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.
N1 - Funding Information:
This work was supported by a grant from the USDA-CSREES (2004-35205-14244) to C.W.B. and the Program for the Promotion of Basic Research Activity for Innovative Biosciences of the Bio-oriented Technology Research Advancement Institution, Japan (H.Y.). It was also supported in part by the Nevada Agricultural Experiment Station, Publication No. 53055520.
PY - 2005/12
Y1 - 2005/12
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.
UR - https://www.scopus.com/pages/publications/28644444279
UR - https://www.scopus.com/pages/publications/28644444279#tab=citedBy
U2 - 10.1016/j.ygeno.2005.08.006
DO - 10.1016/j.ygeno.2005.08.006
M3 - Article
C2 - 16289748
AN - SCOPUS:28644444279
SN - 0888-7543
VL - 86
SP - 731
EP - 738
JO - Genomics
JF - Genomics
IS - 6
ER -