High-density rat radiation hybrid maps containing over 24,000 SSLPs, genes, and ESTs provide a direct link to the rat genome sequence.
The laboratory rat is a major model organism for systems biology. To complement the cornucopia of physiological and pharmacological data generated in the rat, a large genomic toolset has been developed, culminating in the release of the rat draft genome sequence. The rat draft sequence used a variety of assembly packages, as well as data from the Radiation Hybrid (RH) map of the rat as part of their validation. As part of the Rat Genome Project, we have been building a high-density RH map to facilitate data integration from multiple maps and now to help validate the genome assembly. By incorporating vectors from our lab and several other labs, we have doubled the number of simple sequence length polymorphisms (SSLPs), genes, expressed sequence tags (ESTs), and sequence-tagged sites (STSs) compared to any other genome-wide rat map, a total of 24,437 elements. During the process, we also identified a novel approach for integrating the RH placement results from multiple maps. This new integrated RH map contains approximately 10 RH-mapped elements per Mb on the genome assembly, enabling the RH maps to serve as a scaffold for a variety of data visualization tools.
Kwitek
Anne E
AE
Human & Molecular Genetics Center and Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA. akwitek@mcw.edu
Gullings-Handley
Jo
J
Yu
Jiaming
J
Carlos
Danilo C
DC
Orlebeke
Kimberly
K
Nie
Jeff
J
Eckert
Jeffrey
J
Lemke
Angela
A
Andrae
Jaime Wendt
JW
Bromberg
Susan
S
Pasko
Dean
D
Chen
Dan
D
Scheetz
Todd E
TE
Casavant
Thomas L
TL
Soares
M Bento
MB
Sheffield
Val C
VC
Tonellato
Peter J
PJ
Jacob
Howard J
HJ
D000818:Animals; D002874:Chromosome Mapping / Q000379:methods; D002875:Chromosomes / Q000235:genetics; D003433:Crosses, Genetic; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D005796:Genes / Q000235:genetics*; D005819:Genetic Markers / Q000235:genetics / Q000502:physiology; D016678:Genome; D008126:Lod Score; D011110:Polymorphism, Genetic / Q000235:genetics*; D021101:Radiation Hybrid Mapping / Q000379:methods*; D051381:Rats; D011912:Rats, Inbred ACI; D011914:Rats, Inbred BN; D020334:Rats, Inbred OLETF; D011918:Rats, Inbred SHR; D012091:Repetitive Sequences, Nucleic Acid; D016324:Sequence Tagged Sites
D005819:Genetic Markers