CORDIS provides links to public deliverables and publications of HORIZON projects.
Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .
Deliverables
We have established a new genetic marker system for the rat genome based on Interspersed Repetitive Sequence (IRS)-PCR. The IRS-markers allow the large scale high-throughput characterization of genomic rat clones using robotically spotted high density arrays in a hybridization-base fashion. An IRS-marker based strategy is currently used for the assignment of large insert genomic (YAC- and PAC-) DNA clones towards the construction of a genome-wide integrated physical and genetic map for the rat. Based on the mapping data from >2000 IRS markers a physical framework map for >15 % of the rat genome is available.
Several hundred IRS-markers have been screened for polymorsphisms between 39 rat strains commonly used in biomedical research. Thus, a suitable set of IRS-markers is available for first high throughput hybridization-based scanning of multigenic rat crosses, i.e. for genetic linkage studies.
We have established a new genetic markers system for the rat (IRS-markers). About 2000 IRS-markers have been generated from individual PAC-clones and were mapped to the rat genome in a hybridization-based fashion using the rat radiation hybrid panel T55. Based on these data the two available ratiation hybrid maps for this panel were integrated. By hybridization against high density spotted YAC-clone filters about 20.000 YAC-clones were identified, covering >15 % of the rat genome.
A set of 640 markers has been screened for polymorphisms between 39 commonly used rat strains. Subsets of these markers are useful tools for high throughput screening of multigenic crosses between those strains in a hybridization-based fashion. Data about IRS-markers and IRS-marker related results are provided to the scientific community via the project homepage: (http://www.mdc-berlin.de/ratgenom/ )
Increasing attention has focussed in recent years on the rat as a model organism for genetic studies, in particular for the investigation of complex traits, but progress has been limited by the lack of availability of large-insert genomic libraries.
We have therefore constructed and characterized an arrayed yeast artificial chromosome (YAC) library for the rat genome containing approximately 40,000 clones. The estimated insert size is 736kb and the library provides a 10-fold coverage of the rat genome. Clones are arranged in high-density filters and 3-dimensional pooling schemes amenable to both hybridization and PCR-based screening approaches. Clones, pools and library filters can be purchased from The Resource Centre of the German Human Genome Project RZPD (Berlin, Germany) and Research Genetics (Huntsville, Alabama, USA).
We have constructed and characterized an arrayed yeast artificial chromosome (YAC) library for the rat genome containing approximately 40,000 clones in the ABI1380 host using the pCGS966 vector. An average size of 736kb was estimated from 166 randomly chosen clones; thus the library provides 10-fold coverage of the genome, with a 99,9% probability of containing unique sequence. The library was spotted on high-density filters to allow the identification of YAC clones by hybridization. A 3-dimensional pooling scheme was used to prepare pools of YACs amenable to PCR-based screening approaches. Clones, pools and library filters can be purchased from The Resource Centre of the German Human Genome Project RZPD (Berlin, Germany) and Research Genetics (Huntsville, Alabama, USA).
We have successfully constructed a rat PAC library from female Brown Norway (BN/ssNHsd) rat brain DNA cloned into the BamHI sites of the pPAC4 vector. Currently this library was arrayed in 614 384-well microtiter plates consisting of more than 210,000 clones and also gridded onto 22x22cm nylon high density hybridization filters for screening by probe hybridization. Each hybridization membrane represents 18,432 distinct rat PAC clones, stamped in duplicate. Primary DNA plate pools for easy PCR screening has also been developed. An average insert size of 143 kb was estimated from 202 randomly isolated clones, thus representing approximately 10-fold genome coverage and provides a 99% probability of containing a unique sequence. This library is now available to the scientific community and thus provides a new resource for rat genome analysis in particular the identification of genes involved in multifactorial disease in this species.
The construction of a 10-fold genome coverage of rat PAC library provides an important and new biological resources which will surely potentiate the discovery of new genes and SNPs (Single Nucleotide Polymorphics) for fine mapping of genetic disease loci in wide variety of rat models which are important in physiological as well as genetic studies. This new resource will prove to be an important and useful tools in translating rat disease loci into human genetic disease studies and thus provide an essential material needed for any positional cloning involving either monogenic or multifactorial disease loci.
We have established a high resolution mapping cross for the rat genome as a tool for fine mapping of genetic markers. Chromosomal loci (quantitative trait loci= QTL) harboring disease genes have been identified for a large number of rat models in genetic linkage studies. The causative disease genes within these QTL are currently in the process of being identified by positional cloning approaches requiring the dissection and characterization of the QTL regions. Therefore the generation and fine mappig of new genetic markers is required. The high resolution mapping cross offers the potential of mapping new markers with a resolution of > 0.1 cM. The availability of the rat high resolution mapping panel supports the establishment of congenic animals for the further dissection of individual QTLs and the construction of physical maps for the identification of the disease-relevant genes.
We have produced a cross between the inbred rat strains Brown Norway (BN) and the spontaneously hypertensive rat stroke-prone (SHRSP) comprising 999 (BNxSHRSP)xBN backcross offspring in total. Stocks of DNA were prepared and stored for each animal. Each DNA was genotyped for a set of 207 microsatelite markers distributed evenly over the whole rat genome (at least 5 markers per chromosome). Anchor markers are placed with an average distance of 10 cM. About 80 recombinant DNAs can be selected for intervals between two anchor markers. New markers can be placed within the marker framework with a genetic resolution of >0.1 cM. The complete set of genotyping data is stored and administrated in an oracle database. Data are made available to the scientific community via the internet. The DNAs along with the genotyping data and an in-house developed scoring and mapping tool will be provided by the Resource Center/Primary database in Berlin, Germany.
A linkage map of the rat genome integrating 1100 anonymous markers and 400 genes has been constructed. It provides an important tool for the full use of the rat as a model for genetic studies of human complex traits. This high density genetic map will help for the selection and the analysis of congenic lines to localise disease genes to small regions in the genome where candidate genes can be isolated. The inclusion of genes in this map allows the construction of comparative maps between rat, mouse and human.
The production of 1500 microsatellite markers and the construction of a high density linkage map of the rat genome represent important biological resources which facilitate the advancement of genetic studies for a wide variety of rat models characterized for complex phenotypes.
This result also led to the improvement of comparative mapping analysis which allows:
1-Translation of rat disease loci into human genetic studies.
2-Direct application of biological resources derived from the Human Genome Project to the genetics of complex disorders in models.
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