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 IMNpRH2(12,000-rad) porcine WG-RH panel, integrated with the IMpRH(7000-rad) WG-RH, genetic and BAC fingerprinted contig (FPC) maps.

Results: Map vectors from the IMNpRH2(12,000-rad) and IMpRH(7,000-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 cR(7,000) and 1814.5 cR(12,000), respectively. The second group covers SSC10q at map distances of 1336.9 cR(7,000) and 3353.6 cR(12,000), yielding an overall average map resolution of 16.4 kb/cR(12,000) or 393.5 kb per marker on SSC10. This represents an approximately 2.5-fold increase in map resolution over the IMpRH(7,000-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 IMNpRH2(12,000-rad) and IMpRH(7,000-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.

Figure 1

High-resolution RH comprehensive and comparative maps of SSC10. (a) Cytogenetic map of porcine chromosome (SSC) 10. The nucleolus organizer region is indicated as NOR; (b) Genetic map of SSC10. Those MS markers that are mapped in the current 7,000- and 12,000-rad FW maps and non-FW maps are listed in the genetic map. The four singletons that were not in FW maps are marked in italics in a box; (c) The 7000-rad IMpRH framework (FW) map; (d) The 12,000-rad IMNpRH2 FW map. MSs highlighted in black, genes/ESTs in red, and BESs in magenta. Markers listed between the 7,000- and 12,000-rad FW maps are framework markers; those on the right of the IMNpRH2 FW map are non-framework markers; (e) BAC fingerprinted contig (FPC). Contig number, e.g. 10001, corresponds to the FPC maps at ; Question mark (?) indicates that the BES 287A21G01 is lack of information in the FPC maps. (f) Comparative to human chromosome (HSA) 1, 9 and 10. Synteny blocks between pig and human, as well as the orientation of the human sequences in reference to the SSC10 RH map, are indicated by arrows, with HSA1 in blue, HSA9 in red and HSA10 in green. Sequence position of each synteny block in the human genome sequences (Build 36.3) is listed (in Mb) on the right side of the chromosomes.

Figure 2

Comparison of gene order between SSC10 and HSA1, 9, and 10. A total of 127 genes/ESTs and BESs were compared based on their positions on SSC10 and HSA1, 9 and 10. The sequence positions (Mb) of genes on human chromosomes (Build 36.3) are compared with corresponding genes on the SSC10 RH_12,000-rad map (Fig. 1). Map distances (cR) for SSC10 are the accumulated sum of the linkage groups from Fig. 1. Each diamond represents the Cartesian coordinates for a sequence on HSA1, squares for HSA9, and triangles HSA10. Any significant change in coordinates between adjacent genes indicates a rearrangement. The map position of FBP1 at coordinate 1310.0 CR/96.6 Mb is indicated and discussed in the text.