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Hou X, Wang Z, Shi L, Wang L, Zhao F, Liu X, Gao H, Shi L, Yan H, Wang L, Zhang L. Identification of imprinted genes in the skeletal muscle of newborn piglets by high-throughput sequencing. Anim Genet 2022; 53:479-486. [PMID: 35481679 DOI: 10.1111/age.13212] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 04/01/2022] [Accepted: 04/13/2022] [Indexed: 11/28/2022]
Abstract
Imprinted genes - exhibiting parent-specific transcription - play essential roles in the process of mammalian development and growth. Skeletal muscle growth is crucial for meat production. To further understand the role of imprinted genes during the porcine skeletal muscle growth, DNA-seq and RNA-seq were used to explore the characteristics of imprinted genes from porcine reciprocal crosses. A total of 584 545 single-nucleotide variations were discovered in the DNA-seq data of F0 parents, heterozygous in two pig breeds (Yorkshire and Min pigs) but homozygous in each breed. These single-nucleotide variations were used to determine the allelic-specific expression in F1 individuals. Finally, eight paternal expression sites and three maternal expression sites were detected, whereas two paternally expressed imprinted genes (NDN and IGF2) and one maternally expressed imprinted gene (H1-3) were validated by Sanger sequencing. DNA methylation regulates the expression of imprinted genes, and all of the identified imprinted genes in this study were predicted to possess CpG islands. PBX1 and YY1 binding motifs were discovered in the promoter regions of all three imprinted genes, which were candidate elements regulating the transcription of imprinted genes. For these identified imprinted genes, IGF2 and NDN promoted muscle growth whereas H1-3 inhibited cell proliferation, corroborating the 'parental conflict' theory that paternally expressed imprinted genes assisted descendants' growth whereas maternally expressed imprinted genes inhibited it. This study discovered porcine imprinted genes in skeletal muscle and was the first to reveal that H1-3 was expressed by the maternal allele to our knowledge. Our findings provided valuable resources for the potential utilization of imprinted genes in pig breeding.
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Affiliation(s)
- Xinhua Hou
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zishuai Wang
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Liangyu Shi
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,School of Animal Science and Nutritional Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Ligang Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fuping Zhao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xin Liu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongmei Gao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lijun Shi
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hua Yan
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lixian Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Longchao Zhang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Banerjee P, Carmelo VAO, Kadarmideen HN. Integrative Analysis of Metabolomic and Transcriptomic Profiles Uncovers Biological Pathways of Feed Efficiency in Pigs. Metabolites 2020; 10:E275. [PMID: 32640603 PMCID: PMC7408121 DOI: 10.3390/metabo10070275] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 06/24/2020] [Accepted: 07/04/2020] [Indexed: 12/12/2022] Open
Abstract
Feed efficiency (FE) is an economically important trait. Thus, reliable predictors would help to reduce the production cost and provide sustainability to the pig industry. We carried out metabolome-transcriptome integration analysis on 40 purebred Duroc and Landrace uncastrated male pigs to identify potential gene-metabolite interactions and explore the molecular mechanisms underlying FE. To this end, we applied untargeted metabolomics and RNA-seq approaches to the same animals. After data quality control, we used a linear model approach to integrate the data and find significant differently correlated gene-metabolite pairs separately for the breeds (Duroc and Landrace) and FE groups (low and high FE) followed by a pathway over-representation analysis. We identified 21 and 12 significant gene-metabolite pairs for each group. The valine-leucine-isoleucine biosynthesis/degradation and arginine-proline metabolism pathways were associated with unique metabolites. The unique genes obtained from significant metabolite-gene pairs were associated with sphingolipid catabolism, multicellular organismal process, cGMP, and purine metabolic processes. While some of the genes and metabolites identified were known for their association with FE, others are novel and provide new avenues for further research. Further validation of genes, metabolites, and gene-metabolite interactions in larger cohorts will elucidate the regulatory mechanisms and pathways underlying FE.
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Affiliation(s)
| | | | - Haja N. Kadarmideen
- Quantitative Genomics, Bioinformatics and Computational Biology Group, Department of Applied Mathematics and Computer Science, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (P.B.); (V.A.O.C.)
