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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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2
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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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3
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Pan G, Fu Y, Zuo B, Ren Z, Xu D, Lei M, Zheng R, Xiong YZ. Molecular characterization, expression profile and association analysis with fat deposition traits of the porcine APOM gene. Mol Biol Rep 2009; 37:1363-71. [PMID: 19326253 DOI: 10.1007/s11033-009-9518-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2008] [Accepted: 03/17/2009] [Indexed: 10/21/2022]
Abstract
Apolipoprotein M (APOM), a novel apolipoprotein presented mostly in high-density lipoprotein (HDL) in plasma, is involved in lipid and lipoprotein metabolism. Through comparative mapping, we have mapped this gene to SSC7 p1.1 in which many QTLs affecting fat deposition traits have been reported. As a candidate gene for fat deposition traits, in this study, we obtained the 742-bp mRNA sequence of porcine APOM including the full coding region and encoding a protein of 188 amino acids. The sequence was deposited into the GenBank under the accession no. DQ329240. Semi-quantitative RT-PCR results showed that the porcine APOM gene is expressed predominantly in liver and kidney tissue. The genomic sequence of this gene which contains six exons and five introns, is 3,621 bp in length (DQ272488). Bioinformatic analysis of the 5' regulatory region has revealed that classical TATA-box element and species conserved Hepatocyte nuclear factor-1a (HNF-1alpha) biding site were represented in this region. A G2289C single nucleotide polymorphism (SNP) in the intron 2 of porcine APOM gene detected as an Eco130I PCR-restriction fragment length polymorphism (PCR-RFLP) showed allele frequency differences among three purebreds. Association of the genotypes with fat deposition traits showed that different genotypes of porcine APOM gene were significantly associated with leaf fat weight (P < 0.05), backfat thickness at shoulder (P < 0.05), backfat thickness at thorax-waist (P < 0.05), backfat thickness at buttock (P < 0.01) and average backfat thickness over shoulder, thorax-waist and buttock (P < 0.01).
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Affiliation(s)
- Gang Pan
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
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4
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Shimogiri T, Nishibori M, Hiraiwa H, Hayashi T, Yasue H. Assignment of 128 genes localized on human chromosome 14q to the IMpRH map. Anim Genet 2009; 40:538-42. [PMID: 19292706 DOI: 10.1111/j.1365-2052.2009.01852.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
To provide a gene-based comparative map and to examine a porcine genome assembly using bacterial artificial chromosome-based sequence, we have attempted to assign 128 genes localized on human chromosome 14q (HSA14q) to a porcine 7000-rad radiation hybrid (IMpRH) map. This study, together with earlier studies, has demonstrated the following. (i) 126 genes were incorporated into two SSC7 RH linkage groups by CarthaGene analysis. (ii) In the remaining two genes, TOX4 linked to TCRA located in SSC7 by two-point analysis, whereas SIP1 showed no significant linkage with any gene/marker registered in the IMpRH Web Server. (iii) In the two groups, the gene clusters located from 19.9 to 36.5 Mb on HSA14q11.2-q13.3 and from 64.0 to 104.3 Mb on HSA14q23-q32.33 respectively were assigned to SSC7q21-q26. (iv) Comparison of the gene order between the present RH map and the latest porcine sequence assembly revealed some inconsistencies, and a redundant arrangement of 16 genes in the sequence assembly.
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Affiliation(s)
- T Shimogiri
- Faculty of Agriculture, Kagoshima University, Kagoshima 890-0065, Japan
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A new 4016-marker radiation hybrid map for porcine-human genome analysis. Mamm Genome 2008; 19:51-60. [PMID: 18188646 DOI: 10.1007/s00335-007-9081-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2007] [Accepted: 11/02/2007] [Indexed: 10/22/2022]
Abstract
We constructed a 5000-rad comprehensive radiation hybrid (RH) map of the porcine (Sus scrofa) genome and compared the results with the human genome. Of 4475 typed markers, 4016 (89.7%) had LOD >5 compared with the markers used in our previous RH map by means of two-point analysis and were grouped onto the 19 porcine chromosomes (SSCs). All mapped markers had LOD >3 as determined by RHMAPPER analysis. The current map comprised 430 microsatellite (MS) framework markers, 914 other MS markers, and 2672 expressed sequence tags (ESTs). The whole-genome map was 8822.1 cR in length, giving an average marker density of 0.342 Mb/cR. The average retention frequency was 35.8%. Using BLAST searches of porcine ESTs against the RefSeq human nucleotide and amino acid sequences (release 22), we constructed high-resolution comparative maps of each SSC and each human chromosome (HSA). The average distance between ESTs in the human genome was 1.38 Mb. SSC contained 50 human chromosomal syntenic groups, and SSC11, SSC12, and SSC16 were only derived from the HSA13q, HSA17, and HSA5 regions, respectively. Among 38 porcine terminal regions, we found that at least 20 regions have been conserved between the porcine and human genomes; we also found four paralogous regions for the major histocompatibility complex (MHC) on SSC7, SSC2, SSC4, and SSC1.
