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A high resolution physical and RH map of pig chromosome 6q1.2 and comparative analysis with human chromosome 19q13.1.

Martins-Wess F, Milan D, Drögemüller C, Vobeta-Nemitz R, Brenig B, Robic A, Yerle M, Leeb T - BMC Genomics (2003)

Bottom Line: The construction of these contigs was monitored by the results provided by the mapping of 15 markers on the IMpRH(7000rad) and 35 markers on the IMNpRH2(12000rad) radiation hybrid panels.The order of markers on the framework 1000:1 RH map was found totally consistent with the data deduced from the contig map.The integrated physical and RH map of the investigated region on SSC 6q1.2 was used for a comparative analysis with respect to the syntenic regions on HSA 19q13.1 and MMU 7 and revealed a perfectly conserved gene order across the entire studied interval.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Animal Breeding and Genetics, School of Veterinary Medicine Hannover, Bünteweg 17p, 30559 Hannover, Germany. flavia.martins@tiho-hannover.de

ABSTRACT

Background: The generation of BAC/PAC contigs in targeted genome regions is a powerful method to establish high-resolution physical maps. In domestic animal species the generation of such contigs is typically initiated with the screening of libraries with probes derived from human genes that are expected to be located in the region of interest by comparative mapping. However, in many instances the available gene-derived probes are too far apart to allow the cloning of BAC/PAC contigs larger than a few hundred kb. High resolution physical mapping allows to estimate the sizes of gaps and to control the orientation of the individual sub-contigs, which helps to avoid errors during the assembly of smaller contigs into final Mb-sized contigs. The recently constructed porcine IMNpRH2 panel allowed us to use this approach for the construction of high-resolution physical maps of SSC 6q1.2.

Results: Two sequence-ready BAC/PAC contigs of the gene-rich region on porcine chromosome 6q1.2 (SSC 6q1.2) containing the RYRl gene were constructed. The two contigs spanned about 1.2 Mb and 2.0 Mb respectively. The construction of these contigs was monitored by the results provided by the mapping of 15 markers on the IMpRH(7000rad) and 35 markers on the IMNpRH2(12000rad) radiation hybrid panels. Analyses on the IMpRH panel allowed us to globally link and orientate preliminary smaller contigs, whereas analyses on the high resolution IMNpRH2 panel allowed us to finally identify the order of genes and markers.

Conclusions: A framework map of 523 cR12000 was established covering the whole studied region. The order of markers on the framework 1000:1 RH map was found totally consistent with the data deduced from the contig map. The kb/cR ratio was very constant in the whole region, with an average value of 6.6 kb/cR. We estimate that the size of the remaining gap between the two contigs is of about 300 kb. The integrated physical and RH map of the investigated region on SSC 6q1.2 was used for a comparative analysis with respect to the syntenic regions on HSA 19q13.1 and MMU 7 and revealed a perfectly conserved gene order across the entire studied interval.

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Comparison of the clone-based physical map, RH7000 map and RH12000 mapofSSC 6q1.2. The RH maps represent comprehensive maps, where the markers of the 1000:1 framework map are highlighted in bold. Note that there is perfect agreement in the order of framework markers between the IMNpRH2 RH12000 map and the clone-based physical map. For the non-framework markers, altemate positions are indicated by thin vertical lines.
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Figure 3: Comparison of the clone-based physical map, RH7000 map and RH12000 mapofSSC 6q1.2. The RH maps represent comprehensive maps, where the markers of the 1000:1 framework map are highlighted in bold. Note that there is perfect agreement in the order of framework markers between the IMNpRH2 RH12000 map and the clone-based physical map. For the non-framework markers, altemate positions are indicated by thin vertical lines.

Mentions: When the full RH data set was available for both panels, it appeared that at the scale of 10–100 kb, the degree of resolution of the IMpRH panel is not high enough, and furthermore the order of genes that could be determined on this panel is very sensitive to some small genotyping errors. To produce a final reference map we thus computed a 1000:1 framework map using only the 35 vectors produced on IMNpRH2 panel. The framework status of the map was tested by calculation of likelihood of maps produced after all local permutations in a slipping window of 6 markers, and by global local inversions. We confirmed that no altemate order could be identified with a difference of log likelihood of less than 3 compared to the proposed order. The framework map contained 24 of the 35 IMNpRH2 markers. Using this framework map comprehensive maps were produced on each panel. In order to avoid inflation of the map size, we chose to project additional markers at their most likely location, without altering the multipoint distance between framework markers (Fig. 3).


