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Lowe JWE. Humanising and dehumanising pigs in genomic and transplantation research. HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES 2022; 44:66. [PMID: 36417007 PMCID: PMC9684229 DOI: 10.1007/s40656-022-00545-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 10/16/2022] [Indexed: 06/16/2023]
Abstract
Biologists who work on the pig (Sus scrofa) take advantage of its similarity to humans by constructing the inferential and material means to traffic data, information and knowledge across the species barrier. Their research has been funded due to its perceived value for agriculture and medicine. Improving selective breeding practices, for instance, has been a driver of genomics research. The pig is also an animal model for biomedical research and practice, and is proposed as a source of organs for cross-species transplantation: xenotransplantation. Genomics research has informed transplantation biology, which has itself motivated developments in genomics. Both have generated models of correspondences between the genomes of pigs and humans. Concerning genomics, I detail how researchers traverse species boundaries to develop representations of the pig genome, alongside ensuring that such representations are sufficiently porcine. In transplantation biology, the representations of the genomes of humans and pigs are used to detect and investigate immunologically-pertinent differences between the two species. These key differences can then be removed, to 'humanise' donor pigs so that they can become a safe and effective source of organs. In both of these endeavours, there is a tension between practices that 'humanise' the pig (or representations thereof) through using resources from human genomics, and the need to 'dehumanise' the pig to maintain distinctions for legal, ethical and scientific reasons. This paper assesses the ways in which this tension has been managed, observing the differences between its realisations across comparative pig genomics and transplantation biology, and considering the consequences of this.
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Affiliation(s)
- James W E Lowe
- Science, Technology and Innovation Studies, University of Edinburgh, Old Surgeons' Hall, High School Yards, Edinburgh, EH1 1LZ, UK.
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2
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Lowe JWE, Bruce A. Genetics without genes? The centrality of genetic markers in livestock genetics and genomics. HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES 2019; 41:50. [PMID: 31659490 DOI: 10.1007/s40656-019-0290-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 10/18/2019] [Indexed: 05/23/2023]
Abstract
In this paper, rather than focusing on genes as an organising concept around which historical considerations of theory and practice in genetics are elucidated, we place genetic markers at the heart of our analysis. This reflects their central role in the subject of our account, livestock genetics concerning the domesticated pig, Sus scrofa. We define a genetic marker as a (usually material) element existing in different forms in the genome, that can be identified and mapped using a variety (and often combination) of quantitative, classical and molecular genetic techniques. The conjugation of pig genome researchers around the common object of the marker from the early-1990s allowed the distinctive theories and approaches of quantitative and molecular genetics concerning the size and distribution of gene effects to align (but never fully integrate) in projects to populate genome maps. Critical to this was the nature of markers as ontologically inert, internally heterogeneous and relational. Though genes as an organising and categorising principle remained important, the particular concatenation of limitations, opportunities, and intended research goals of the pig genetics community, meant that a progressively stronger focus on the identification and mapping of markers rather than genes per se became a hallmark of the community. We therefore detail a different way of doing genetics to more gene-centred accounts. By doing so, we reveal the presence of practices, concepts and communities that would otherwise be hidden.
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Affiliation(s)
- James W E Lowe
- Science, Technology and Innovation Studies, University of Edinburgh, Old Surgeons' Hall, High School Yards, Edinburgh, EH1 1LZ, UK.
| | - Ann Bruce
- Science, Technology and Innovation Studies, University of Edinburgh, Old Surgeons' Hall, High School Yards, Edinburgh, EH1 1LZ, UK
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3
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Perelman PL, Pichler R, Gaggl A, Larkin DM, Raudsepp T, Alshanbari F, Holl HM, Brooks SA, Burger PA, Periasamy K. Construction of two whole genome radiation hybrid panels for dromedary (Camelus dromedarius): 5000 RAD and 15000 RAD. Sci Rep 2018; 8:1982. [PMID: 29386528 PMCID: PMC5792482 DOI: 10.1038/s41598-018-20223-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 01/11/2018] [Indexed: 01/08/2023] Open
Abstract
The availability of genomic resources including linkage information for camelids has been very limited. Here, we describe the construction of a set of two radiation hybrid (RH) panels (5000RAD and 15000RAD) for the dromedary (Camelus dromedarius) as a permanent genetic resource for camel genome researchers worldwide. For the 5000RAD panel, a total of 245 female camel-hamster radiation hybrid clones were collected, of which 186 were screened with 44 custom designed marker loci distributed throughout camel genome. The overall mean retention frequency (RF) of the final set of 93 hybrids was 47.7%. For the 15000RAD panel, 238 male dromedary-hamster radiation hybrid clones were collected, of which 93 were tested using 44 PCR markers. The final set of 90 clones had a mean RF of 39.9%. This 15000RAD panel is an important high-resolution complement to the main 5000RAD panel and an indispensable tool for resolving complex genomic regions. This valuable genetic resource of dromedary RH panels is expected to be instrumental for constructing a high resolution camel genome map. Construction of the set of RH panels is essential step toward chromosome level reference quality genome assembly that is critical for advancing camelid genomics and the development of custom genomic tools.
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Affiliation(s)
- Polina L Perelman
- Animal Production and Health Laboratory, Joint FAO/IAEA Division, International Atomic Energy Agency, Vienna, Austria
- Institute of Molecular and Cellular Biology and Novosibirsk State University, Novosibirsk, Russia
| | - Rudolf Pichler
- Animal Production and Health Laboratory, Joint FAO/IAEA Division, International Atomic Energy Agency, Vienna, Austria
| | - Anna Gaggl
- Animal Production and Health Laboratory, Joint FAO/IAEA Division, International Atomic Energy Agency, Vienna, Austria
| | - Denis M Larkin
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, NW1 0TU, United Kingdom
| | | | | | | | | | - Pamela A Burger
- Research Institute of Wildlife Ecology, Vetmeduni, Vienna, Austria
| | - Kathiravan Periasamy
- Animal Production and Health Laboratory, Joint FAO/IAEA Division, International Atomic Energy Agency, Vienna, Austria.
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Zambonelli P, Comella M, Braglia S, Buttazzoni L, Davoli R. Skeletal muscle expression analysis of fat metabolism genes in pig. ITALIAN JOURNAL OF ANIMAL SCIENCE 2016. [DOI: 10.4081/ijas.2009.s2.171] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Paolo Zambonelli
- DIPROVAL, Sezione di Allevamenti Zootecnici, Università di Bologna, Italy
| | - Marco Comella
- DIPROVAL, Sezione di Allevamenti Zootecnici, Università di Bologna, Italy
| | - Silvia Braglia
- DIPROVAL, Sezione di Allevamenti Zootecnici, Università di Bologna, Italy
| | | | - Roberta Davoli
- DIPROVAL, Sezione di Allevamenti Zootecnici, Università di Bologna, Italy
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Porcine EEF1A1 and EEF1A2 genes: genomic structure, polymorphism, mapping and expression. Mol Biol Rep 2015; 42:1257-64. [DOI: 10.1007/s11033-015-3866-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 03/04/2015] [Indexed: 11/26/2022]
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Tong X, Zhang Z, Jiao Y, Xu J, Dang H, Chen Y, Jiang Z, Duan J, Zhang H, Li J, Wang C. Association of eight EST-derived SNPs with carcass and meat quality traits in pigs. J Appl Genet 2014; 56:85-95. [PMID: 25081836 DOI: 10.1007/s13353-014-0234-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 06/29/2014] [Accepted: 07/07/2014] [Indexed: 12/01/2022]
Abstract
The identification of genetic markers associated with important economic traits is fundamental to improving the productivity and quality of livestock. In this investigation, we searched for 177 expressed sequence tags (ESTs) putatively involved in meat quality from the available pig EST database, and detected eight single nucleotide polymorphisms (SNPs) in eight ESTs. We investigated the associations of these SNPs with 18 carcass and meat quality traits in a Landrace × Lantang F2 resource population (n = 257). Association analysis revealed that seven SNPs (except E42) were associated with some of the carcass- and meat quality-related traits. Particularly, significant associations of three SNPs (E53, E82, and E36) with backfat thickness traits were observed. Further, the genetic effects of E53 on four live backfat thickness traits were validated in an independent population (n = 221). More investigations about E53 sequence characteristics were performed, i.e., radiation hybrid (RH) mapping, 3'-RACE, and screening analysis of the positive BAC clones. Our research identified the genetic effects of eight EST-derived SNPs on carcass and meat quality traits, and suggested that E53 may be a useful marker for live backfat thickness traits in pig breeding programs.
