Dog genetics and whole genome mapping. UMR-CNRS 6061

dog genetics

The 10,000 Canine Gene Map

Accurate and comprehensive sequence coverage for large genomes has been restricted to only a few species of specific interest. Lower sequence coverage (survey sequenci ng) of related species can yield a wealth of information regarding gene content and putative regulatory elements. But survey sequences lack long-range continuity and provide only a fragmented view of a genome.

Here we show the utility of combining survey sequencing with dense radiation hybrid (RH) maps for extracting maximal comparative genome information from model organism s of choice. Based on results from the canine system we propose that henceforth all low pass sequencing projects be accompanied by a dense, gene-based RH map construction effort to extract max imum information from the genome with a marginal additional cost

Reference for this work : Facilitating Genome Navigation: Survey Sequencing and Dense Radiation Hybrid Gene Mapping.

Hitte et al., Nature Review Genetics, 2005, Aug 6, 643-648. [-abstract-] [-pubmed-]

Download Supplementary Information file1 (S1-to-S8) [ Supplementary1.pdf ]

Download Supplementary Information file2 (S9-to-S10) [ Supplementary2.pdf ]

METHODS :

[- The RH panel -] [- Markers Identification -] [- Map Construction -] [- Map Data : Get RH vectors ; Gene Sequences & RH Panel -]

MARKER CHARACTERISTICS :

Gene_based Markers distribution - [-all data -]

The microsatellites-containing gene screening set - [- Characteristics - sequences - primers & PCR conditions - genome localization - polymorphism content -]

Optimized marker selection : [- display -]

Query the RH map through DOG_DB : a relational MySQL database [- DOG_DB home -] [- General Query -] [- Advanced Query -]

RADIATION HYBRID MAPS & COMPARATIVE MAPPING :

Canine RH maps [ raw txt format ] :
Select a chromosome map : [- 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 X -]

Canine and Human Comparative Mapping : Display Oxford grid to represent Dog/Human conserved evolutionnary relationships : [- oxford grid -]

Canine/Human comparative mapping rearrangement figures:



Canine/Human/Mouse/Rat Comparative Mapping : Dog as master

Human as master

Mouse as master

Rat as master

RADIATION HYBRID MAPS VALIDATION :

Plots of marker order as determined by RH map and whole genome sequence assembly (WGSA) release1.0 :

Integration of the canine RH map with the whole genome sequence assembly (WGSA) release1.0 :

THE 10,000 GENE MAP RADIATION HYBRID SERVER :

A RH Server has been developped to give the possibilty of the in silico placement of markers on the 10,000 gene canine RH map : [- The CRH10K_Server -]

CANINE RH10,000-FISH-RH5,000 INTEGRATED MAPS :

Integrated map Figures :

The RH10K mapping project is a collaborative work between :

¹Pr Francis GALIBERT group at CNRS-University of Rennes1 - Rennes France - [-web site -]

^2,6Dr Elaine A. OSTRANDER group at FHCRC - Seattle USA - [- web site -]
current address : NHGRI/NIH, 50 South Drive, MSC 8000, Building 50, Room 5339, Bethesda MD 20892-8000

³Dr Ewen KIRKNESS group at TIGR - Rockeville USA [- web site -]

⁴Dr Panos DELOUKAS group from the Sanger Centre - Cambridge GB [- web site -]

⁵Dr Kerstin LINDBLAD-TOH group at the BROAD Institute of MIT&Harvard - Cambridge USA [- web site -]

SUPPORT for this work

We acknowledge the American Kennel Club Canine Health Foundation and NIH R01CA-92167 (E.A.O, E.K. and F.G.). E.A.O was supported by K05 CA90754 and is the recipient of a Burroughs Wellcome Award in Functional Genomics; F.G. is supported by the Centre National Recherche Scientifique (CNRS), the UniversitC) de Rennes, and Conseil RC)gional de Bretagne (France). Canine HQD sequence was supported by 5 K01 HG02304 from NHGRI. DT., C.S. and P.D. were supported by the Wellcome Trust.

Questions or comments, please email : christophe

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