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A physical map of large segments of pig Chromosome 7q11–q14: comparative analysis with human Chromosome 6p21

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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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Authors and Affiliations

  1. 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

    Angela Barbosa, Céline Urien, Patrick Chardon & Christine Renard

  2. Laboratoire de génétique cellulaire, Institut national de la recherche agronomique, Castanet Tolosan, France

    Olivier Demeure & Denis Milan

Authors
  1. Angela Barbosa
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  2. Olivier Demeure
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  3. Céline Urien
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  4. Denis Milan
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  5. Patrick Chardon
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  6. Christine Renard
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Corresponding author

Correspondence to Christine Renard.

Additional information

The nucleotide sequence data reported in this article have been submitted to EMBL/GenBank and have been assigned the following accession numbers: gene amplicons (AJ629177–AJ629187), microsatellites (AJ544106–AJ544111, AJ544188–AJ544192, and AJ544212–AJ5442217), BAC-end sequences (AJ628956–974, AJ629076–9108, AJ629125–149, AJ629152–176, AJ629222–46, AJ629414–453, AJ630314–355, and AJ634055. Locus name, gene name (EMBL accession number): SLA class II telomeric end: COL11A2, collagen type XI alpha2 (BX324144); RXRB, retinoid X receptor beta; KE4, HLA class II region expressed gene KE4; KE6 (HSD17B8), estradiol 17 beta-dehydrogenase; and RING1, ring finger protein 1 (BX640585), BMP5, bone morphogenetic protein 6-like id EST SSC2B02 (F14943); LANO (FLJ10775, TINAG), LAP (leucine-rich repeats and PDZ) and no PDZ protein (NM_018214)

GAP: SACM2I, suppressor of actin mutations 2-like (BI360056); BAG2, BCL2-associated athanogene 2 (NM_004282)

Contig1: RPS18 (KE3), ribosomal protein S18 (AJ629092); HKE2, HLA class II region expressed gene KE2 (AJ629178); RAB2L, RAB2, member RAS oncogene family-like (NM_00476 l); TAPBP, tapasin binding protein (BE234046); ZNF297 (BING1), Zn finger protein with POZ motif (AJ629088); DAXX (Fas binding protein) death-associated protein 6 (AJ629179); SYNGAP (RASA5, KIAA1938), synaptic Ras GTPase activating protein 1 homolog (AJ629106); BAK1, BCL2 antagonist killer 1 (AJ629098); ITPR3, inosotol triphosphate receptor 3 (AJ634055); HMGA1(HMGY), high mobility group protein 1 (AJ62180); NUDT3(DIPP), nucleoside diphosphate linked moiety X or diphosphoinositol polyphosphate (BE749729)

Contig 2: ZNF76, Zn finger protein 76 (expressed in testis) (AJ629181, AJ629163); PPARD, peroxisome proliferative activated receptor (AJ629182, AY188501); CLPS, colipase (AJ306320, AF012819); SRPK1, serine/arginine protein kinase (BP172161); SOCS5 (CISH6, KIAA0671), suppressor of cytokine signaling 5 (HSA2p21), or cytokine-inductible SH2 containing element (AJ629418, AJ629422); SLC26A8, solute carrier family 26, member 8 (AJ629426); MAPK14, mitogen-activated protein kinase 14 (AJ629427); MAPK13, mitogen-activated protein kinase 13 (BF713204)

Contig 3: STK38 (NDR), serine/threonine kinase 38 (AJ629183); CDKN1A (p21, WAF), cyclin-dependent kinase inhibitor 1A (AJ629184); PPIL1 (CYPL1), peptidylprolyl isomerase (cyclophilin)-like 1 (AJ629228)

Contig4: MTCH1 (CGI-64, PSAP), mitochondrial carrier homolog 1 (AJ620434); PIM1, protein kinase 1 related oncogen (AJ629185); RNF8, ring finger protein (C3HC4 type) (AJ629445)

Small contigs: GLO1, glyoxalase 1 (NM_006708); TPX, testis-specific protein 1 (AJ006634); CCND3, cyclin D3 (AJ629186); NFYA, nuclear transcription factor Y alpha (AJ629187); GSTA3, gluthation S-transferase (BP447660); CEBPE (CRP1), CCAAT/enhancer binding protein (C/EBP) epsilon (BF652076)

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Barbosa, A., Demeure, O., Urien, C. et al. A physical map of large segments of pig Chromosome 7q11–q14: comparative analysis with human Chromosome 6p21. Mamm Genome 15, 982–995 (2004). https://doi.org/10.1007/s00335-004-3008-6

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  • DOI: https://doi.org/10.1007/s00335-004-3008-6

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