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Author(s): Vingborg RKK; Gregersen VR; Zhan BJ; Panitz F; Hoj A; Sorensen KK; Madsen LB; Larsen K; Hornshoj H; Wang XF; Bendixen C
Title: A robust linkage map of the porcine autosomes based on gene-associated SNPs
Source: BMC GENOMICS 10: Art. No. 134
Date: 2009 MAR 27
Document Type: Journal : Review
DOI:
Language: English
Comment:
Address: Aarhus Univ, Fac Agr Sci, Dept Genet & Biotechnol, DK-8830 Tjele, Denmark.
Reprint: Bendixen, C, Aarhus Univ, Fac Agr Sci, Dept Genet & Biotechnol, POB 50,
DK-8830 Tjele, Denmark. E-mail: rikkek.vingborg@agrsci.dk
vivi.gregersen@agrsci.dk zhan.bujie@agrsci.dk frank.panitz@agrsci.dk Anette.hoj@agrsci.dk kirstenk.sorensen@agrsci.dk loneb.madsen@agrsci.dk knud.larsen@agrsci.dk henrikh.jensen@agrsci.dk xuefei1216@agrsci.dk christian.bendixen@agrsci.dk Author Keywords:
KeyWords Plus: EXPRESSED SEQUENCE TAGS; RADIATION HYBRID PANEL; PIG COMPARATIVE MAP;
HIGH-RESOLUTION; HUMAN GENOME; IMPRH MAP; RAPID COMMUNICATION; HUMAN-
CHROMOSOME; CANDIDATE GENES; MOLECULAR CHARACTERIZATION
Abstract: Background: Genetic linkage maps are necessary for mapping of mendelian traits and quantitative trait loci (QTLs). To identify the actual genes, which control these traits, a map based on gene-associated single nucleotide polymorphism (SNP) markers is highly valuable. In this study, the SNPs were genotyped in a large family material comprising more than 5,000 piglets derived from 12 Duroc boars crossed with 236 Danish Landrace/Danish Large White sows. The SNPs were identified in sequence alignments of 4,600 different amplicons obtained from the 12 boars and containing coding regions of genes derived from expressed sequence tags (ESTs) and genomic shotgun sequences. Results: Linkage maps of all 18 porcine autosomes were constructed based on 456 gene-associated and six porcine EST-based SNPs. The total length of the averaged-sex whole porcine autosome was estimated to 1,711.8 cM resulting in an average SNP spacing of 3.94 cM. The female and male maps were estimated to 2,336.1 and 1,441.5 cM, respectively. The gene order was validated through comparisons to the cytogenetic and/or physical location of 203 genes, linkage to evenly spaced microsatellite markers as well as previously reported conserved synteny. A total of 330 previously unmapped genes and ESTs were mapped to the porcine autosome while ten genes were mapped to unexpected locations. Conclusion: The linkage map presented here shows high accuracy in gene order. The pedigree family network as well as the large amount of meiotic events provide good reliability and make this map suitable for QTL and association studies. In addition, the linkage to the RH-map of microsatellites makes it suitable for comparison to other QTL studies.
Cited References: ALDENHOVEN J, 2003, CYTOGENET GENOME RES, V102, P121 ALDENHOVEN J, 2005, ANIM GENET, V36, P540 ALTSCHUL SF, 1990, J MOL BIOL, V215, P403 ANDERSEN PK, 2007, MOL MEMBR BIOL, V24, P519 ARCHIBALD AL, 1995, MAMM GENOME, V6, P157 ARCHIBALD AL, 1996, ANIM GENET, V27, P351 BARBOSA A, 2004, MAMM GENOME, V15, P982 BEECKMANN P, 2003, J ANIM BREED GENE S1, V120, P1 BERTANI GR, 2003, ANIM GENET, V34, P132 BILTUEVA LS, 2004, MAMM GENOME, V15, P809 BJERRE D, 2006, BIOCHEM BIOPH RES CO, V347, P803 BOETTCHER D, 2007, CYTOGENET GENOME RES, V118, P67 BOSAK N, 2003, CYTOGENET GENOME RES, V102, P109 BOSAK N, 2005, CYTOGENET GENOME RES, V108, P317 BROOKES AJ, 1999, GENE, V234, P177 CARGILL EJ, 1998, J ANIM SCI, V76, P2211 CHAUDHARY R, 1997, CHROMOSOME RES, V5, P545 DAVOLI R, 2002, ANIM