An integrated RH map of porcine chromosome 10

Jian Gang Ma, Hiroshi Yasue, Katie E. Eyer, Hideki Hiraiwa, Takeshi Shimogiri, Stacey N. Meyers, Jonathan E. Beever, Lawrence B. Schook, Craig W. Beattie, Wansheng Liu

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

Background: Whole genome radiation hybrid (WG-RH) maps serve as "scaffolds" to significantly improve the orientation of small bacterial artificial chromosome (BAC) contigs, order genes within the contigs and assist assembly of a sequence-ready map for virtually any species. Here, we report the construction of a porcine: human comparative map for pig (Sus scrofa) chromosome 10 (SSC10) using the IMNpRH212,000-rad porcine WG-RH panel, integrated with the IMpRH7000-rad WG-RH, genetic and BAC fingerprinted contig (FPC) maps. Results: Map vectors from the IMNpRH212,000-rad and IMpRH7,000-rad panels were merged to construct parallel framework (FW) maps, within which FW markers common to both panels have an identical order. This strategy reduced map discrepancies between the two panels and significantly improved map accuracy. A total of 216 markers, including 50 microsatellites (MSs), 97 genes and ESTs, and 69 BAC end sequences (BESs), were ordered within two linkage groups at two point (2 pt) LOD score of 8. One linkage group covers SSC10p with accumulated map distances of 738.2 cR7,000 and 1814.5 cR12,000, respectively. The second group covers SSC10q at map distances of 1336.9 cR7,000 and 3353.6 cR12,000, yielding an overall average map resolution of 16.4 kb/cR12,000 or 393.5 kb per marker on SSC10. This represents a ∼2.5-fold increase in map resolution over the IMpRH7,000-rad panel. Based on 127 porcine markers that have homologous sequences in the human genome, a detailed comparative map between SSC10 and human (Homo sapiens) chromosome (HSA) 1, 9 and 10 was built. Conclusion: This initial comparative RH map of SSC10 refines the syntenic regions between SSC10 and HSA1, 9 and 10. It integrates the IMNpRH212,000-rad and IMpRH7,000-rad, genetic and BAC FPC maps and provides a scaffold to close potential gaps between contigs prior to genome sequencing and assembly. This map is also useful in fine mapping of QTLs on SSC10.

Original languageEnglish (US)
Article number211
JournalBMC genomics
Volume10
DOIs
StatePublished - May 8 2009

Fingerprint

Chromosomes, Human, Pair 10
Sus scrofa
Swine
Bacterial Artificial Chromosomes
Radiation Hybrid Mapping
Genome
Radiation Genetics
Chromosomes, Human, Pair 9
Gene Order
Chromosomes, Human, Pair 1
Expressed Sequence Tags
Human Genome
Sequence Homology
Microsatellite Repeats
Genes