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Affiliation(s)
- Xiong Tong
- College of Animal Science, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China
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Lee MO, Yang E, Morisson M, Vignal A, Huang YZ, Cheng HH, Muir WM, Lamont SJ, Lillehoj HS, Lee SH, Womack JE. Mapping and genotypic analysis of the NK-lysin gene in chicken. Genet Sel Evol 2014; 46:43. [PMID: 25001618 PMCID: PMC4120735 DOI: 10.1186/1297-9686-46-43] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 05/13/2014] [Indexed: 11/10/2022] Open
Abstract
Background Antimicrobial peptides (AMP) are important elements of the first line of defence against pathogens in animals. NK-lysin is a cationic AMP that plays a critical role in innate immunity. The chicken NK-lysin gene has been cloned and its antimicrobial and anticancer activity has been described but its location in the chicken genome remains unknown. Here, we mapped the NK-lysin gene and examined the distribution of a functionally significant single nucleotide polymorphism (SNP) among different chicken inbred lines and heritage breeds. Results A 6000 rad radiation hybrid panel (ChickRH6) was used to map the NK-lysin gene to the distal end of chromosome 22. Two additional genes, the adipocyte enhancer-binding protein 1-like gene (AEBP1) and the DNA polymerase delta subunit 2-like (POLD2) gene, are located in the same NW_003779909 contig as NK-lysin, and were thus indirectly mapped to chromosome 22 as well. Previously, we reported a functionally significant SNP at position 271 of the NK-lysin coding sequence in two different chicken breeds. Here, we examined this SNP and found that the A allele appears to be more common than the G allele in these heritage breeds and inbred lines. Conclusions The chicken NK-lysin gene mapped to the distal end of chromosome 22. Two additional genes, AEBP1 and POLD2, were indirectly mapped to chromosome 22 also. SNP analyses revealed that the A allele, which encodes a peptide with a higher antimicrobial activity, is more common than the G allele in our tested inbred lines and heritage breeds.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - James E Womack
- Department of Veterinary Pathobiology, Texas A & M University, College Station, TX 77843, USA.
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Henriksen C, Kjaer-Sorensen K, Einholm AP, Madsen LB, Momeni J, Bendixen C, Oxvig C, Vilsen B, Larsen K. Molecular cloning and characterization of porcine Na⁺/K⁺-ATPase isoforms α1, α2, α3 and the ATP1A3 promoter. PLoS One 2013; 8:e79127. [PMID: 24236096 PMCID: PMC3827302 DOI: 10.1371/journal.pone.0079127] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 09/17/2013] [Indexed: 11/18/2022] Open
Abstract
Na⁺/K⁺-ATPase maintains electrochemical gradients of Na⁺ and K⁺ essential for a variety of cellular functions including neuronal activity. The α-subunit of the Na⁺/K⁺-ATPase exists in four different isoforms (α1-α4) encoded by different genes. With a view to future use of pig as an animal model in studies of human diseases caused by Na⁺/K⁺-ATPase mutations, we have determined the porcine coding sequences of the α1-α3 genes, ATP1A1, ATP1A2, and ATP1A3, their chromosomal localization, and expression patterns. Our ATP1A1 sequence accords with the sequences from several species at five positions where the amino acid residue of the previously published porcine ATP1A1 sequence differs. These corrections include replacement of glutamine 841 with arginine. Analysis of the functional consequences of substitution of the arginine revealed its importance for Na⁺ binding, which can be explained by interaction of the arginine with the C-terminus, stabilizing one of the Na⁺ sites. Quantitative real-time PCR expression analyses of porcine ATP1A1, ATP1A2, and ATP1A3 mRNA showed that all three transcripts are expressed in the embryonic brain as early as 60 days of gestation. Expression of α3 is confined to neuronal tissue. Generally, the expression patterns of ATP1A1, ATP1A2, and ATP1A3 transcripts were found similar to their human counterparts, except for lack of α3 expression in porcine heart. These expression patterns were confirmed at the protein level. We also report the sequence of the porcine ATP1A3 promoter, which was found to be closely homologous to its human counterpart. The function and specificity of the porcine ATP1A3 promoter was analyzed in transgenic zebrafish, demonstrating that it is active and drives expression in embryonic brain and spinal cord. The results of the present study provide a sound basis for employing the ATP1A3 promoter in attempts to generate transgenic porcine models of neurological diseases caused by ATP1A3 mutations.
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Affiliation(s)
- Carina Henriksen
- Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
- Department of Biomedicine, Aarhus University, Aarhus C, Denmark
| | | | | | - Lone Bruhn Madsen
- Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
| | - Jamal Momeni
- Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
| | - Christian Bendixen
- Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
| | - Claus Oxvig
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | - Bente Vilsen
- Department of Biomedicine, Aarhus University, Aarhus C, Denmark
| | - Knud Larsen
- Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
- * E-mail:
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Ma J, Gilbert H, Iannuccelli N, Duan Y, Guo B, Huang W, Ma H, Riquet J, Bidanel JP, Huang L, Milan D. Fine mapping of fatness QTL on porcine chromosome X and analyses of three positional candidate genes. BMC Genet 2013; 14:46. [PMID: 23725562 PMCID: PMC3691627 DOI: 10.1186/1471-2156-14-46] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Accepted: 05/06/2013] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Porcine chromosome X harbors four QTL strongly affecting backfat thickness (BFT), ham weight (HW), intramuscular fat content (IMF) and loin eye area (LEA). The confidence intervals (CI) of these QTL overlap and span more than 30 cM, or approximately 80 Mb. This study therefore attempts to fine map these QTL by joint analysis of two large-scale F₂ populations (Large White × Meishan and White Duroc × Erhualian constructed by INRA and JXAU respectively) and furthermore, to determine whether these QTL are caused by mutations in three positional candidate genes (ACSL4, SERPINA7 and IRS4) involved in lipid biosynthesis. RESULTS A female-specific linkage map with an average distance of 2 cM between markers in the initial QTL interval (SW2456-SW1943) was created and used here. The CI of QTL for BFT, HW and LEA were narrowed down to 6-7 cM, resulting from the joint analysis. For IMF, two linked QTL were revealed in the INRA population but not in the JXAU population, causing a wider CI (13 cM) for IMF QTL. Linkage analyses using two subsets of INRA F₁ dam families demonstrate that the BFT and HW QTL were segregating in the Meishan pigs. Moreover, haplotype comparisons between these dams suggest that within the refined QTL region, the recombination coldspot (~34 Mb) flanked by markers MCSE3F14 and UMNP1218 is unlikely to contain QTL genes. Two SNPs in the ACSL4 gene were identified and showed significant association with BFT and HW, but they and the known polymorphisms in the other two genes are unlikely to be causal mutations. CONCLUSION The candidate QTL regions have been greatly reduced and the QTL are most likely located downstream of the recombination coldspot. The segregation of SSCX QTL for BFT and HW within Meishan breed provides an opportunity for us to make effective use of Meishan chromosome X in crossbreeding. Further studies should attempt to identify the impact of additional DNA sequence (e.g. CNV) and expression variation in the three genes or their surrounding genes on these traits.
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Affiliation(s)
- Junwu Ma
- INRA, UMR444 Laboratoire de Génétique Cellulaire, Castanet-Tolosan F-31326, France
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Zhou X, Jiang T, Du X, Zhou P, Jiang Z, Michal JJ, Liu B. Molecular characterization of porcine SARM1 and its role in regulating TLRs signaling during highly pathogenic porcine reproductive and respiratory syndrome virus infection in vivo. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2013; 39:117-126. [PMID: 22366489 DOI: 10.1016/j.dci.2012.02.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Revised: 02/07/2012] [Accepted: 02/08/2012] [Indexed: 05/31/2023]
Abstract
Toll-like receptors (TLRs) are important pattern-recognition receptors (PRRs) that trigger innate immune response and mediate acquired immunity. Evidence has shown that SARM1 (sterile-α and TIR motif containing protein 1) is one of five TIR domain-containing adaptor proteins involved in TLRs signaling transduction. In the present study, a full-length cDNA sequence was cloned for the porcine SARM1 gene, which contains nine exons. Using the radiation hybrid mapping approach, we assigned the porcine gene to SSC12 q13. Under the normal condition, porcine SARM1 was highly expressed in brain and spleen. Polyinosinic-polycytidylic acid (poly (I:C)) weakly induced the porcine SARM1 expression in the early stimulation. We found that porcine SARM1 protein is localized in mitochondria and attenuates NF-κB activation induced by stimulation and infection. The quantitative real-time PCR (Q-PCR) analysis showed that the expression of porcine SARM1 significantly decreased in several tissues of Tongcheng pigs infected with highly pathogenic porcine reproductive and respiratory syndrome virus (HP-PRRSV). Gene-interaction network analysis for porcine SARM1 in porcine alveolar macrophages (PAMs) showed that down-regulation of SARM1 gene in infected Tongcheng pig may modulate TRIF-depend TLRs signaling and regulate the expression of disease-resistant genes and inflammatory genes. Our findings provide evidence that porcine SARM1 may play an important role in immune regulation with PRRSV infection.