GENET, V33, P3 DROGEMULLER C, 2006, MAMM GENOME, V17, P58 DVORAK CMT, 2006, ANIM GENET, V37, P62 FENG Z, 2007, GENE, V403, P170 FRIDOLFSSON AK, 1997, MAMM GENOME, V8, P907 GORODKIN J, 2007, GENOME BIOL, V8, ARR45 GRAPES L, 2006, MAMM GENOME, V17, P657 GREEN P, 1990, DOCUMENTATION CRIMAP GRINDFLEK E, 2000, J ANIM SCI, V78, P1391 GU F, 1992, CYTOGENET CELL GENET, V59, P63 HAWKEN RJ, 1999, MAMM GENOME, V10, P824 HAYES H, 2003, CYTOGENET GENOME RES, V102, P16 HEBINCK A, 2000, CYTOGENET CELL GENET, V90, P68 HIRAIWA H, 2003, CYTOGENET GENOME RES, V101, P84 HUBBARD T, 2005, NUCLEIC ACIDS RES, V33, PD447 HUMPHRAY SJ, 2007, GENOME BIOL, V8, ARR139 JIANG ZH, 2005, CHROMOSOME RES, V13, P707 JORGENSEN CB, 1997, MAMM GENOME, V8, P423 JORGENSON E, 2006, NAT REV GENET, V7, P885 JUNG KC, 2003, CYTOGENET GENOME RES, V103, PC202 JUNGERIUS BJ, 2003, ANIM GENET, V34, P429 KARNUAH AB, 2001, MAMM GENOME, V12, P518 KAROLCHIK D, 2003, NUCLEIC ACIDS RES, V31, P51 KAROLCHIK D, 2004, NUCLEIC ACIDS RES, V32, PD493 KIERSTEIN S, 2003, CYTOGENET GENOME RES, V101, PF92 KUEHN LA, 2007, J ANIM SCI, V85, P1111 LAHBIBMANSAIS Y, 1999, MAMM GENOME, V10, P145 LAHBIBMANSAIS Y, 2000, MAMM GENOME, V11, P1098 LAHBIBMANSAIS Y, 2003, MAMM GENOME, V14, P275 LAHBIBMANSAIS Y, 2006, GENOMICS, V88, P504 LANDER ES, 2001, NATURE, V409, P860 LARSEN K, 2007, CYTOGENET GENOME RES, V116, P93 LIU XG, 2007, ANIM GENET, V38, P184 MARKLUND L, 1996, ANIM GENET, V27, P255 MARKLUND L, 2000, J ANIM SCI, V78, P2992 MARTINSWESS F, 2003, CYTOGENET GENOME RES, V102, P116 MEIJERINK E, 1997, MAMM GENOME, V8, P736 MEYERS SN, 2005, GENOMICS, V86, P739 MIKAWA S, 1999, ANIM GENET, V30, P407 MILAN D, 2000, BIOINFORMATICS, V16, P558 MOLLER M, 2004, MAMM GENOME, V15, P717 MORTON NE, 1991, P NATL ACAD SCI USA, V88, P7474 MOTE BE, 2006, ANIM GENET, V37, P295 MURPHY WJ, 2003, GENOME RES, V13, P1880 NICKERSON DA, 1997, NUCLEIC ACIDS RES, V25, P2745 NONNEMAN D, 2002, ANIM GENET, V33, P472 NONNEMAN D, 2004, ANIM GENET, V35, P338 NONNEMAN D, 2005, ANIM GENET, V36, P532 NONNEMAN DJ, 2006, BMC VET RES, V2, P28 NONNEMAN DJ, 2008, ANIMAL GENOME, V16, P578 OKUMURA N, 2006, ANIM GENET, V37, P80 PANITZ F, 2007, BIOINFORMATICS, V23, P387 PINTON P, 2000, MAMM GENOME, V11, P306 PRUITT KD, 2007, NUCLEIC ACIDS RES, V35, PD61 RAMOS PL, 2008, PIG GENOME, V2 RATTINK AP, 2001, MAMM GENOME, V12, P366 RENARD C, 2006, GENOMICS, V88, P96 RINK A, 2002, MAMM GENOME, V13, P578 RIQUET J, 1995, MAMM GENOME, V6, P623 ROBIC A, 2001, MAMM GENOME, V12, P380 ROHRER GA, 1996, GENOME RES, V6, P371 ROZEN S, 2000, METH MOL B, V132, P365 SAMBROOK J, 1989, MOL CLONING LABORATO, V9, P16 SAWERA M, 2006, ANIM GENET, V37, P199 SEELOW D, 2008, PLOS ONE, V3, ARE3874 SHIGENARI A, 2004, IMMUNOGENETICS, V55, P695 SHIMOGIRI T, 2006, ANIM GENET, V37, P503 SPLAN RK, 1998, J ANIM SCI, V76, P658 SPOTTER A, 2001, CYTOGENET CELL GENET, V95, P92 STRATIL A, 2004, COMP BIOCHEM PHYS B, V138, P377 SUN HS, 2002, ANIM GENET, V33, P91 TANAKA M, 2006, ANIM GENET, V37, P10 THOMSEN PD, 1998, MAMM GENOME, V9, P394 TUGGLE CK, 2003, MAMM GENOME, V14, P565 VAN PM, 2001, CYTOGENET CELL GENET, V93, P297 VAN PM, 2003, CYTOGENET GENOME RES, V102, P133 WAGENKNECHT D, 2006, J ANIM BREED GENET, V123, P280 WANG H, 2005, CYTOGENET GENOME RES, V108, P363 WANG XM, 2006, ANIM BIOTECHNOL, V17, P99 WERNERSSON R, 2005, BMC GENOMICS, V6, AR70 WIMMERS K, 2005, ANIM GENET, V36, P152 WIMMERS K, 2007, ANIM GENET, V38, P474 YASUE H, 2006, CYTOGENET GENOME RES, V112, P121 YERLE M, 1998, CYTOGENET CELL GENET, V82, P182 ZHANG B, 2008, ANIM GENET, V39, P258 ZHU ZM, 2006, BIOCHEM BIOPH RES CO, V346, P7 |