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Bakoev S, Getmantseva L, Bakoev F, Kolosova M, Gabova V, Kolosov A, Kostyunina O. Survey of SNPs Associated with Total Number Born and Total Number Born Alive in Pig. Genes (Basel) 2020; 11:E491. [PMID: 32365801 PMCID: PMC7291110 DOI: 10.3390/genes11050491] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 04/24/2020] [Accepted: 04/29/2020] [Indexed: 12/26/2022] Open
Abstract
Reproductive productivity depend on a complex set of characteristics. The number of piglets at birth (Total number born, Litter size, TNB) and the number of alive piglets at birth (Total number born alive, NBA) are the main indicators of the reproductive productivity of sows in pig breeding. Great hopes are pinned on GWAS (Genome-Wide Association Studies) to solve the problems associated with studying the genetic architecture of reproductive traits of pigs. This paper provides an overview of international studies on SNP (Single nucleotide polymorphism) associated with TNB and NBA in pigs presented in PigQTLdb as "Genome map association". Currently on the base of Genome map association results 306 SNPs associated with TNB (218 SNPs) and NBA (88 SNPs) have been identified and presented in the Pig QTLdb database. The results are based on research of pigs such as Large White, Yorkshire, Landrace, Berkshire, Duroc and Erhualian. The presented review shows that most SNPs found in chromosome areas where candidate genes or QTLs (Quantitative trait locus) have been identified. Further research in the given direction will allow to obtain new data that will become an impulse for creating breakthrough breeding technologies and increase the production efficiency in pig farming.
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Affiliation(s)
- Siroj Bakoev
- Federal Science Center for Animal Husbandry named after Academy Member L.K. Ernst, Dubrovitsy 142132, Russian; (S.B.); (F.B.); (M.K.); (A.K.); (O.K.)
| | - Lyubov Getmantseva
- Federal Science Center for Animal Husbandry named after Academy Member L.K. Ernst, Dubrovitsy 142132, Russian; (S.B.); (F.B.); (M.K.); (A.K.); (O.K.)
| | - Faridun Bakoev
- Federal Science Center for Animal Husbandry named after Academy Member L.K. Ernst, Dubrovitsy 142132, Russian; (S.B.); (F.B.); (M.K.); (A.K.); (O.K.)
- Department of Biology and Biotechnology, Southern Federal University, Rostov-on-Don 344006, Russia;
| | - Maria Kolosova
- Federal Science Center for Animal Husbandry named after Academy Member L.K. Ernst, Dubrovitsy 142132, Russian; (S.B.); (F.B.); (M.K.); (A.K.); (O.K.)
- Department of Biotechnology, Don State Agrarian University, Persianovski 346493, Russia
| | - Valeria Gabova
- Department of Biology and Biotechnology, Southern Federal University, Rostov-on-Don 344006, Russia;
| | - Anatoly Kolosov
- Federal Science Center for Animal Husbandry named after Academy Member L.K. Ernst, Dubrovitsy 142132, Russian; (S.B.); (F.B.); (M.K.); (A.K.); (O.K.)
- Department of Biotechnology, Don State Agrarian University, Persianovski 346493, Russia
| | - Olga Kostyunina
- Federal Science Center for Animal Husbandry named after Academy Member L.K. Ernst, Dubrovitsy 142132, Russian; (S.B.); (F.B.); (M.K.); (A.K.); (O.K.)