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Affiliation(s)
- Xiang Zhou
- Key Lab of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070 Hubei, PR China
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11
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Wang W, Tao C, Zhou P, Zhou X, Zhang Q, Liu B. Molecular characterization, expression profiles of the porcine SDC2 and HSPG2 genes and their association with hematologic parameters. Mol Biol Rep 2012; 40:2549-56. [PMID: 23264070 DOI: 10.1007/s11033-012-2340-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Accepted: 12/09/2012] [Indexed: 11/25/2022]
Abstract
Heparan sulfate proteoglycans (HSPGs) located at the cell surface and in the extracellular matrix of most animal tissues are proteoglycan coreceptors that carry heparan sulfate chains, and play a vital role in infections of many diseases. HSPGs are classified as glypican, syndecan, perlecan and agrin according to different core proteins. Syndecan-2 (SDC2) is one of the four coding genes of syndecan, while heparan sulfate proteoglycan 2 (HSPG2) is for perlecan. In this study, we cloned the cDNA of porcine SDC2 and analyzed its genomic structure. The porcine SDC2 and HSPG2 were mapped to SSC4p12-13 and SSC6q24-25 by the SCHP panel respectively, further IMpRH panel analysis showed that they were most closely linked to the marker SWR362 and SW709. One special domain named the 4.1 m domain (putative band 4.1 homologues' binding motif) was found in the prediction amino acid sequence of porcine SDC2. RT-PCR showed that both of porcine SDC2 and HSPG2 were expressed widely in detected tissues: heart, liver, spleen, lung, kidney, stomach, muscle, fat and lymph. Upon stimulation in healthy Tongcheng piglets with PRRSV, SDC2 mRNA did not induce a prominent change in the PAMs, while HSPG2 mRNA displayed a dramatic decline. In addition, synonymous mutation g.32A>G of the SDC2 gene was detected and confirmed to be significantly associated with hematocrit, mean corpuscular volume and hemoglobin concentration in the peripheral blood (p < 0.05). A single nucleotide polymorphism g.83.A>G was found in the HSPG2 gene and the association analysis showed that it was significantly associated with mean corpuscular hemoglobin (p < 0.05). Our results confirmed the relation of porcine SDC2 and HSPG2 to the immunity in pigs, and these two genes could be used as candidate genes for improving immune traits in industrial pig breeding.
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Affiliation(s)
- Weimin Wang
- Lab of Molecular Biology and Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
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Gallardo D, Amills M, Quintanilla R, Pena RN. Mapping and tissue mRNA expression analysis of the pig solute carrier 27A (SLC27A) multigene family. Gene 2012; 515:220-3. [PMID: 23219995 DOI: 10.1016/j.gene.2012.11.029] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2012] [Revised: 10/20/2012] [Accepted: 11/27/2012] [Indexed: 12/31/2022]
Abstract
Solute-carrier family 27A molecules are integral transmembrane proteins that play a fundamental role in the uptake of long-chain fatty acids into mammalian cells. Our goal was to characterize this multigene family in pigs. Chromosomal location of the six porcine SLC27A genes was determined by radiation hybrid mapping and indicated that the six genes map to six different chromosomal locations. Moreover, we analyzed SLC27A mRNA expression in six pig tissues by quantitative RT-PCR. While SLC27A1, SLC27A3 and SLC27A4 were expressed in most, if not all, analyzed tissues, SLC27A2, SLC27A5 and SLC27A6 were predominantly expressed in the liver. In general, pig and human SLC27A mRNA expression profiles were remarkably concordant, although important differences were observed for SLC27A1 and SLC27A6 mRNAs. Discrepancies between mRNA expression profiles have been observed even in closely related primate species, and they might reflect the acquisition of regulatory changes promoting evolutionary adaptation.
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Affiliation(s)
- D Gallardo
- Genètica i Millora Animal, IRTA, Lleida, 25198, Spain
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13
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Servin B, Faraut T, Iannuccelli N, Zelenika D, Milan D. High-resolution autosomal radiation hybrid maps of the pig genome and their contribution to the genome sequence assembly. BMC Genomics 2012; 13:585. [PMID: 23153393 PMCID: PMC3499281 DOI: 10.1186/1471-2164-13-585] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Accepted: 10/25/2012] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND The release of the porcine genome sequence offers great perspectives for Pig genetics and genomics, and more generally will contribute to the understanding of mammalian genome biology and evolution. The process of producing a complete genome sequence of high quality, while facilitated by high-throughput sequencing technologies, remains a difficult task. The porcine genome was sequenced using a combination of a hierarchical shotgun strategy and data generated with whole genome shotgun. In addition to the BAC contig map used for the clone-by-clone approach, genomic mapping resources for the pig include two radiation hybrid (RH) panels at two different resolutions. These two panels have been used extensively for the physical mapping of pig genes and markers prior to the availability of the pig genome sequence. RESULTS In order to contribute to the assembly of the pig genome, we genotyped the two radiation hybrid (RH) panels with a SNP array (the Illumina porcineSNP60 array) and produced high density physical RH maps for each pig autosome. We first present the methods developed to obtain high density RH maps with 38,379 SNPs from the SNP array genotyping. We then show how they were useful to identify problems in a draft of the pig genome assembly, and how the RH maps enabled the problems to be corrected in the porcine genome sequence. Finally, we used the RH maps to predict the position of 2,703 SNPs and 1,328 scaffolds currently unplaced on the porcine genome assembly. CONCLUSIONS A complete process, from genotyping of a high density SNP array on RH panels, to the construction of genome-wide high density RH maps, and finally their exploitation for validating and improving a genome assembly is presented here. The study includes the cross-validation of RH based findings with independent information from genetic data and comparative mapping with the Human genome. Several additional resources are also provided, in particular the predicted genomic location of currently unplaced SNPs and associated scaffolds summing up to a total of 72 megabases, that can be useful for the exploitation of the pig genome assembly.
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Affiliation(s)
- Bertrand Servin
- Laboratoire de Génétique Cellulaire, Animal Genetics Division, INRA, Chemin de Borde-Rouge Auzeville, 31326 Castanet-Tolosan, France.
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Molecular cloning and characterization of the anti-obesity gene adipose in pig. Gene 2012; 509:110-9. [PMID: 23010425 DOI: 10.1016/j.gene.2012.07.087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Revised: 07/22/2012] [Accepted: 07/30/2012] [Indexed: 11/20/2022]
Abstract
Obesity has become an epidemic health problem characterized by aberrant energy metabolism. As the major player in energy homeostasis, adipose tissue has a decisive role in the development of obesity. Many genes involved in adipogenesis are also correlated with obesity. Adipose (Adp) has been established as an anti-obesity gene to repress adipogenesis and fat accumulation in mice, which inhibits the transcriptional activity of PPARγ by forming a chromatin remodeling complex with histones and HDAC3. Here, we reported the cloning and characterization of the pig Adp gene. Pig Adp cDNA had an ORF of 2034 nucleotides and was highly conserved among various species. Genomic sequence analysis indicated that pig Adp gene contains 16 exons and 15 introns, spanning more than 60kb on chromosome 6q21-24. The expression of pig Adp was high in testis, lung, kidney and adipose tissues, and relatively low in skeletal muscle. Bioinformatic analysis of 5'-flanking region of Adp has identified several potential binding sites for pivotal transcriptional factors related to both adipocyte differentiation and inflammation, highlighting the significance of Adp in energy metabolism. We have confirmed that KLF6, a positive regulator of adipogenesis, can enhance the promoter activity of Adp and up-regulate its mRNA expression. Taken together, our results would be helpful for further study of Adp regulation in the process of fat accumulation.
