Martin Jirout1,2, Drahomira Krenova2, Vladimir Kren2,3, Laura Breen1, Michal Pravenec3,2, Nicholas J Schork4, Morton P Printz1
Mammalian Genome (In Press)
1) Dept of Pharmacology, University of California San Diego, La Jolla, CA, USA, 2) Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic, 3) The Academy of Sciences of the Czech Republic and Centre for Integrated Genomics, Videnska, Prague, CR, 4) Dept of Psychiatry, University of California San Diego, La Jolla, CA, USA
Abstract
A new contiguous genetic linkage map of the HXB/BXH set of rat recombinant inbred (RI) strains was constructed to enhance QTL mapping power and precision, and thereby, make the RI strain set a better genomics resource. The HXB/BXH rat RI strains were developed from a cross between the hypertensive SHR/OlaIpcv and normotensive BN-Lx/Cub rat strains, and have been shown useful for identifying quantitative trait loci (QTL) for a variety of cardiovascular, metabolic and behavioural phenotypes. In the current analysis, the DNA from 31 existing strains, 1 substrain and 4 extinct strains were genotyped for a selection of polymorphic microsatellite marker loci, predominantly polymorphic framework markers from the high-density integrated rat genome maps of Steen et al., (1999). The resulting linkage map consists of 245 microsatellite markers spanning a total length of 1789 cM with an average inter-marker distance of ~ 8.0 cM. This map covers the rat genome contiguously and completely with an exception of two locations on chromosomes 11 and 16. The new genotypic information obtained also permitted further genetic characterization of the RI strain set including strain independence, genetic similarity among the individual strains and non-syntenic associations between loci.
|
New SDP | |||
|---|---|---|---|
| Chromosome | Length (cM) | Number of markers | Average spacing (cM) |
| 1 | 176.3 | 26 | 6.79 |
| 2 | 123.1 | 20 | 6.16 |
| 3 | 99.8 | 17 | 6.24 |
| 4 | 106.8 | 16 | 7.11 |
| 5 | 123.1 | 16 | 8.22 |
| 6 | 119.8 | 17 | 7.50 |
| 7 | 106.6 | 16 | 6.67 |
| 8 | 84.4 | 11 | 8.43 |
| 9 | 109.9 | 13 | 9.17 |
| 10 | 112.0 | 14 | 8.00 |
| 11 | 72.7 | 8 | 12.13 |
| 12 | 45.4 | 8 | 6.51 |
| 13 | 61.9 | 6 | 12.40 |
| 14 | 37.3 | 6 | 7.48 |
| 15 | 68.7 | 8 | 9.83 |
| 16 | 90.8 | 10 | 10.11 |
| 17 | 55.8 | 6 | 11.18 |
| 18 | 65.5 | 10 | 6.56 |
| 19 | 67.1 | 8 | 8.39 |
| 20 | 62.4 | 9 | 7.81 |
| Total | 1789.40 | 245 | 7.96 |
Comparison of rat genome reference map and new framework marker based map for rat HXB/BXH RI strain set. The last column shows the average between marker spacing on individual chromosomes.