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Yin Z, Zhang X, Li J, Jiao Y, Kong Q, Mu Y. Identification of Imprinted Genes and Their Differentially Methylated Regions in Porcine. RUSS J GENET+ 2020. [DOI: 10.1134/s1022795419120135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Jiang Z, Dong H, Zheng X, Marjani SL, Donovan DM, Chen J, Tian XC. mRNA Levels of Imprinted Genes in Bovine In Vivo Oocytes, Embryos and Cross Species Comparisons with Humans, Mice and Pigs. Sci Rep 2015; 5:17898. [PMID: 26638780 PMCID: PMC4671149 DOI: 10.1038/srep17898] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 11/02/2015] [Indexed: 12/30/2022] Open
Abstract
Twenty-six imprinted genes were quantified in bovine in vivo produced oocytes and embryos using RNA-seq. Eighteen were detectable and their transcriptional patterns were: largely decreased (MEST and PLAGL1); first decreased and then increased (CDKN1C and IGF2R); peaked at a specific stage (PHLDA2, SGCE, PEG10, PEG3, GNAS, MEG3, DGAT1, ASCL2, NNAT, and NAP1L5); or constantly low (DIRAS3, IGF2, H19 and RTL1). These patterns reflect mRNAs that are primarily degraded, important at a specific stage, or only required at low quantities. The mRNAs for several genes were surprisingly abundant. For instance, transcripts for the maternally imprinted MEST and PLAGL1, were high in oocytes and could only be expressed from the maternal allele suggesting that their genomic imprints were not yet established/recognized. Although the mRNAs detected here were likely biallelically transcribed before the establishment of imprinted expression, the levels of mRNA during these critical stages of development have important functional consequences. Lastly, we compared these genes to their counterparts in mice, humans and pigs. Apart from previously known differences in the imprinting status, the mRNA levels were different among these four species. The data presented here provide a solid reference for expression profiles of imprinted genes in embryos produced using assisted reproductive biotechnologies.
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Affiliation(s)
- Zongliang Jiang
- Center for Regenerative Biology, Department of Animal Science, University of Connecticut, Storrs, Connecticut, 06269, USA
| | - Hong Dong
- Institute of Animal Science, Xinjiang Academy of Animal Science, Urumqi, Xinjiang, P.R. China
| | - Xinbao Zheng
- Institute of Animal Science, Xinjiang Academy of Animal Science, Urumqi, Xinjiang, P.R. China
| | - Sadie L Marjani
- Department of Biology, Central Connecticut State University, New Britain, Connecticut, 06050, USA
| | - David M Donovan
- Animal Biosciences and Biotechnology Laboratory, Agricultural Research Services, United States Department of Agriculture, Beltsville, Maryland, 20705, USA
| | - Jingbo Chen
- Institute of Animal Science, Xinjiang Academy of Animal Science, Urumqi, Xinjiang, P.R. China
| | - Xiuchun Cindy Tian
- Center for Regenerative Biology, Department of Animal Science, University of Connecticut, Storrs, Connecticut, 06269, USA
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Bomba L, Nicolazzi EL, Milanesi M, Negrini R, Mancini G, Biscarini F, Stella A, Valentini A, Ajmone-Marsan P. Relative extended haplotype homozygosity signals across breeds reveal dairy and beef specific signatures of selection. Genet Sel Evol 2015; 47:25. [PMID: 25888030 PMCID: PMC4383072 DOI: 10.1186/s12711-015-0113-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 03/19/2015] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND A number of methods are available to scan a genome for selection signatures by evaluating patterns of diversity within and between breeds. Among these, "extended haplotype homozygosity" (EHH) is a reliable approach to detect genome regions under recent selective pressure. The objective of this study was to use this approach to identify regions that are under recent positive selection and shared by the most representative Italian dairy and beef cattle breeds. RESULTS A total of 3220 animals from Italian Holstein (2179), Italian Brown (775), Simmental (493), Marchigiana (485) and Piedmontese (379) breeds were genotyped with the Illumina BovineSNP50 BeadChip v.1. After standard quality control procedures, genotypes were phased and core haplotypes were identified. The decay of linkage disequilibrium (LD) for each core haplotype was assessed by measuring the EHH. Since accurate estimates of local recombination rates were not available, relative EHH (rEHH) was calculated for each core haplotype. Genomic regions that carry frequent core haplotypes and with significant rEHH values were considered as candidates for recent positive selection. Candidate regions were aligned across to identify signals shared by dairy or beef cattle breeds. Overall, 82 and 87 common regions were detected among dairy and beef cattle breeds, respectively. Bioinformatic analysis identified 244 and 232 genes in these common genomic regions. Gene annotation and pathway analysis showed that these genes are involved in molecular functions that are biologically related to milk or meat production. CONCLUSIONS Our results suggest that a multi-breed approach can lead to the identification of genomic signatures in breeds of cattle that are selected for the same production goal and thus to the localisation of genomic regions of interest in dairy and beef production.