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Bach LH, Gandolfi B, Grahn JC, Millon LV, Kent MS, Narfstrom K, Cole SA, Mullikin JC, Grahn RA, Lyons LA. A high-resolution 15,000(Rad) radiation hybrid panel for the domestic cat. Cytogenet Genome Res 2012; 137:7-14. [PMID: 22777158 DOI: 10.1159/000339416] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/02/2012] [Indexed: 11/19/2022] Open
Abstract
The current genetic and recombination maps of the cat have fewer than 3,000 markers and a resolution limit greater than 1 Mb. To complement the first-generation domestic cat maps, support higher resolution mapping studies, and aid genome assembly in specific areas as well as in the whole genome, a 15,000(Rad) radiation hybrid (RH) panel for the domestic cat was generated. Fibroblasts from the female Abyssinian cat that was used to generate the cat genomic sequence were fused to a Chinese hamster cell line (A23), producing 150 hybrid lines. The clones were initially characterized using 39 short tandem repeats (STRs) and 1,536 SNP markers. The utility of whole-genome amplification in preserving and extending RH panel DNA was also tested using 10 STR markers; no significant difference in retention was observed. The resolution of the 15,000(Rad) RH panel was established by constructing framework maps across 10 different 1-Mb regions on different feline chromosomes. In these regions, 2-point analysis was used to estimate RH distances, which compared favorably with the estimation of physical distances. The study demonstrates that the 15,000(Rad) RH panel constitutes a powerful tool for constructing high-resolution maps, having an average resolution of 40.1 kb per marker across the ten 1-Mb regions. In addition, the RH panel will complement existing genomic resources for the domestic cat, aid in the accurate re-assemblies of the forthcoming cat genomic sequence, and support cross-species genomic comparisons.
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Affiliation(s)
- L H Bach
- Population Health and Reproduction,, School of Veterinary Medicine, University of California-Davis, Davis, CA 95616, USA
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Characterization, tissue expression, and imprinting analysis of the porcine CDKN1C and NAP1L4 genes. J Biomed Biotechnol 2012; 2012:946527. [PMID: 22500112 PMCID: PMC3303864 DOI: 10.1155/2012/946527] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2011] [Revised: 10/25/2011] [Accepted: 11/15/2011] [Indexed: 01/07/2023] Open
Abstract
CDKN1C and NAP1L4 in human CDKN1C/KCNQ1OT1 imprinted domain are two key candidate genes responsible for BWS (Beckwith-Wiedemann syndrome) and cancer. In order to increase understanding of these genes in pigs, their cDNAs are characterized in this paper. By the IMpRH panel, porcine CDKN1C and NAP1L4 genes were assigned to porcine chromosome 2, closely linked with IMpRH06175 and with LOD of 15.78 and 17.94, respectively. By real-time quantitative RT-PCR and polymorphism-based method, tissue and allelic expression of both genes were determined using F1 pigs of Rongchang and Landrace reciprocal crosses. The transcription levels of porcine CDKN1C and NAP1L4 were significantly higher in placenta than in other neonatal tissues (P < 0.01) although both genes showed the highest expression levels in the lung and kidney of one-month pigs (P < 0.01). Imprinting analysis demonstrated that in pigs, CDKN1C was maternally expressed in neonatal heart, tongue, bladder, ovary, spleen, liver, skeletal muscle, stomach, small intestine, and placenta and biallelically expressed in lung and kidney, while NAP1L4 was biallelically expressed in the 12 neonatal tissues examined. It is concluded that imprinting of CDKN1C is conservative in mammals but has tissue specificity in pigs, and imprinting of NAP1L4 is controversial in mammalian species.
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Huang J, Ma G, Zhu M, Pan J, Zhang W, Zhao SH. Molecular characterization of the porcine STAT4 and STAT6 genes. Mol Biol Rep 2012; 39:6959-65. [DOI: 10.1007/s11033-012-1523-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Accepted: 01/24/2012] [Indexed: 10/14/2022]
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Han X, Jiang T, Yu L, Zeng C, Fan B, Liu B. Molecular characterization of the porcine MTPAP gene associated with meat quality traits: chromosome localization, expression distribution, and transcriptional regulation. Mol Cell Biochem 2012; 364:173-80. [PMID: 22297614 DOI: 10.1007/s11010-011-1216-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Accepted: 12/21/2011] [Indexed: 11/28/2022]
Abstract
MTPAP (mitochondrial poly(A) polymerase) gene plays a role in stabilizing the level of mitochondrial mRNAs and controlling the poly(A) length of human mitochondrial mRNAs. In this study, 2,296 bp partial cDNA sequences of the porcine MTPAP gene were obtained, which contained 1,746 bp full-length coding regions flanked by a 500 bp partial 3′-UTR. The porcine MTPAP gene was assigned to SSC10q14-q16 using the radiation hybrid (IMpRH) panel and chromosome electric location methods. Q-PCR analysis showed that MTPAP was expressed in all analyzed tissues, and has higher expression in heart, liver, skeletal muscles, and fat. One single nucleotide polymorphism g.2421T>A in intron5 of MTPAP gene was identified and detected by DdeI PCR–RFLP. Association of the genotypes with economic traits showed that different genotypes were significantly associated with juiciness, individuals with genotype AT displayed a significantly higher juiciness compared to genotype TT. The C/EBPβ transcription factors was up-regulation the expression of MTPAP by analyzing a series of MTPAP promoter reporter constructs using the dual-luciferase assay system, it indicated that MTPAP gene maybe play a critical role in fat deposition regulation which is regulated by C/EBPβ transcription factor. These findings provide an important basis for further understanding of porcine MTPAP regulation and function in swine.
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Affiliation(s)
- Xuelei Han
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, People's Republic of China
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Polymorphisms in an obesity-related gene (PCSK1) are associated with fat deposition and production traits in Italian heavy pigs. Animal 2012; 6:1913-24. [DOI: 10.1017/s1751731112001280] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
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21
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Sun N, Liu D, Chen H, Liu X, Meng F, Zhang X, Chen H, Xie S, Li X, Wu Z. Localization, expression change in PRRSV infection and association analysis of the porcine TAP1 gene. Int J Biol Sci 2011; 8:49-58. [PMID: 22211104 PMCID: PMC3226032 DOI: 10.7150/ijbs.8.49] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Accepted: 11/01/2011] [Indexed: 12/22/2022] Open
Abstract
The transporter associated with antigen processing (TAP) translocates antigenic peptides from the cytosol into the lumen of the endoplasmic reticular and plays a critical role in the major histocompatibility complex (MHC) class I molecule-mediated antigenic presentation pathway. In this study, the porcine TAP1 gene was mapped to the pig chromosome 7 (SSC7) and was closely linked to the marker SSC2B02 (retention fraction=43%, LOD=15.18). Subcellular localization of TAP1 by transient transfection of PK15 cells indicated that the TAP1 protein might be located in the endoplasmic reticulum (ER) in pig kidney epithelial cells (PK-15). Gene expression analysis by semi-quantitative RT-PCR revealed that TAP1 was selectively expressed in some immune and immune-related tissues. Quantitative real-time PCR (qRT-PCR) analysis revealed that this gene was up-regulated after treatments that mimic viral and bacterial infection (polyriboinosinic-polyribocytidylic acid (poly(I:C)) and lipopolysaccharide (LPS), respectively). In addition, elevated TAP1 expression was detected after porcine reproductive and respiratory syndrome virus (PRRSV) infection in porcine white blood cells (WBCs). One single nucleotide polymorphism (SNP) in exon 3 of TAP1 was detected in a Landrace pig population by Bsp143I restriction enzyme digestion. Different genotypes of this SNP had significant associations (P<0.05) with the red blood cell distribution width (RDW) of 1-day-old (1 d) pigs (P=0.0168), the PRRSV antibody level (PRRSV Ab) (P=0.0445) and the absolute lymphocyte count (LYM#) (P=0.024) of 17 d pigs. Our results showed that the TAP1 gene might have important roles in swine immune responses, and these results provide useful information for further functional studies.