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Genetics

Cite this

Ma, J. G., Yasue, H., Eyer, K. E., Hiraiwa, H., Shimogiri, T., Meyers, S. N., ... Liu, W. (2009). An integrated RH map of porcine chromosome 10. BMC genomics, 10, [211]. https://doi.org/10.1186/1471-2164-10-211
Ma, Jian Gang ; Yasue, Hiroshi ; Eyer, Katie E. ; Hiraiwa, Hideki ; Shimogiri, Takeshi ; Meyers, Stacey N. ; Beever, Jonathan E. ; Schook, Lawrence B. ; Beattie, Craig W. ; Liu, Wansheng. / An integrated RH map of porcine chromosome 10. In: BMC genomics. 2009 ; Vol. 10.
@article{d30f15394eb2489ea3778e65204ca392,
title = "An integrated RH map of porcine chromosome 10",
abstract = "Background: Whole genome radiation hybrid (WG-RH) maps serve as {"}scaffolds{"} to significantly improve the orientation of small bacterial artificial chromosome (BAC) contigs, order genes within the contigs and assist assembly of a sequence-ready map for virtually any species. Here, we report the construction of a porcine: human comparative map for pig (Sus scrofa) chromosome 10 (SSC10) using the IMNpRH212,000-rad porcine WG-RH panel, integrated with the IMpRH7000-rad WG-RH, genetic and BAC fingerprinted contig (FPC) maps. Results: Map vectors from the IMNpRH212,000-rad and IMpRH7,000-rad panels were merged to construct parallel framework (FW) maps, within which FW markers common to both panels have an identical order. This strategy reduced map discrepancies between the two panels and significantly improved map accuracy. A total of 216 markers, including 50 microsatellites (MSs), 97 genes and ESTs, and 69 BAC end sequences (BESs), were ordered within two linkage groups at two point (2 pt) LOD score of 8. One linkage group covers SSC10p with accumulated map distances of 738.2 cR7,000 and 1814.5 cR12,000, respectively. The second group covers SSC10q at map distances of 1336.9 cR7,000 and 3353.6 cR12,000, yielding an overall average map resolution of 16.4 kb/cR12,000 or 393.5 kb per marker on SSC10. This represents a ∼2.5-fold increase in map resolution over the IMpRH7,000-rad panel. Based on 127 porcine markers that have homologous sequences in the human genome, a detailed comparative map between SSC10 and human (Homo sapiens) chromosome (HSA) 1, 9 and 10 was built. Conclusion: This initial comparative RH map of SSC10 refines the syntenic regions between SSC10 and HSA1, 9 and 10. It integrates the IMNpRH212,000-rad and IMpRH7,000-rad, genetic and BAC FPC maps and provides a scaffold to close potential gaps between contigs prior to genome sequencing and assembly. This map is also useful in fine mapping of QTLs on SSC10.",
author = "Ma, {Jian Gang} and Hiroshi Yasue and Eyer, {Katie E.} and Hideki Hiraiwa and Takeshi Shimogiri and Meyers, {Stacey N.} and Beever, {Jonathan E.} and Schook, {Lawrence B.} and Beattie, {Craig W.} and Wansheng Liu",
year = "2009",
month = "5",
day = "8",
doi = "10.1186/1471-2164-10-211",
language = "English (US)",
volume = "10",
journal = "BMC Genomics",
issn = "1471-2164",
publisher = "BioMed Central",

}

Ma, JG, Yasue, H, Eyer, KE, Hiraiwa, H, Shimogiri, T, Meyers, SN, Beever, JE, Schook, LB, Beattie, CW & Liu, W 2009, 'An integrated RH map of porcine chromosome 10', BMC genomics, vol. 10, 211. https://doi.org/10.1186/1471-2164-10-211

An integrated RH map of porcine chromosome 10. / Ma, Jian Gang; Yasue, Hiroshi; Eyer, Katie E.; Hiraiwa, Hideki; Shimogiri, Takeshi; Meyers, Stacey N.; Beever, Jonathan E.; Schook, Lawrence B.; Beattie, Craig W.; Liu, Wansheng.

In: BMC genomics, Vol. 10, 211, 08.05.2009.

Research output: Contribution to journalArticle

TY - JOUR

T1 - An integrated RH map of porcine chromosome 10

AU - Ma, Jian Gang

AU - Yasue, Hiroshi

AU - Eyer, Katie E.

AU - Hiraiwa, Hideki

AU - Shimogiri, Takeshi

AU - Meyers, Stacey N.

AU - Beever, Jonathan E.

AU - Schook, Lawrence B.

AU - Beattie, Craig W.