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Demars J, Riquet J, Sanchez MP, Billon Y, Hocquette JF, Lebret B, Iannuccelli N, Bidanel JP, Milan D, Gondret F. Metabolic and histochemical characteristics of fat and muscle tissues in homozygous or heterozygous pigs for the body composition QTL located on chromosome 7. Physiol Genomics 2007; 30:232-41. [PMID: 17426114 DOI: 10.1152/physiolgenomics.00270.2006] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Quantitative trait loci (QTL) influencing many traits including backfat thickness and carcass composition have been detected on porcine chromosome 7 (SSC7) in an F2 cross between Large White (LW) and Meishan (MS) pigs. However, the genes and controlled pathways underlying the QTL effects on body phenotype remain unknown. This study aimed at investigating the tissue characteristics at metabolic and cellular levels in pigs that were either homozygous or heterozygous for a body composition SSC7 QTL. A backcross pig (BC3) was first progeny tested to confirm its heterozygoty for the SSC7 QTL; results on all offspring (n = 80) confirmed the QTL effects on body fatness. This boar was then mated with three sows known to be heterozygous for this QTL. In the subset of pigs per genotype, we found that heterozygous LW(QTL7)/MS(QTL7) pigs had smaller adipocytes in backfat, together with a lower basal rate of glucose incorporation into lipids and lower activities of selected lipogenic enzymes in backfat isolated cells, compared with homozygous LW(QTL7)/LW(QTL7) pigs. A higher number of adipocytes was also estimated in backfat of LW(QTL7)/MS(QTL7) animals compared with LW(QTL7)/LW(QTL7) pigs. The SSC7 QTL did not influence oxidative and glycolytic metabolisms of longissimus and trapezius muscles, as estimated by the activities of specific energy metabolism enzymes, or the myofiber type properties. Altogether, this study provides new evidence for an altered adipocyte cellularity in backfat of pigs carrying at least one MS allele for the SSC7 QTL. Some candidate genes known for their functions on adipocyte growth and differentiation are suggested.
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Affiliation(s)
- Julie Demars
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 444, Laboratoire de Génétique Cellulaire, BP52627, Castanet-Tolosan, France
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Gouin N, Deakin JE, Miska KB, Miller RD, Kammerer CM, Graves JAM, VandeBerg JL, Samollow PB. Linkage mapping and physical localization of the major histocompatibility complex region of the marsupial Monodelphis domestica. Cytogenet Genome Res 2006; 112:277-85. [PMID: 16484784 DOI: 10.1159/000089882] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2005] [Accepted: 06/28/2005] [Indexed: 12/14/2022] Open
Abstract
We used genetic linkage mapping and fluorescence in situ hybridization (FISH) to conduct the first analysis of genic organization and chromosome localization of the major histocompatibility complex (MHC) of a marsupial, the gray, short-tailed opossum Monodelphis domestica. Family based linkage analyses of two M. domestica MHC Class I genes (UA1, UG) and three MHC Class II genes (DAB, DMA, and DMB) revealed that these genes were tightly linked and positioned in the central region of linkage group 3 (LG3). This cluster of MHC genes was physically mapped to the centromeric region of chromosome 2q by FISH using a BAC clone containing the UA1 gene. An interesting finding from the linkage analyses is that sex-specific recombination rates were virtually identical within the MHC region. This stands in stark contrast to the genome-wide situation, wherein males exhibit approximately twice as much recombination as females, and could have evolutionary implications for maintaining equality between males and females in the ability to generate haplotype diversity in this region. These analyses also showed that three non-MHC genes that flank the MHC region on human chromosome 6, myelin oligodendrocyte glycoprotein (MOG), bone morphogenetic protein 6 (BMP6), and prolactin (PRL), are split among two separate linkage groups (chromosomes) in M. domestica. Comparative analysis with eight other vertebrate species suggests strong conservation of the BMP6-PRL synteny among birds and mammals, although the BMP6-PRL-MHC-ME1 synteny is not conserved.
