A 12,000-rad porcine radiation hybrid (IMNpRH2) panel refines the conserved synteny between SSC12 and HSA17

Wan Sheng Liu, Katie Eyer, Hiroshi Yasue, Benjamin Roelofs, Hideki Hiraiwa, Takeshi Shimogiri, Earl Landrito, Joseph Ekstrand, Michael Treat, Anette Rink, Martine Yerle, Denis Milan, Craig W. Beattie

Research output: Contribution to journalArticle

16 Citations (Scopus)

Abstract

Reverse or bidirectional Zoo-FISH suggests that synteny between porcine chromosome 12 (SSC12) and human chromosome 17 (HSA17) is completely conserved. The construction of a high-resolution radiation hybrid (RH) map for SSC12 provides a unique opportunity to determine whether chromosomal synteny is reflected at the molecular level by comparative gene mapping of SSC12 and HSA17. We report an initial, high-resolution RH map of SSC12 on the 12,000-rad IMNpRH2 panel using CarthaGene software. This map contains a total of 320 markers, including 20 microsatellites and 300 ESTs/genes, covering ∼4836.9 cR 12,000. The markers were ordered in 16 linkage groups at LOD 6.0 using framework markers previously mapped on the IMpRH7000-rad SSC12 and porcine genetic maps. Ten linkage groups ordered more than 10 markers, with the largest containing 101 STSs. The resolution of the current RH map is ∼15.3 kb/cR on SSC12, a significant improvement over the second-generation EST SSC12 RH7000-rad map of 103 ESTs and 15 framework markers covering ∼2287.2 cR7000. Compared to HSA17, six distinct segments were identified, revealing macro-rearrangements within the apparently complete synteny between SSC12 and HSA17. Further analysis of the order of 245 genes (ESTs) on HSA17 and SSC12 also revealed several micro-rearrangements within a synteny segment. A high-resolution SSC12 RH12,000-rad map will be useful in fine-mapping QTL and as a scaffold for sequencing this chromosome.

Original languageEnglish (US)
Pages (from-to)731-738
Number of pages8
JournalGenomics
Volume86
Issue number6
DOIs
StatePublished - Dec 1 2005

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Radiation Hybrid Mapping
Synteny
Expressed Sequence Tags
Swine
Chromosomes, Human, Pair 12
Chromosomes, Human, Pair 17
Gene Order
Chromosome Mapping
Human Chromosomes
Microsatellite Repeats
Software
Chromosomes
Genes

All Science Journal Classification (ASJC) codes

  • Genetics

Cite this

Liu, Wan Sheng ; Eyer, Katie ; Yasue, Hiroshi ; Roelofs, Benjamin ; Hiraiwa, Hideki ; Shimogiri, Takeshi ; Landrito, Earl ; Ekstrand, Joseph ; Treat, Michael ; Rink, Anette ; Yerle, Martine ; Milan, Denis ; Beattie, Craig W. / A 12,000-rad porcine radiation hybrid (IMNpRH2) panel refines the conserved synteny between SSC12 and HSA17. In: Genomics. 2005 ; Vol. 86, No. 6. pp. 731-738.
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title = "A 12,000-rad porcine radiation hybrid (IMNpRH2) panel refines the conserved synteny between SSC12 and HSA17",
abstract = "Reverse or bidirectional Zoo-FISH suggests that synteny between porcine chromosome 12 (SSC12) and human chromosome 17 (HSA17) is completely conserved. The construction of a high-resolution radiation hybrid (RH) map for SSC12 provides a unique opportunity to determine whether chromosomal synteny is reflected at the molecular level by comparative gene mapping of SSC12 and HSA17. We report an initial, high-resolution RH map of SSC12 on the 12,000-rad IMNpRH2 panel using CarthaGene software. This map contains a total of 320 markers, including 20 microsatellites and 300 ESTs/genes, covering ∼4836.9 cR 12,000. The markers were ordered in 16 linkage groups at LOD 6.0 using framework markers previously mapped on the IMpRH7000-rad SSC12 and porcine genetic maps. Ten linkage groups ordered more than 10 markers, with the largest containing 101 STSs. The resolution of the current RH map is ∼15.3 kb/cR on SSC12, a significant improvement over the second-generation EST SSC12 RH7000-rad map of 103 ESTs and 15 framework markers covering ∼2287.2 cR7000. Compared to HSA17, six distinct segments were identified, revealing macro-rearrangements within the apparently complete synteny between SSC12 and HSA17. Further analysis of the order of 245 genes (ESTs) on HSA17 and SSC12 also revealed several micro-rearrangements within a synteny segment. A high-resolution SSC12 RH12,000-rad map will be useful in fine-mapping QTL and as a scaffold for sequencing this chromosome.",
author = "Liu, {Wan Sheng} and Katie Eyer and Hiroshi Yasue and Benjamin Roelofs and Hideki Hiraiwa and Takeshi Shimogiri and Earl Landrito and Joseph Ekstrand and Michael Treat and Anette Rink and Martine Yerle and Denis Milan and Beattie, {Craig W.}",
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Liu, WS, Eyer, K, Yasue, H, Roelofs, B, Hiraiwa, H, Shimogiri, T, Landrito, E, Ekstrand, J, Treat, M, Rink, A, Yerle, M, Milan, D & Beattie, CW 2005, 'A 12,000-rad porcine radiation hybrid (IMNpRH2) panel refines the conserved synteny between SSC12 and HSA17', Genomics, vol. 86, no. 6, pp. 731-738. https://doi.org/10.1016/j.ygeno.2005.08.006

