A robust linkage map of the porcine autosome based on gene-associated SNPs

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A robust linkage map of the porcine autosome based on gene-associated SNPs. / Vingborg, Rikke K K; Gregersen, Vivi R; Zhan, Bujie; Panitz, Frank; Hoj, Anette; Sorensen, Kirsten K; Madsen, Lone B; Larsen, Knud; Hornshøj, Henrik; Wang, Xuefei; Bendixen, Christian.

In: B M C Genomics, Vol. 10, No. 134, 2009.

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaperJournal articleResearchpeer-review

Harvard

Vingborg, RKK, Gregersen, VR, Zhan, B, Panitz, F, Hoj, A, Sorensen, KK, Madsen, LB, Larsen, K, Hornshøj, H, Wang, X & Bendixen, C 2009, 'A robust linkage map of the porcine autosome based on gene-associated SNPs', B M C Genomics, vol. 10, no. 134. https://doi.org/10.1186/1471-2164-10-134

APA

Vingborg, R. K. K., Gregersen, V. R., Zhan, B., Panitz, F., Hoj, A., Sorensen, K. K., Madsen, L. B., Larsen, K., Hornshøj, H., Wang, X., & Bendixen, C. (2009). A robust linkage map of the porcine autosome based on gene-associated SNPs. B M C Genomics, 10(134). https://doi.org/10.1186/1471-2164-10-134

CBE

Vingborg RKK, Gregersen VR, Zhan B, Panitz F, Hoj A, Sorensen KK, Madsen LB, Larsen K, Hornshøj H, Wang X, Bendixen C. 2009. A robust linkage map of the porcine autosome based on gene-associated SNPs. B M C Genomics. 10(134). https://doi.org/10.1186/1471-2164-10-134

MLA

Vancouver

Author

Vingborg, Rikke K K ; Gregersen, Vivi R ; Zhan, Bujie ; Panitz, Frank ; Hoj, Anette ; Sorensen, Kirsten K ; Madsen, Lone B ; Larsen, Knud ; Hornshøj, Henrik ; Wang, Xuefei ; Bendixen, Christian. / A robust linkage map of the porcine autosome based on gene-associated SNPs. In: B M C Genomics. 2009 ; Vol. 10, No. 134.

Bibtex

@article{073b8f3021e711dfa28b000ea68e967b,
title = "A robust linkage map of the porcine autosome based on gene-associated SNPs",
abstract = "BackgroundGenetic 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.ResultsLinkage 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.ConclusionsThe 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. ",
author = "Vingborg, {Rikke K K} and Gregersen, {Vivi R} and Bujie Zhan and Frank Panitz and Anette Hoj and Sorensen, {Kirsten K} and Madsen, {Lone B} and Knud Larsen and Henrik Hornsh{\o}j and Xuefei Wang and Christian Bendixen",
year = "2009",
doi = "10.1186/1471-2164-10-134",
language = "English",
volume = "10",
journal = "B M C Genomics",
issn = "1471-2164",
publisher = "BioMed Central Ltd.",
number = "134",

}

RIS

TY - JOUR

T1 - A robust linkage map of the porcine autosome based on gene-associated SNPs

AU - Vingborg, Rikke K K

AU - Gregersen, Vivi R

AU - Zhan, Bujie

AU - Panitz, Frank

AU - Hoj, Anette

AU - Sorensen, Kirsten K

AU - Madsen, Lone B

AU - Larsen, Knud

AU - Hornshøj, Henrik

AU - Wang, Xuefei

AU - Bendixen, Christian

PY - 2009

Y1 - 2009

N2 - BackgroundGenetic 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.ResultsLinkage 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.ConclusionsThe 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.

AB - BackgroundGenetic 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.ResultsLinkage 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.ConclusionsThe 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.

U2 - 10.1186/1471-2164-10-134

DO - 10.1186/1471-2164-10-134

M3 - Journal article

VL - 10

JO - B M C Genomics

JF - B M C Genomics

SN - 1471-2164

IS - 134

ER -