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Affiliation(s)
- N Gouin
- Department of Genetics, Southwest Foundation for Biomedical Research, San Antonio, TX 78245-0549, USA.
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Tanaka M, Suzuki K, Morozumi T, Kobayashi E, Matsumoto T, Domukai M, Eguchi-Ogawa T, Shinkai H, Awata T, Uenishi H. Genomic structure and gene order of swine chromosome 7q1.1q1.2. Anim Genet 2006; 37:10-6. [PMID: 16441290 DOI: 10.1111/j.1365-2052.2005.01362.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
To clarify the structure of the porcine genomic region that contains quantitative trait loci (QTL) related to fat, we constructed a bacterial artificial chromosome (BAC) contig of the region from DST to SRPK1 on porcine chromosome 7 and performed low-redundancy 'skim' shotgun sequencing of the clones that composed a minimum tiling path of the contig. This analysis revealed that the gene order from VPS52 to SRPK1 is conserved between human and swine and that comparison with the human sequence identified a rearrangement in the swine genome at the proximal end of VPS52. Analysis of the nucleotide sequences of three BAC clones that included the rearrangement point demonstrated that COL21A1 and DST, which were not present in the corresponding human region, were located adjacent to the rearrangement point. These results provide useful information about the genomic region containing QTL for fat in pigs and help to clarify the structure of the so-called 'extended-class II' region distal to the porcine major histocompatibility complex class II region.
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Affiliation(s)
- M Tanaka
- Animal Genome Research Program, National Institute of Agrobiological Sciences/STAFF-Institute, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
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Demars J, Riquet J, Feve K, Gautier M, Morisson M, Demeure O, Renard C, Chardon P, Milan D. High resolution physical map of porcine chromosome 7 QTL region and comparative mapping of this region among vertebrate genomes. BMC Genomics 2006; 7:13. [PMID: 16433907 PMCID: PMC1420295 DOI: 10.1186/1471-2164-7-13] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2005] [Accepted: 01/24/2006] [Indexed: 11/10/2022] Open
Abstract
Background On porcine chromosome 7, the region surrounding the Major Histocompatibility Complex (MHC) contains several Quantitative Trait Loci (QTL) influencing many traits including growth, back fat thickness and carcass composition. Previous studies highlighted that a fragment of ~3.7 Mb is located within the Swine Leucocyte Antigen (SLA) complex. Internal rearrangements of this fragment were suggested, and partial contigs had been built, but further characterization of this region and identification of all human chromosomal fragments orthologous to this porcine fragment had to be carried out. Results A whole physical map of the region was constructed by integrating Radiation Hybrid (RH) mapping, BAC fingerprinting data of the INRA BAC library and anchoring BAC end sequences on the human genome. 17 genes and 2 reference microsatellites were ordered on the high resolution IMNpRH212000rad Radiation Hybrid panel. A 1000:1 framework map covering 550 cR12000 was established and a complete contig of the region was developed. New micro rearrangements were highlighted between the porcine and human genomes. A bovine RH map was also developed in this region by mapping 16 genes. Comparison of the organization of this region in pig, cattle, human, mouse, dog and chicken genomes revealed that 1) the translocation of the fragment described previously is observed only on the bovine and porcine genomes and 2) the new internal micro rearrangements are specific of the porcine genome. Conclusion We estimate that the region contains several rearrangements and covers 5.2 Mb of the porcine genome. The study of this complete BAC contig showed that human chromosomal fragments homologs of this heavily rearranged QTL region are all located in the region of HSA6 that surrounds the centromere. This work allows us to define a list of all candidate genes that could explain these QTL effects.