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Affiliation(s)
- Nunu Sun
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, P. R. China
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Sanz G, Jiménez-Marín Á, Barbancho M, Garrido JJ. Molecular cloning, characterization and gene expression of the full length cDNA encoding the porcine CD11b(αM) and chromosomal localization of the porcine CD11a(αL)-CD11b(αM)-CD11b(αD) gene cluster. Vet Immunol Immunopathol 2011; 145:505-10. [PMID: 22129786 DOI: 10.1016/j.vetimm.2011.10.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2011] [Revised: 10/19/2011] [Accepted: 10/26/2011] [Indexed: 11/16/2022]
Abstract
CD11b (α(M)) is a cell-surface glycoprotein mainly expressed on myeloid cells, required for important interactions during the immune response and involved in the pathogenesis of several diseases. The full length cDNA encoding porcine CD11b protein has been cloned and sequenced. Pig CD11b cDNA sequence contains an ORF of 3459 nucleotides that encodes a deduced polypeptide of 1152 amino acid residues that share with CD11b from other species: High % amino acid identity, common domains (α-I, Ca(++) binding, MIDAS), N-glycosylation sites, and the seven FG-GAP tandem repeats. Real time quantitative PCR expression analysis revealed that CD11b transcripts were highly expressed in neutrophils, showing a lower expression in spleen. The CD11a-CD11b-CD11c gene cluster locates on the porcine chromosome region SSC3p15-17.
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Affiliation(s)
- Gema Sanz
- Unidad de Genómica y Mejora Animal, Departamento de Genética, Universidad de Córdoba, Campus de Rabanales, 14071 Córdoba, Spain
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Zhao S, Zhao Y, Niu P, Wang N, Tang Z, Zan L, Li K. Molecular characterization of porcine MMP19 and MMP23B genes and its association with immune traits. Int J Biol Sci 2011; 7:1101-13. [PMID: 21927579 PMCID: PMC3174387 DOI: 10.7150/ijbs.7.1101] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2011] [Accepted: 07/03/2011] [Indexed: 12/28/2022] Open
Abstract
MMP19 and MMP23B belong to the Matrix metalloproteases (MMPs) family, which are zinc-binding endopeptidases that are capable of degrading various components of the extracellular matrix. They are thought to play important roles in embryonic development, reproduction and tissue remodeling, as well as in cell proliferation, differentiation, migration, angiogenesis, apoptosis and host defense. However, they are poorly understood in pigs. Here, we obtained the full length coding region sequence and genomic sequence of the porcine MMP19 and MMP23B genes and analyzed their genomic structures. The deduced amino acid sequence shares similar precursor protein domains with human and mouse MMP19 and MMP23B protein, respectively. Using IMpRH panel, MMP19 was mapped to SSC5p12-q11 (closely linked to microsatellite DK) and MMP23B was mapped to SSC8q11-q12 (linked to microsatellite Sw2521). Quantitative real-time PCR showed that MMP19 was abundantly expressed in the liver, while MMP23B was strongly expressed in the ovarian and heart. Furthermore, both genes were all expressed increasingly in prenatal skeletal muscle during development. Three SNPs were detected by sequencing and PCR-RFLP methods, and association analysis indicated that C203T at exon 5 of MMP19 has a significant association with the blood parameters WBC (G/L) and IgG2 (mg/mL) (P<0.05), SNP C131T at exon 3 of MMP23B is significantly associated with the blood parameters HGB (g/L) and MCH (P<0.05), and A150G in exon 4 has no significant association with the economic traits in pigs.
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Affiliation(s)
- Shuanping Zhao
- College of Animal Science and Technology, Northwest A & F University, No. 22 Xinong Road, 712100 Yangling, Shaanxi, China
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Characterization of porcine endogenous retrovirus clones from the NIH miniature pig BAC library. J Biomed Biotechnol 2011; 2012:482568. [PMID: 21912484 PMCID: PMC3168785 DOI: 10.1155/2012/482568] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Revised: 06/08/2011] [Accepted: 06/16/2011] [Indexed: 02/03/2023] Open
Abstract
Pigs have been considered as donors for xenotransplantation in the replacement of human organs and tissues. However, porcine endogenous retroviruses (PERVs) might transmit new infectious disease to humans during xenotransplantation. To investigate PERV integration sites, 45 PERV-positive BAC clones, including 12 PERV-A, 16 PERV-B, and 17 PERV-C clones, were identified from the NIH miniature pig BAC library. The analysis of 12 selected full-length sequences of PERVs, including the long terminal repeat (LTR) region, identified the expected of open reading frame length, an indicative of active PERV, in all five PERV-C clones and one of the four PERV-B clones. Premature stop codons were observed in only three PERV-A clones. Also, eleven PERV integration sites were mapped using a 5000-rad IMpRH panel. The map locations of PERV-C clones have not been reported before, thus they are novel PERV clones identified in this study. The results could provide basic information for the elimination of site-specific PERVs in selection of pigs for xenotransplantation.
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Wang F, Qiu H, Zhang Q, Peng Z, Liu B. Association of two porcine reproductive and respiratory syndrome virus (PRRSV) receptor genes, CD163 and SN with immune traits. Mol Biol Rep 2011; 39:3971-6. [DOI: 10.1007/s11033-011-1177-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Accepted: 07/02/2011] [Indexed: 10/18/2022]
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26
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NUDT6, the FGF-2’s antisense gene, showed associations with fat deposition related traits in pigs. Mol Biol Rep 2011; 39:4119-26. [DOI: 10.1007/s11033-011-1194-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Accepted: 07/11/2011] [Indexed: 11/25/2022]
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27
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Wu X, Pan Y. Molecular characterization, mapping, and haplotype analysis of porcine matrix metalloproteinase genes MMP1 and MMP10. Biochem Genet 2011; 47:763-74. [PMID: 19639408 DOI: 10.1007/s10528-009-9275-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2008] [Accepted: 05/12/2009] [Indexed: 11/26/2022]
Abstract
Matrix metalloproteinases (MMPs) are a family of enzymes that cleave protein components of the extracellular matrix, such as collagens, laminin, fibronectin, and proteoglycans, playing a role in degradation of the matrix of the uterus and in embryo implantation. We report the identification of two members of the MMP gene family in swine. The porcine MMP1 and MMP10 genes comprise 10 exons and 9 introns spanning approximately 8,460 and 7,030 bp. Of 28 potential single nucleotide polymorphisms found in the genomic region, five polymorphic positions were analyzed using PCR-RFLP. Allelic frequencies and haplotypes were analyzed in five pig breeds (n = 280). The AC haplotype of MMP1 and ATG haplotype of MMP10 were not detected in two foreign pig breeds. Association analysis in a French Large White population (n = 164, total four traits) showed no association between haplotypes and reproduction performance. In addition, porcine MMP1 and MMP10 were mapped on SSC9p(13) and SSC2q(21), respectively, in agreement with comparative mapping data.
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Affiliation(s)
- Xiao Wu
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, China
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28
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Rothschild MF. Advances in pig genomics and functional gene discovery. Comp Funct Genomics 2011; 4:266-70. [PMID: 18629119 PMCID: PMC2447406 DOI: 10.1002/cfg.261] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2003] [Accepted: 01/28/2003] [Indexed: 11/11/2022] Open
Abstract
Advances in pig gene identification, mapping and functional analysis have continued to make rapid progress. The porcine genetic linkage map now has nearly 3000 loci, including several hundred genes, and is likely to expand considerably in the next few years, with many more genes and amplified fragment length polymorphism (AFLP) markers being added to the map. The physical genetic map is also growing rapidly and has over 3000 genes and markers. Several recent quantitative trait loci (QTL) scans and candidate gene analyses have identified important chromosomal regions and individual genes associated with traits of economic interest. The commercial pig industry is actively using this information and traditional performance information to improve pig production by marker-assisted selection (MAS). Research to study the co-expression of thousands of genes is now advancing and methods to combine these approaches to aid in gene discovery are under way. The pig's role in xenotransplantation and biomedical research makes the study of its genome important for the study of human disease. This review will briefly describe advances made, directions for future research and the implications for both the pig industry and human health.