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Affiliation(s)
- Lorenzo Bomba
- Istituto di Zootecnica, UCSC, via Emilia Parmense 84, Piacenza, 29122, Italy.
| | - Ezequiel L Nicolazzi
- Fondazione Parco Tecnologico Padano, Via Einstein, Loc. Cascina Codazza, Lodi, 26900, Italy.
| | - Marco Milanesi
- Istituto di Zootecnica, UCSC, via Emilia Parmense 84, Piacenza, 29122, Italy.
| | - Riccardo Negrini
- Associazione Italiana Allevatori (AIA), Via Tomassetti 9, Rome, 00161, Italy.
| | - Giordano Mancini
- Center for Computational Chemistry and Cosmology, Scuola Normale Superiore, Via Consoli del Mare 2, Pisa, 56126, Italy.
| | - Filippo Biscarini
- Fondazione Parco Tecnologico Padano, Via Einstein, Loc. Cascina Codazza, Lodi, 26900, Italy.
| | - Alessandra Stella
- Fondazione Parco Tecnologico Padano, Via Einstein, Loc. Cascina Codazza, Lodi, 26900, Italy. .,Istituto di biologia e biotecnologia Agraria (IBBA-CNR), Consiglio Nazionale delle Ricerche, Via Einstein, Cascina Codazza, Lodi, 26900, Italy.
| | - Alessio Valentini
- Dipartimento per l'Innovazione nei Sistemi Biologici, Agroalimentari e Forestali (DIBAF), via de Lellis, Viterbo, 01100, Italy.
| | - Paolo Ajmone-Marsan
- Istituto di Zootecnica, UCSC, via Emilia Parmense 84, Piacenza, 29122, Italy.
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Congras A, Yerle-Bouissou M, Pinton A, Vignoles F, Liaubet L, Ferchaud S, Acloque H. Sperm DNA methylation analysis in swine reveals conserved and species-specific methylation patterns and highlights an altered methylation at the GNAS locus in infertile boars. Biol Reprod 2014; 91:137. [PMID: 25320151 DOI: 10.1095/biolreprod.114.119610] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Male infertility is an increasing health issue in today's society for both human and livestock populations. In livestock, male infertility slows the improvement of animal selection programs and agricultural productivity. There is increasing evidence that epigenetic marks play an important role in the production of good-quality sperm. We therefore screened for specific or common epigenetic signatures of livestock infertility. To do so, we compared DNA methylation level in sperm DNA from fertile and infertile boars. We evaluated first the global level of sperm DNA methylation and found no difference between the two groups of boars. We then selected 42 loci of interest, most of them known to be imprinted in human or mice, and assessed the imprinting status of five of them not previously described in swine tissues: WT1, CNTN3, IMPACT, QPCT, and GRB10. DNA methylation level was then quantified in fertile and infertile boars at these 42 loci. Results from fertile boars indicated that the methylation level of the selected loci is highly conserved between pig, human, and mice, with a few exceptions, including the POU5F1 (OCT4) promoter and RTL1. Comparison between fertile and infertile boars revealed that one imprinted region, the GNAS locus, shows an increase in sperm DNA methylation in three out of eight infertile boars with low semen quality. This increase in DNA methylation is associated with an altered expression of the genes belonging to the GNAS locus, suggesting a new role for GNAS in the proper formation of functional gametes.
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Affiliation(s)
- Annabelle Congras
- INRA, UMR1388 Génétique, Physiologie et Systèmes d'Elevage, GenPhySE, Castanet-Tolosan, France
| | - Martine Yerle-Bouissou
- INRA, UMR1388 Génétique, Physiologie et Systèmes d'Elevage, GenPhySE, Castanet-Tolosan, France
| | - Alain Pinton
- Université de Toulouse INPT ENVT, UMR1388 Génétique Physiologie et Systèmes d'Elevage GenPhySE, Toulouse, France
| | - Florence Vignoles
- INRA, UMR1388 Génétique, Physiologie et Systèmes d'Elevage, GenPhySE, Castanet-Tolosan, France
| | - Laurence Liaubet
- INRA, UMR1388 Génétique, Physiologie et Systèmes d'Elevage, GenPhySE, Castanet-Tolosan, France
| | - Stéphane Ferchaud
- UE1372 GenESI Génétique, Expérimentation et Système Innovants, Surgères, France
| | - Hervé Acloque
- INRA, UMR1388 Génétique, Physiologie et Systèmes d'Elevage, GenPhySE, Castanet-Tolosan, France
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