A high resolution physical and RH map of pig chromosome 6q1.2 and comparative analysis with human chromosome 19q13.1.

Martins-Wess F, Milan D, Drögemüller C, Vobeta-Nemitz R, Brenig B, Robic A, Yerle M, Leeb T - BMC Genomics (2003)

Comparison of the clone-based physical map, RH7000 map and RH12000 mapofSSC 6q1.2. The RH maps represent comprehensive maps, where the markers of the 1000:1 framework map are highlighted in bold. Note that there is perfect agreement in the order of framework markers between the IMNpRH2 RH12000 map and the clone-based physical map. For the non-framework markers, altemate positions are indicated by thin vertical lines.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC161799&req=5

Figure 3: Comparison of the clone-based physical map, RH7000 map and RH12000 mapofSSC 6q1.2. The RH maps represent comprehensive maps, where the markers of the 1000:1 framework map are highlighted in bold. Note that there is perfect agreement in the order of framework markers between the IMNpRH2 RH12000 map and the clone-based physical map. For the non-framework markers, altemate positions are indicated by thin vertical lines.
Mentions: When the full RH data set was available for both panels, it appeared that at the scale of 10–100 kb, the degree of resolution of the IMpRH panel is not high enough, and furthermore the order of genes that could be determined on this panel is very sensitive to some small genotyping errors. To produce a final reference map we thus computed a 1000:1 framework map using only the 35 vectors produced on IMNpRH2 panel. The framework status of the map was tested by calculation of likelihood of maps produced after all local permutations in a slipping window of 6 markers, and by global local inversions. We confirmed that no altemate order could be identified with a difference of log likelihood of less than 3 compared to the proposed order. The framework map contained 24 of the 35 IMNpRH2 markers. Using this framework map comprehensive maps were produced on each panel. In order to avoid inflation of the map size, we chose to project additional markers at their most likely location, without altering the multipoint distance between framework markers (Fig. 3).

Bottom Line: The construction of these contigs was monitored by the results provided by the mapping of 15 markers on the IMpRH(7000rad) and 35 markers on the IMNpRH2(12000rad) radiation hybrid panels.The order of markers on the framework 1000:1 RH map was found totally consistent with the data deduced from the contig map.The integrated physical and RH map of the investigated region on SSC 6q1.2 was used for a comparative analysis with respect to the syntenic regions on HSA 19q13.1 and MMU 7 and revealed a perfectly conserved gene order across the entire studied interval.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Animal Breeding and Genetics, School of Veterinary Medicine Hannover, Bünteweg 17p, 30559 Hannover, Germany. flavia.martins@tiho-hannover.de

ABSTRACT

Background: The generation of BAC/PAC contigs in targeted genome regions is a powerful method to establish high-resolution physical maps. In domestic animal species the generation of such contigs is typically initiated with the screening of libraries with probes derived from human genes that are expected to be located in the region of interest by comparative mapping. However, in many instances the available gene-derived probes are too far apart to allow the cloning of BAC/PAC contigs larger than a few hundred kb. High resolution physical mapping allows to estimate the sizes of gaps and to control the orientation of the individual sub-contigs, which helps to avoid errors during the assembly of smaller contigs into final Mb-sized contigs. The recently constructed porcine IMNpRH2 panel allowed us to use this approach for the construction of high-resolution physical maps of SSC 6q1.2.

Results: Two sequence-ready BAC/PAC contigs of the gene-rich region on porcine chromosome 6q1.2 (SSC 6q1.2) containing the RYRl gene were constructed. The two contigs spanned about 1.2 Mb and 2.0 Mb respectively. The construction of these contigs was monitored by the results provided by the mapping of 15 markers on the IMpRH(7000rad) and 35 markers on the IMNpRH2(12000rad) radiation hybrid panels. Analyses on the IMpRH panel allowed us to globally link and orientate preliminary smaller contigs, whereas analyses on the high resolution IMNpRH2 panel allowed us to finally identify the order of genes and markers.

Conclusions: A framework map of 523 cR12000 was established covering the whole studied region. The order of markers on the framework 1000:1 RH map was found totally consistent with the data deduced from the contig map. The kb/cR ratio was very constant in the whole region, with an average value of 6.6 kb/cR. We estimate that the size of the remaining gap between the two contigs is of about 300 kb. The integrated physical and RH map of the investigated region on SSC 6q1.2 was used for a comparative analysis with respect to the syntenic regions on HSA 19q13.1 and MMU 7 and revealed a perfectly conserved gene order across the entire studied interval.

Show MeSH