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 approximately 4836.9 cR12,000. 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 approximately 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 approximately 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.

High-resolution comprehensive radiation hybrid maps of the porcine chromosomes 2p and 9p compared with the human chromosome 11

“…Therefore, the kb/cR ratio in the IMNpRH2 12,000-rad FW maps was 15.8 for SSC2p, and 15.4 for SSC9p, while the ratio in the IMpRH 7,000-rad FW maps was 47.1 and 36.3, respectively. The kb/cR 12,000 ratio is consistent with the observation of 15.3 kb/cR for the entire SSC12 (Liu et al, 2005), suggesting that a realized average map resolution is ϳ 15 kb/cR for the IMNpRH2 12,000-rad panel. This represents a 3-fold increase in resolution over that of the 7,000-rad panel on SSC2p, and a 2.4-fold increase on SSC9p ( Table 1 ).…”

“…All primers were optimized by determining the highest annealing temperature at which successful amplification of porcine genomic DNA took place. Primers were then tested with porcine and Chinese hamster genomic DNA at species specific temperatures (Liu et al, 2005).…”

“…RH typing was carried out in duplicate as described (Liu et al, 2005). Consensus vectors were established by two individuals using GelScore data (http://www.wesbarris.com/GelScore/) as a baseline.…”

“…rich' genomes of human and other sequenced and assembled organisms to the 'information-poor' maps of farm animals and to increase the number of gene loci (Burt, 2002;Liu et al, 2005) and reveal the degree of synteny conservation between species (Goldammer et al, 2002(Goldammer et al, , 2004Martins-Wess et al, 2003a;Liu et al, 2005).…”

“…A 12,000-rad porcine WG-RH panel (IMNpRH2) has been used for highresolution mapping of several chromosome regions in swine Martins-Wess et al, 2003a;Demars et al, 2006). We recently reported a detailed comparison of SSC12 with HSA17 using the IMNpRH2 panel at an overall resolution of ϳ 252 kb/STS or ϳ 15 kb/cR 12,000 , and indicated that the IMNpRH2 panel provides a highresolution scaffold for interval mapping and sequence assembly (Liu et al, 2005).…”