respectively. Gene ontology (GO) and Kyoto encyclopedia of genes and genome (KEGG) were performed to compare the transcriptome data between different treatments. From GO analysis, the majority of differentially expressed genes (DEGs) (pH 3.0_1 h-VS-pH 4.8_1 h, pH 3.0_1 h-VS-pH 4.8_0 h, and pH 4.8_1 h-VS-pH 4.8_0 h) were found to be involved in the metabolic process, catalytic activity, cellular process, and binding. KEGG analysis reveals that the most functional gene categories affected by acid are membrane transport, amino acid metabolism and carbohydrate metabolism. Some genes, like the heat shock protein Hsp20, malate transporter and malate permease, were also over-expressed in response to acid stress. In addition, a considerable proportion of gene indicate a significantly different expression in this study, are novel, which needs to be investigated further. These results provide a new viewpoint and crucial resource on the acid stress response in O. oeni.
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Affiliation(s)
- Longxiang Liu
- College of Enology, Northwest A&F UniversityYangling, China
| | - Hongyu Zhao
- College of Enology, Northwest A&F UniversityYangling, China
| | - Shuai Peng
- College of Enology, Northwest A&F UniversityYangling, China
| | - Tao Wang
- College of Enology, Northwest A&F UniversityYangling, China.,College of Bioengineering, Sichuan University of Science and EngineeringZigong, China
| | - Jing Su
- College of Enology, Northwest A&F UniversityYangling, China.,College of Food Science and Engineering, Shanxi Agricultural UniversityTaigu, China
| | - Yanying Liang
- College of Enology, Northwest A&F UniversityYangling, China
| | - Hua Li
- College of Enology, Northwest A&F UniversityYangling, China.,Shaanxi Engineering Research Center for Viti-VinicultureYangling, China.,Heyang Experimental and Demonstrational Stations for Grape, Northwest A&F UniversityWeinan, China
| | - Hua Wang
- College of Enology, Northwest A&F UniversityYangling, China.,Shaanxi Engineering Research Center for Viti-VinicultureYangling, China.,Heyang Experimental and Demonstrational Stations for Grape, Northwest A&F UniversityWeinan, China
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24
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Chu Q, Zhou B, Xu F, Chen R, Shen C, Liang T, Li Y, Schinckel AP. Genome-wide differential mRNA expression profiles in follicles of two breeds and at two stages of estrus cycle of gilts. Sci Rep 2017; 7:5052. [PMID: 28698542 PMCID: PMC5506030 DOI: 10.1038/s41598-017-04336-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 05/11/2017] [Indexed: 12/11/2022] Open
Abstract
Estrus expression by gilts and sows is hereditable and important for heat detection. To better understand the molecular biological mechanisms of estrus expression in gilts, the mRNA expression profiles of follicular tissue from Large White gilts in diestrus (LD, n = 3) and estrus (LE, n = 3), and Chinese indigenous Mi gilts in diestrus (MD, n = 2) and estrus (ME, n = 3) were investigated using RNA sequencing. We detected 122,804-335,295 SNPs, 6,140-14,947 InDel and 12 types of AS events (39.57% TSS, 34.90% TTS) in 11 samples. A total of 2,838 differentially expressed genes (DEGs) were found in LD vs MD, LE vs ME, LE vs LD, or ME vs MD comparisons. Two DEGs (ACP5 and PIGS) were observed in all comparisons. Two new genes (ENSSSCG00000028235 and ENSSSCG00000021903) were exclusively expressed in Mi and Large White gilts, respectively. Bioinformatics analyses indicate that these DEGs are involved in single-organism process, catalytic activity, cell adhesion and enriched in ECM-receptor interaction, olfactory transduction, ovarian steroidogenesis, steroid biosynthesis and CAMs signaling pathways. These results of RNA-Seq have provided important information for screening the key functional genes or molecular markers of estrus expression in gilts.
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Affiliation(s)
- Qingpo Chu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, P.R. China
| | - Bo Zhou
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, P.R. China.
| | - Feilong Xu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, P.R. China
| | - Ruonan Chen
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, P.R. China
| | - Chunyan Shen
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, P.R. China
| | - Tingting Liang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, P.R. China
| | - Yuan Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, P.R. China
| | - Allan P Schinckel
- Department of Animal Sciences, Purdue University, West Lafayette, IN, 47907-2054, USA
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