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Affiliation(s)
- Max F Rothschild
- 2255 Kildee Hall Department of Animal Science Center for Integrated Animal Genomics Iowa State University Ames IA 50011 USA
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Yuan J, Cao JY, Tang ZL, Wang N, Li K. Molecular characterization of Tob1 in muscle development in pigs. Int J Mol Sci 2011; 12:4315-26. [PMID: 21845080 PMCID: PMC3155353 DOI: 10.3390/ijms12074315] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2011] [Revised: 05/18/2011] [Accepted: 05/20/2011] [Indexed: 11/17/2022] Open
Abstract
Cell proliferation is an important biological process during myogenesis. Tob1 encoded a member of the Tob/BTG family of anti-proliferative proteins. Our previous LongSAGE (Long Serial Analysis of Gene Expression) analysis suggested that Tob1 was differentially expressed during prenatal skeletal muscle development. In this study, we isolated and characterized the swine Tob1 gene. Subsequently, we examined Tob1 chromosome assignment, subcellular localization and dynamic expression profile in prenatal skeletal muscle (33, 65 and 90 days post-conception, dpc) from Landrace (lean-type) and Tongcheng pigs (obese-type). The Tob1 gene was mapped to pig chromosome 12 (SSC12). The Tob1 protein was distributed throughout the nucleus and cytoplasm of PK15 cells. During prenatal skeletal muscle development, Tob1 was up-regulated and highly expressed in skeletal muscle at 90 dpc in Tongcheng pigs but peaked at 65 dpc in Landrace pigs. This result suggested that there were different proliferation patterns during myogenesis between Tongcheng and Landrace pigs. During postnatal skeletal muscle development, the expression of Tob1 increased with aging, indicating that the proliferation potential of myoblasts decreased in postnatal muscle development. In tissues of adult wuzhishan miniature pigs, the Tob1 gene was highly expressed in skeletal muscle. The expression of Tob1 was significantly increased at day 6 during C2C12 differentiation time, suggesting a possible role in skeletal muscle development. Therefore, this study indicated that Tob1 perhaps played an important role in skeletal muscle development.
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Affiliation(s)
- Jing Yuan
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China; E-Mail:
- Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; E-Mail:
| | - Ji-Yue Cao
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China; E-Mail:
- Authors to whom correspondence should be addressed; E-Mails: (J.-Y.C.); (Z.-L.T.); Tel.: +86-27-87281593 (J.-Y.C.); +86-10-62818180 (Z.-L.T.); Fax: +86-10-62818180 (Z.-L.T.)
| | - Zhong-Lin Tang
- Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; E-Mail:
- Authors to whom correspondence should be addressed; E-Mails: (J.-Y.C.); (Z.-L.T.); Tel.: +86-27-87281593 (J.-Y.C.); +86-10-62818180 (Z.-L.T.); Fax: +86-10-62818180 (Z.-L.T.)
| | - Ning Wang
- College of Animal Science, Northeast Agricultural University, Haerbin, Helongjiang 150030, China; E-Mail:
| | - Kui Li
- Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; E-Mail:
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Larsen K, Bendixen C. Characterization of the porcine FBX07 gene: the first step towards generation of a pig model for Parkinsonian pyramidal syndrome. Mol Biol Rep 2011; 39:1517-26. [PMID: 21611747 DOI: 10.1007/s11033-011-0890-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2011] [Accepted: 05/17/2011] [Indexed: 12/20/2022]
Abstract
Parkinsonian pyramidal syndrome, also named pallido-pyramidal syndrome (PKPS), is the combination of early-onset progressive Parkinsonism with pyramidal tract signs. FBXO7, an F-box protein, is a component of modular E3 ubiquitin protein ligases called SCFs (SKP1, cullin, F-box proteins), which functions in phosphorylation-dependent ubiquitination. FBXO7 mutations cause autosomal recessive, early-onset PKPS. Here we report the molecular cloning and characterization of two isoforms of FBXO7 cDNA from pigs. The encoded FBXO7 protein displays a very high homology to human FBXO7 with an amino acid identity of 90%. Phylogenetic analysis demonstrated that porcine FBXO7 is closely related to other mammalian FBXO7 proteins. Furthermore, the genomic structure of the porcine FBXO7 gene was determined. The intron-exon structure is similar to that of the human FBXO7 gene. The promoter sequence for the porcine FBXO7 gene was also identified. A recognition site for miR-301a was found in the 3'UTR region of porcine FBXO7. Investigating the genetic variation in the porcine FBXO7 gene revealed a missense A/G SNP in exon 5. The A/G SNP results in a substitution of an asparagine to a serine residue (N269S). Using a radiation hybrid map the FBXO7 gene was mapped to pig chromosome 5. Real-time quantitative RT-PCR analysis revealed that FBXO7 mRNA is differentially expressed in many tissues and organs, and that FBXO7 transcript can be detected early in embryo development.
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Affiliation(s)
- Knud Larsen
- Department of Genetics and Biotechnology, Faculty of Science and Technology, Aarhus University, Blichers Alle 20, P.O. Box 50, 8830, Tjele, Denmark.
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Wu X, Wang Y, Sun Y. Molecular characterization, expression analysis and association study with immune traits of porcine PSMB6 gene. Mol Biol Rep 2011; 38:5465-70. [DOI: 10.1007/s11033-011-0866-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2010] [Accepted: 05/12/2011] [Indexed: 11/24/2022]
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Chen H, Lunney JK, Cheng L, Li X, Cao J, Zhu M, Zhao S. Porcine S100A8 and S100A9: molecular characterizations and crucial functions in response to Haemophilus parasuis infection. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2011; 35:490-500. [PMID: 21185856 DOI: 10.1016/j.dci.2010.11.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2010] [Revised: 11/15/2010] [Accepted: 11/15/2010] [Indexed: 05/30/2023]
Abstract
S100 calcium-binding protein A8 (S100A8) and S100 calcium-binding protein A9 (S100A9) are pivotal mediators of inflammatory and protective anti-infection responses for the mammalian host. In this study, we present the molecular cloning of porcine S100A8 (pS100A8) and porcine S100A9 (pS100A9). Both genes comprise 3 exons and 2 introns and are located on pig chromosome 4q21-q23 (closely linked to SW512). Homology comparison to other mammalian species affirmed that critical functional amino acids for post-transcriptional modification, inflammatory regulation, and formation of heterodimeric complexes exist in pS100A8 and pS100A9. Under normal conditions, both genes are preferentially expressed in porcine immune or immune-related organs, e.g., bone marrow, spleen, lymph nodes, and lung. Upon stimulation in porcine whole blood cultures with LPS or Poly(I:C), they are dramatically induced. Interestingly, the maximum increase of mRNA levels in blood cultures of Meishan pigs is significantly greater than that in Duroc pigs. We previously showed that pS100A8 and pS100A9 mRNA were up-regulated following Haemophilus parasuis (HPS) infection. We herein further confirm their up-regulation at the protein level in multiple HPS infected tissues (spleen, lung and liver). Functional cluster and network analysis based on our previous microarray data discovered that CEBPB may be one of the key transcription factors. A pS100A8/pS100A9-CASP3-SLC1A2 pathway regulating lipid metabolism was found. Both of their pro- and anti-inflammatory functions in response to HPS infection are highlighted.
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Affiliation(s)
- Hongbo Chen
- Key Lab of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, Hubei, PR China
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Chen Z, Gao X, Lei T, Chen X, Zhou L, Yu A, Lei P, Zhang R, Long H, Yang Z. Molecular characterization, expression and chromosomal localization of porcine PNPLA3 and PNPLA4. Biotechnol Lett 2011; 33:1327-37. [DOI: 10.1007/s10529-011-0591-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2010] [Accepted: 03/07/2011] [Indexed: 01/04/2023]
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Isolation and molecular characterization of the porcine SLC6A14 gene excludes it as a candidate gene for fat deposition and growth. J Appl Genet 2011; 51:299-308. [PMID: 20720304 DOI: 10.1007/bf03208859] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The gene encoding solute carrier family 6 member 14 (SLC6A14) has been considered as a candidate gene affecting human obesity. In this study, full-length cDNA (2237 bp) and DNA sequence (24 541 bp) of the porcine SLC6A14 gene were isolated. The porcine SLC6A14 cDNA contains a 5’-untranslated region of 57 bp, a 3’-untranslated region of 254 bp, and an open reading frame of 1926 bp, encoding a deduced protein of 642 amino acids with a molecular mass of 72. 475 kDa and an isoelectric point of 7.82. The genomic structure of the porcine SLC6A14 gene is similar to mammalian orthologs, particularly in terms of exon size and exon/intron boundaries. It comprises 14 exons and 13 introns. A semi-quantitative RT-PCR showed that the porcine SLC6A14 mRNA expression was tissue-specific. Four SLC6A14 single-nucleotide polymorphisms (SNPs) were identified, and 3 informative SNPs were chosen for genotyping in a White Duroc × Erhualian resource population with phenotype data of growth and fatness traits. The association analysis showed that the c.1438 G>A nonsynonymous polymorphism was associated with birth weight and 21-day body weight (P < 0.05), while g.7944 A>T was associated with 46-day body weight. Linkage and radiation hybrid mapping assigned SLC6A14 to a region around SW1522 on SSCXp13, which did not fall in the confidence interval of the quantitative trait locus (QTL) for growth and fatness traits on SSCX in the resource population. These results indicate that SLC6A14 is not a positional candidate gene for the QTL affecting fatness and growth traits in pigs.
