Abstract
BackgroundWhole 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.ResultsMap 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.ConclusionThis 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.
Highlights
Whole genome radiation hybrid (WG-Radiation hybrid (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
The accumulated map distance of SSC10 was 2075.1 cR7,000 on the IMpRH7,000-rad and 5168.1 cR12,000 on the IMNpRH212,000-rad FW maps. This represents a 2.5 fold increase in map resolution over the IMpRH7,000-rad panel (Table 1), which is consistent with our previous observations on SSC2p, 9p and 12, [15,16], and within the 2.2– 3.0 fold range reported on SSC6q1.2 [17], SSC7q11-14 [18], and SSC15q25 [1]
If we assume the DNA content of SSC10 is ~85 Mb [25], the kb/cR ratio is ~16.4 for the IMNpRH212,000-rad FW map, and 41 kb/cR in the IMpRH7,000-rad FW map, close to the genome average of 15 kb/cR12,000 reported for the IMNpRH2 panel [1,15], and slightly better than the 47.5 kb/cR7,000 genome average reported for the IMpRH7,000-rad panel [7]
Summary
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. Radiation hybrid (RH) mapping is an important tool in the construction of high-resolution physical maps, which are key to efficient sequencing and successful genome sequence assembly [1,2,3,4,5] and the construction of comparative maps between species [6,7,8]. Current RH maps of SSC10 are built on the IMpRH7,000-rad panel [8,1922] where map resolution and marker density are not optimal for either fine-mapping QTLs or genome sequence assembly. An integrated, high-resolution RH and comparative map for SSC10 should help in resolving discrepancies
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