A 12,000-rad porcine radiation hybrid (IMNpRH2) panel refines the conserved synteny between SSC12 and HSA17. / Liu, Wan Sheng; Eyer, Katie; Yasue, Hiroshi; Roelofs, Benjamin; Hiraiwa, Hideki; Shimogiri, Takeshi; Landrito, Earl; Ekstrand, Joseph; Treat, Michael; Rink, Anette; Yerle, Martine; Milan, Denis; Beattie, Craig W.

In: Genomics, Vol. 86, No. 6, 01.12.2005, p. 731-738.

Research output: Contribution to journalArticle

TY - JOUR

T1 - A 12,000-rad porcine radiation hybrid (IMNpRH2) panel refines the conserved synteny between SSC12 and HSA17

AU - Liu, Wan Sheng

AU - Eyer, Katie

AU - Yasue, Hiroshi

AU - Roelofs, Benjamin

AU - Hiraiwa, Hideki

AU - Shimogiri, Takeshi

AU - Landrito, Earl

AU - Ekstrand, Joseph

AU - Treat, Michael

AU - Rink, Anette

AU - Yerle, Martine

AU - Milan, Denis

AU - Beattie, Craig W.

PY - 2005/12/1

Y1 - 2005/12/1

N2 - Reverse or bidirectional Zoo-FISH suggests that synteny between porcine chromosome 12 (SSC12) and human chromosome 17 (HSA17) is completely conserved. The construction of a high-resolution radiation hybrid (RH) map for SSC12 provides a unique opportunity to determine whether chromosomal synteny is reflected at the molecular level by comparative gene mapping of SSC12 and HSA17. We report an initial, high-resolution RH map of SSC12 on the 12,000-rad IMNpRH2 panel using CarthaGene software. This map contains a total of 320 markers, including 20 microsatellites and 300 ESTs/genes, covering ∼4836.9 cR 12,000. The markers were ordered in 16 linkage groups at LOD 6.0 using framework markers previously mapped on the IMpRH7000-rad SSC12 and porcine genetic maps. Ten linkage groups ordered more than 10 markers, with the largest containing 101 STSs. The resolution of the current RH map is ∼15.3 kb/cR on SSC12, a significant improvement over the second-generation EST SSC12 RH7000-rad map of 103 ESTs and 15 framework markers covering ∼2287.2 cR7000. Compared to HSA17, six distinct segments were identified, revealing macro-rearrangements within the apparently complete synteny between SSC12 and HSA17. Further analysis of the order of 245 genes (ESTs) on HSA17 and SSC12 also revealed several micro-rearrangements within a synteny segment. A high-resolution SSC12 RH12,000-rad map will be useful in fine-mapping QTL and as a scaffold for sequencing this chromosome.

AB - Reverse or bidirectional Zoo-FISH suggests that synteny between porcine chromosome 12 (SSC12) and human chromosome 17 (HSA17) is completely conserved. The construction of a high-resolution radiation hybrid (RH) map for SSC12 provides a unique opportunity to determine whether chromosomal synteny is reflected at the molecular level by comparative gene mapping of SSC12 and HSA17. We report an initial, high-resolution RH map of SSC12 on the 12,000-rad IMNpRH2 panel using CarthaGene software. This map contains a total of 320 markers, including 20 microsatellites and 300 ESTs/genes, covering ∼4836.9 cR 12,000. The markers were ordered in 16 linkage groups at LOD 6.0 using framework markers previously mapped on the IMpRH7000-rad SSC12 and porcine genetic maps. Ten linkage groups ordered more than 10 markers, with the largest containing 101 STSs. The resolution of the current RH map is ∼15.3 kb/cR on SSC12, a significant improvement over the second-generation EST SSC12 RH7000-rad map of 103 ESTs and 15 framework markers covering ∼2287.2 cR7000. Compared to HSA17, six distinct segments were identified, revealing macro-rearrangements within the apparently complete synteny between SSC12 and HSA17. Further analysis of the order of 245 genes (ESTs) on HSA17 and SSC12 also revealed several micro-rearrangements within a synteny segment. A high-resolution SSC12 RH12,000-rad map will be useful in fine-mapping QTL and as a scaffold for sequencing this chromosome.

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