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Restriction of porcine endogenous retrovirus by porcine APOBEC3 cytidine deaminases. J Virol 2011; 85:3842-57. [PMID: 21307203 DOI: 10.1128/jvi.01880-10] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Xenotransplantation of porcine cells, tissues, and organs shows promise to surmount the shortage of human donor materials. Among the barriers to pig-to-human xenotransplantation are porcine endogenous retroviruses (PERV) since functional representatives of the two polytropic classes, PERV-A and PERV-B, are able to infect human embryonic kidney cells in vitro, suggesting that a xenozoonosis in vivo could occur. To assess the capacity of human and porcine cells to counteract PERV infections, we analyzed human and porcine APOBEC3 (A3) proteins. This multigene family of cytidine deaminases contributes to the cellular intrinsic immunity and act as potent inhibitors of retroviruses and retrotransposons. Our data show that the porcine A3 gene locus on chromosome 5 consists of the two single-domain genes A3Z2 and A3Z3. The evolutionary relationships of the A3Z3 genes reflect the evolutionary history of mammals. The two A3 genes encode at least four different mRNAs: A3Z2, A3Z3, A3Z2-Z3, and A3Z2-Z3 splice variant A (SVA). Porcine and human A3s have been tested toward their antiretroviral activity against PERV and murine leukemia virus (MuLV) using novel single-round reporter viruses. The porcine A3Z2, A3Z3 and A3Z2-Z3 were packaged into PERV particles and inhibited PERV replication in a dose-dependent manner. The antiretroviral effect correlated with editing by the porcine A3s with a trinucleotide preference for 5' TGC for A3Z2 and A3Z2-Z3 and 5' CAC for A3Z3. These results strongly imply that human and porcine A3s could inhibit PERV replication in vivo, thereby reducing the risk of infection of human cells by PERV in the context of pig-to-human xenotransplantation.
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Jiang X, Cai Z, Zhao X, Zhang L, Chen Z, Wang Y, Guo X, Xu N. Mapping, CDNA Cloning and Tissue Expression of the Porcine Thyrotropin-Releasing Hormone Receptor Gene. Anim Biotechnol 2011; 22:30-6. [DOI: 10.1080/10495398.2011.547745] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Fan B, Gorbach DM, Rothschild MF. The pig genome project has plenty to squeal about. Cytogenet Genome Res 2011; 134:9-18. [PMID: 21304247 DOI: 10.1159/000324043] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/27/2010] [Indexed: 11/19/2022] Open
Abstract
Significant progress on pig genetics and genomics research has been witnessed in recent years due to the integration of advanced molecular biology techniques, bioinformatics and computational biology, and the collaborative efforts of researchers in the swine genomics community. Progress on expanding the linkage map has slowed down, but the efforts have created a higher-resolution physical map integrating the clone map and BAC end sequence. The number of QTL mapped is still growing and most of the updated QTL mapping results are available through PigQTLdb. Additionally, expression studies using high-throughput microarrays and other gene expression techniques have made significant advancements. The number of identified non-coding RNAs is rapidly increasing and their exact regulatory functions are being explored. A publishable draft (build 10) of the swine genome sequence was available for the pig genomics community by the end of December 2010. Build 9 of the porcine genome is currently available with Ensembl annotation; manual annotation is ongoing. These drafts provide useful tools for such endeavors as comparative genomics and SNP scans for fine QTL mapping. A recent community-wide effort to create a 60K porcine SNP chip has greatly facilitated whole-genome association analyses, haplotype block construction and linkage disequilibrium mapping, which can contribute to whole-genome selection. The future 'systems biology' that integrates and optimizes the information from all research levels can enhance the pig community's understanding of the full complexity of the porcine genome. These recent technological advances and where they may lead are reviewed.
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Affiliation(s)
- B Fan
- Department of Animal Science, Iowa State University, Ames, Iowa 50011, USA
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Long H, Bock HH, Lei T, Chai X, Yuan J, Herz J, Frotscher M, Yang Z. Identification of alternatively spliced Dab1 and Fyn isoforms in pig. BMC Neurosci 2011; 12:17. [PMID: 21294906 PMCID: PMC3044655 DOI: 10.1186/1471-2202-12-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2010] [Accepted: 02/05/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Disabled-1 (Dab1) is an adaptor protein that is essential for the intracellular transduction of Reelin signaling, which regulates the migration and differentiation of postmitotic neurons during brain development in vertebrates. Dab1 function depends on its tyrosine phosphorylation by Src family kinases, especially Fyn. RESULTS We have isolated alternatively spliced forms of porcine Dab1 from brain (sDab1) and liver (sDab1-Li) and Fyn from brain (sFyn-B) and spleen (sFyn-T). Radiation hybrid mapping localized porcine Dab1 (sDab1) and Fyn (sFyn) to chromosomes 6q31-35 and 1p13, respectively. Real-time quantitative RT-PCR (qRT-PCR) demonstrated that different isoforms of Dab1 and Fyn have tissue-specific expression patterns, and sDab1 and sFyn-B display similar temporal expression characteristics in the developing porcine cerebral cortex and cerebellum. Both sDab1 isoforms function as nucleocytoplasmic shuttling proteins. It was further shown that sFyn phosphorylates sDab1 at tyrosyl residues (Tyr) 185, 198/200 and 232, whereas sDab1-Li was phosphorylated at Tyr 185 and Tyr 197 (corresponding to Y232 in sDab1) in vitro. CONCLUSIONS Alternative splicing generates natural sDab1-Li that only carries Y185 and Y197 (corresponding to Y232 in sDab1) sites, which can be phosphorylated by Fyn in vitro. sDab1-Li is an isoform that is highly expressed in peripheral organs. Both isoforms are suggested to be nucleocytoplasmic shuttling proteins. Our results imply that the short splice form sDab1-Li might regulate cellular responses to different cell signals by acting as a dominant negative form against the full length sDab1 variant and that both isoforms might serve different signaling functions in different tissues.
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Affiliation(s)
- Huan Long
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China
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Liu XD, Chen HB, Tong Q, Li XY, Zhu MJ, Wu ZF, Zhou R, Zhao SH. Molecular characterization of caveolin-1 in pigs infected with Haemophilus parasuis. THE JOURNAL OF IMMUNOLOGY 2011; 186:3031-46. [PMID: 21282513 DOI: 10.4049/jimmunol.0902687] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Caveolin-1 (Cav1) plays a critical role in the invasion of pathogenic microbes into host cells, yet little is known about porcine Cav1. In this study, we provide the molecular characterization of Cav1 in pigs following stimulation with LPS/polyinosinic-polycytidylic acid as well as during infection with Haemophilus parasuis. The porcine Cav1 gene is 35 kb long and is located at SSC18q21; two isoforms (Cav1-α and Cav1-β) are produced by alternative splicing. Three point mutations were identified in the coding region of the gene, two of which were significantly associated with nine immunological parameters in Landrace pigs, including the Ab response against porcine reproductive and respiratory syndrome virus and lymphocyte counts. Promoter analysis indicated that NF-κB activates both Cav1 transcripts, but the forkhead gene family specifically regulates Cav1-β in the pig. Porcine Cav1 is expressed ubiquitously, with Cav1-α more abundantly expressed than Cav1-β in all tissues investigated. Basal expression levels of Cav1 in PBMCs are relatively similar across different pig breeds. LPS and polyinosinic-polycytidylic acid markedly induced the expression of Cav1 in porcine kidney-15 cells in vitro, likely through NF-κB activation. Pigs infected with H. parasuis exhibited decreased expression of Cav1, particularly in seriously impaired organs such as the brain. This study provides new evidence that supports the use of Cav1 as a potential diagnostic and genetic marker for disease resistance in animal breeding. In addition, our results suggest that Cav1 may be implicated in the pathogenesis of Glasser's disease, which is caused by H. parasuis.