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Affiliation(s)
- Julie Demars
- Laboratoire de Génétique Cellulaire, INRA, BP52627, 31326 Castanet-Tolosan, France
| | - Juliette Riquet
- Laboratoire de Génétique Cellulaire, INRA, BP52627, 31326 Castanet-Tolosan, France
| | - Katia Feve
- Laboratoire de Génétique Cellulaire, INRA, BP52627, 31326 Castanet-Tolosan, France
| | - Mathieu Gautier
- Laboratoire de Génétique Biochimique et de Cytogénétique, INRA, 78352 Jouy en Josas, France
| | - Mireille Morisson
- Laboratoire de Génétique Cellulaire, INRA, BP52627, 31326 Castanet-Tolosan, France
| | - Olivier Demeure
- Laboratoire de Génétique animale, INRA, 35042 Rennes, France
| | - Christine Renard
- Laboratoire de Radiobiologie et d'Etude du Génome, INRA-CEA, 78352 Jouy en Josas, France
| | - Patrick Chardon
- Laboratoire de Radiobiologie et d'Etude du Génome, INRA-CEA, 78352 Jouy en Josas, France
| | - Denis Milan
- Laboratoire de Génétique Cellulaire, INRA, BP52627, 31326 Castanet-Tolosan, France
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Barbosa A, Demeure O, Urien C, Milan D, Chardon P, Renard C. A physical map of large segments of pig chromosome 7q11-q14: comparative analysis with human chromosome 6p21. Mamm Genome 2005; 15:982-95. [PMID: 15599557 DOI: 10.1007/s00335-004-3008-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2004] [Accepted: 07/20/2004] [Indexed: 11/29/2022]
Abstract
The aim of this study was to establish a porcine physical map along the chromosome SSC7q by construction of BAC contigs between microsatellites Sw1409 and S0102. The SLA class II contig, located on SSC7q, was lengthened. Four major BAC contigs and 10 short contigs span a region equivalent to 800 cR measured by IMpRH7000 mapping. The BAC contigs were initiated by PCR screening with primers derived from human orthologous segments, extended by chromosome walking, and controlled and oriented by RH mapping with the two available panels, IMpRH7000Rad and IMNpRH12000Rad. The location of 43 genes was revealed by sequenced segments, either from BAC ends or PCR products from BAC clones. The 220 BAC end sequences (BES) were also used to analyze the different marks of evolution. Comparative mapping analysis between pigs and humans demonstrated that the gene organization on HSA6p21 and on SSC7p11 and q11-q14 segments was conserved during evolution, with the exception of long fragments of HSA6p12 which shuffled and spliced the SLA extended class II region. Additional punctual variations (unique gene insertion/deletion) were observed, even within conserved segments, revealing the evolutionary complexity of this region. In addition, 18 new polymorphic microsatellites have been selected in order to cover the entire SSC7p11-q14 region.
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Affiliation(s)
- Angela Barbosa
- Laboratoire mixte de Radiobiologie et d'Etude du Génome, Institut National de la Recherche Agronomigue et Center d'Energie Atomique, Domaine de Vilvert, 78352, Jouy en Josas cedex, France
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Kim KS, Thomsen H, Bastiaansen J, Nguyen NT, Dekkers JCM, Plastow GS, Rothschild MF. Investigation of obesity candidate genes on porcine fat deposition quantitative trait loci regions. OBESITY RESEARCH 2004; 12:1981-94. [PMID: 15687400 DOI: 10.1038/oby.2004.249] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
OBJECTIVES To investigate possible obesity candidate genes in regions of porcine quantitative trait loci (QTL) for fat deposition and obesity-related phenotypes. RESEARCH METHODS AND PROCEDURES Chromosome mapping and QTL analyses of obesity candidate genes were performed using DNA panels from a reference pig family. Statistical association analyses of these genes were performed for fat deposition phenotypes in several other commercial pig populations. RESULTS Eight candidate genes were mapped to QTL regions of pig chromosomes in this study. These candidate genes also served as anchor loci to determine homologous human chromosomal locations of pig fat deposition QTL. Preliminary analyses of relationships among polymorphisms of individual candidate genes and a variety of phenotypic measurements in a large number of pigs were performed. On the basis of available data, gene-gene interactions were also studied. DISCUSSION Comparative analysis of obesity-related genes in the pig is not only important for development of marker-assisted selection on growth and fat deposition traits in the pig but also provides for an understanding of their genetic roles in the development of human obesity.
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Affiliation(s)
- Kwan-Suk Kim
- Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, Ames, Iowa 50011-3150, USA
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