AU - Liu, Wansheng

PY - 2009/5/8

Y1 - 2009/5/8

N2 - Background: Whole genome radiation hybrid (WG-RH) maps serve as "scaffolds" to significantly improve the orientation of small bacterial artificial chromosome (BAC) contigs, order genes within the contigs and assist assembly of a sequence-ready map for virtually any species. Here, we report the construction of a porcine: human comparative map for pig (Sus scrofa) chromosome 10 (SSC10) using the IMNpRH212,000-rad porcine WG-RH panel, integrated with the IMpRH7000-rad WG-RH, genetic and BAC fingerprinted contig (FPC) maps. Results: Map vectors from the IMNpRH212,000-rad and IMpRH7,000-rad panels were merged to construct parallel framework (FW) maps, within which FW markers common to both panels have an identical order. This strategy reduced map discrepancies between the two panels and significantly improved map accuracy. A total of 216 markers, including 50 microsatellites (MSs), 97 genes and ESTs, and 69 BAC end sequences (BESs), were ordered within two linkage groups at two point (2 pt) LOD score of 8. One linkage group covers SSC10p with accumulated map distances of 738.2 cR7,000 and 1814.5 cR12,000, respectively. The second group covers SSC10q at map distances of 1336.9 cR7,000 and 3353.6 cR12,000, yielding an overall average map resolution of 16.4 kb/cR12,000 or 393.5 kb per marker on SSC10. This represents a ∼2.5-fold increase in map resolution over the IMpRH7,000-rad panel. Based on 127 porcine markers that have homologous sequences in the human genome, a detailed comparative map between SSC10 and human (Homo sapiens) chromosome (HSA) 1, 9 and 10 was built. Conclusion: This initial comparative RH map of SSC10 refines the syntenic regions between SSC10 and HSA1, 9 and 10. It integrates the IMNpRH212,000-rad and IMpRH7,000-rad, genetic and BAC FPC maps and provides a scaffold to close potential gaps between contigs prior to genome sequencing and assembly. This map is also useful in fine mapping of QTLs on SSC10.

AB - Background: Whole genome radiation hybrid (WG-RH) maps serve as "scaffolds" to significantly improve the orientation of small bacterial artificial chromosome (BAC) contigs, order genes within the contigs and assist assembly of a sequence-ready map for virtually any species. Here, we report the construction of a porcine: human comparative map for pig (Sus scrofa) chromosome 10 (SSC10) using the IMNpRH212,000-rad porcine WG-RH panel, integrated with the IMpRH7000-rad WG-RH, genetic and BAC fingerprinted contig (FPC) maps. Results: Map vectors from the IMNpRH212,000-rad and IMpRH7,000-rad panels were merged to construct parallel framework (FW) maps, within which FW markers common to both panels have an identical order. This strategy reduced map discrepancies between the two panels and significantly improved map accuracy. A total of 216 markers, including 50 microsatellites (MSs), 97 genes and ESTs, and 69 BAC end sequences (BESs), were ordered within two linkage groups at two point (2 pt) LOD score of 8. One linkage group covers SSC10p with accumulated map distances of 738.2 cR7,000 and 1814.5 cR12,000, respectively. The second group covers SSC10q at map distances of 1336.9 cR7,000 and 3353.6 cR12,000, yielding an overall average map resolution of 16.4 kb/cR12,000 or 393.5 kb per marker on SSC10. This represents a ∼2.5-fold increase in map resolution over the IMpRH7,000-rad panel. Based on 127 porcine markers that have homologous sequences in the human genome, a detailed comparative map between SSC10 and human (Homo sapiens) chromosome (HSA) 1, 9 and 10 was built. Conclusion: This initial comparative RH map of SSC10 refines the syntenic regions between SSC10 and HSA1, 9 and 10. It integrates the IMNpRH212,000-rad and IMpRH7,000-rad, genetic and BAC FPC maps and provides a scaffold to close potential gaps between contigs prior to genome sequencing and assembly. This map is also useful in fine mapping of QTLs on SSC10.

UR - http://www.scopus.com/inward/record.url?scp=66749152524&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=66749152524&partnerID=8YFLogxK

U2 - 10.1186/1471-2164-10-211

DO - 10.1186/1471-2164-10-211

M3 - Article

VL - 10

JO - BMC Genomics

JF - BMC Genomics

SN - 1471-2164

M1 - 211

ER -

Ma JG, Yasue H, Eyer KE, Hiraiwa H, Shimogiri T, Meyers SN et al. An integrated RH map of porcine chromosome 10. BMC genomics. 2009 May 8;10. 211. https://doi.org/10.1186/1471-2164-10-211