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Affiliation(s)
- Xiang-Dong Liu
- Key Laboratory of Agricultural Animal Genetics and Breeding, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
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Cai ZW, Sheng YF, Zhang LF, Wang Y, Jiang XL, Lv ZZ, Xu NY. Mapping, expression and regulation of the TRα gene in porcine adipose tissue. GENETICS AND MOLECULAR RESEARCH 2011; 10:1320-30. [PMID: 21751158 DOI: 10.4238/vol10-3gmr1113] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Z-W Cai
- College of Animal Science, Zhejiang University, Hang Zhou, P.R. China
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Han X, Xu X, Liu B. Molecular Characteristics of the Porcine MUSTN1 Gene and its Significant Association with Economic Traits. ACTA ACUST UNITED AC 2010. [DOI: 10.3923/javaa.2010.2351.2356] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Xu X, Xu X, Yin Q, Sun L, Liu B, Wang Y. The molecular characterization and associations of porcine cardiomyopathy asssociated 5 (CMYA5) gene with carcass trait and meat quality. Mol Biol Rep 2010; 38:2085-90. [PMID: 20859690 DOI: 10.1007/s11033-010-0334-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2009] [Accepted: 09/03/2010] [Indexed: 10/19/2022]
Abstract
The cardiomyopathy associated 5 (CMYA5) gene was also called TRIM76, which was belonged to the tripartite motif super family of proteins (TRIM). It was a direct transcriptional target for MEF2A and it played an important role in myofibrillogenesis. In the present study, a 12056 bp cDNA sequence of the porcine CMYA5 gene was obtained by RT-PCR. The sequence encoded a large protein consisting of 4003 amino acids and the carboxyl terminus of the predicted CMYA5 protein comprised of a B-box coiled-coil, two fibronectin type III (FN3) repeats, and SPRY domains. The porcine CMYA5 gene was assigned to chromosome 2q21-24 by using the radiation hybrid (IMpRH) panel, and it was significantly linked to microsatellite Sw1602 with LOD scores of 6.74. Semi-quantitative RT-PCR revealed that the porcine CMYA5 gene was broadly expressed in all seven tissues(heart, liver, spleen, lung, kidney, skeletal muscle and adipose)harvested from different developmental stages(new born, five weeks and adult tongcheng pigs), with a high level in heart and skeletal muscle. One SNP (A7189C), leading to the amino acid alteration from the Ile residue to the Leu residue, was found and detected by BspTI PCR-restriction fragment length polymorphism. The association analysis revealed that the substitution of A7189C had significant associations with the percentage of ham (p < 0.05), water loss (p < 0.01) and intramuscular fat (p < 0.05). These results provide the evidence that the porcine CMYA5 gene can act as a potential candidate gene affecting pig meat quality.
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Affiliation(s)
- Xiaoling Xu
- Lab of Molecular Biology and Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
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Liu C, Gao H, Zhai S, Liu B. Molecular characterization, chromosomal localization, expression profile and association analysis with carcass traits of the porcine dickkopf homolog1 gene. Mol Biol Rep 2010; 38:1929-34. [DOI: 10.1007/s11033-010-0313-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2010] [Accepted: 09/03/2010] [Indexed: 11/28/2022]
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Fontanesi L, Colombo M, Tognazzi L, Scotti E, Buttazzoni L, Dall'Olio S, Davoli R, Russo V. The porcine TBC1D1 gene: mapping, SNP identification, and association study with meat, carcass and production traits in Italian heavy pigs. Mol Biol Rep 2010; 38:1425-31. [PMID: 20730498 DOI: 10.1007/s11033-010-0247-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2010] [Accepted: 08/10/2010] [Indexed: 12/18/2022]
Abstract
TBC1D1 [TBC1 (tre-2/USP6, BUB2, cdc16) domain family, member 1] is a Rab-GTPase-activating related protein implicated in regulating the trafficking of glucose transporter 4 (GLUT4 or SLC2A4) storage vesicles to the cell surface in response to insulin and AMPK-activating stimuli in skeletal muscle. Mutations in the human and mouse TBC1D1 genes confer risk of obesity or leanness. We identified five single nucleotide polymorphisms (SNPs) in the porcine TBC1D1 gene. One of them (FN677935:g.219G>A) was genotyped either by high resolution melting and PCR-RFLP analyses to study allele frequencies in a few pig breeds and evaluate association with meat production and carcass traits in five groups of sib-tested pigs of Italian Large White and Italian Duroc breeds. The g.219G>A SNP was associated (P < 0.05) with ham weight, back fat thickness and lean cuts content in Italian Large White and with visible intermuscular fat in Italian Duroc pigs.
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Affiliation(s)
- Luca Fontanesi
- DIPROVAL, Sezione di Allevamenti Zootecnici, Faculty of Agriculture, University of Bologna, Via F.lli Rosselli 107, 42100, Reggio Emilia, Italy.
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Gorni C, Garino C, Iacuaniello S, Castiglioni B, Stella A, Restelli GL, Pagnacco G, Mariani P. Transcriptome analysis to identify differential gene expression affecting meat quality in heavy Italian pigs. Anim Genet 2010; 42:161-71. [PMID: 20726855 DOI: 10.1111/j.1365-2052.2010.02098.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Suppressive subtractive hybridization (SSH) was used to analyse the muscle transcriptome and identify genes affecting meat quality within an Italian pig population of Large White and Landrace purebred individuals. Seven phenotypes were recorded at slaughter: dorsal fat thickness, ham fat thickness, ham fat coverage, muscle compactness, marbling, meat colour and colour uniformity. Two subtractive libraries were created from longissimus dorsi tissue of selected pigs with extreme phenotypes for meat quality. Eighty-four differentially expressed ESTs were identified, which showed homology to expressed pig sequences and/or to genomic pig sequences produced within the pig genome project. Sixty-eight sequences were mapped on the pig genome, and most of these sequences co-localized with the same chromosomal positions as QTLs that have been previously identified for meat quality. Thirty sequences, including eight matching known genes previously related to muscle metabolic pathways, were selected to statistically validate their differential expression. Association analysis and t-test results indicated that 28 ESTs of the 30 analysed were associated with phenotypes investigated here and have significant differential expression levels (P≤ 0.05) between the two tails of the phenotypic distribution.
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Affiliation(s)
- C Gorni
- Parco Tecnologico Padano, 26900 Lodi, Italy.Dipartimento di Scienze e Tecnologie Veterinarie per la Sicurezza Alimentare, Università Degli Studi di Milano, 20134 Milano, Italy.Istituto di Biologia e Biotecnologia Agraria, CNR, 20133 Milano, Italy
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Localization of 31 porcine transcripts to the pig genome by SSRH radiation hybrid mapping. Genes Genomics 2010. [DOI: 10.1007/s13258-010-0024-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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47
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Li A, Chen Y, Zhao X, Niu Y, Cong P, Zhang Z, Chen W, Jiang W, Mo D. Characterization and transcriptional regulation analysis of the porcine TNFAIP8L2 gene. Mol Genet Genomics 2010; 284:185-95. [DOI: 10.1007/s00438-010-0558-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2010] [Accepted: 06/30/2010] [Indexed: 12/14/2022]
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Molecular characterization of thyroid peroxidase gene in porcine (sus scrofa). J Genet Genomics 2010; 37:381-8. [PMID: 20621020 DOI: 10.1016/s1673-8527(09)60056-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2009] [Revised: 05/07/2010] [Accepted: 05/08/2010] [Indexed: 11/21/2022]
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49
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Fontanesi L, Speroni C, Buttazzoni L, Scotti E, Costa LN, Davoli R, Russo V. Association between cathepsin L (CTSL) and cathepsin S (CTSS) polymorphisms and meat production and carcass traits in Italian Large White pigs. Meat Sci 2010; 85:331-8. [DOI: 10.1016/j.meatsci.2010.01.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2009] [Revised: 01/25/2010] [Accepted: 01/29/2010] [Indexed: 10/19/2022]
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Bendixen E, Danielsen M, Larsen K, Bendixen C. Advances in porcine genomics and proteomics--a toolbox for developing the pig as a model organism for molecular biomedical research. Brief Funct Genomics 2010; 9:208-19. [DOI: 10.1093/bfgp/elq004] [Citation(s) in RCA: 122] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
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