Radiation hybrid mapping of 70 rat genes from a data set of
differentially expressed genes
Caroline A. Wallace,
Anne M. Glazier,
Penny J. Norsworthy,
Danilo C. Carlos,
Tom C. Freeman,
Lawrence W. Stanton,
Anne E. Kwitek,
Timothy J. Aitman
Physiological Genomics and Medicine Group, MRC Clinical Sciences Centre, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
Medical College of Wisconsin, Department of Physiology, Human and Molecular Genetics Center, Milwaukee, Wisconsin 53226, USA
Genomic and Molecular Medicine Group, MRC Clinical Sciences Centre and Imperial College Genetics and Genomics Research Institute,
Hammersmith Hospital, London W12 0NN, UK
MRC UK HGMP Resource Centre, Genome Campus, Huxton, Cambridge CB10 15B, UK
Scios Inc., Sunnyvale, California 94086, USA
Received: 1 November 2001 / Accepted: 9 January 2002
Abstract. The spontaneously hypertensive rat (SHR) is a model
of human essential hypertension. Increased blood pressure in SHR
is associated with other risk factors associated with cardiovascular
disease, including insulin resistance and dyslipidemia. DNA mi-
croarray studies identified over 200 differentially expressed genes
and ESTs between SHR and normotensive control rats. These
clones represent candidate genes that may underlie previously de-
tected QTLs in SHR. This study made use of the publication of two
whole-genome maps to identify positional QTL candidates. Ra-
diation hybrid (RH) mapping was used to determine the chromo-
somal locations of 70 rat genes and ESTs from this dataset. Most
of the locations are novel, but in five cases we identified a defini-
tive map location for genes previously mapped by somatic cell
hybrids and/or linkage analysis. Genes for which the mouse ge-
nome map location was already determined mapped to syntenic
segments in the rat genome map, except for two rat genes whose
map locations confirmed previous findings. Where synteny com-
parisons could be made only with the human, 74% of the genes
mapped in this study lay in a conserved syntenic segment. Chro-
mosomal localisation of these mouse and human orthologs to syn-
tenic segments produces a high level of confidence in the data
presented in this study. The data provide new map locations for rat
genes and will aid efforts to advance the rat genome map. The data
may also be used to prioritize candidate QTL genes in SHR and
other rat strains on the basis of their map location.
The rat is an important model organism for physiological and
pharmacological research, but until recently the mouse has been
the preferred model for studies of polygenic diseases (James and
Lindpainter 1997; Jacob 1999). The previous paucity of rat ge-
nome maps has been addressed, in part, by the publication of three
whole-genome RH framework maps of the rat (Steen et al. 1999;
Watanabe et al. 1999; Scheetz et al. 2001), which provide a means
to integrate genetic and physical maps (Bihoreau et al. 2001).
These framework maps can be used in the identification of posi-
tional candidate genes for known QTLs in disease models and will
also be of use in assembling a rat framework genome sequence
(Marshall 2001). Additionally, the maps allow comparative analy-
sis between the rat, human, and mouse genomes (Watanabe et al.
1999; Kwitek et al. 2001).
RH mapping provides a rapid and convenient method for or-
dering DNA markers at a resolution that cannot be obtained using
other mapping methods (Cox et al. 1990; Burmeister et al. 1991).
A major advantage of RH mapping is that it allows the use of
non-polymorphic DNA markers that cannot be used in meiotic
mapping in inbred rat strains.
The spontaneously hypertensive rat (SHR) is the most widely
studied model of human essential hypertension (Yamori 1984). As
in many humans with essential hypertension, increased blood pres-
sure in this rat strain is associated with other risk factors for car-
diovascular disease, including insulin resistance and dyslipidemia
(Reaven et al. 1989; Aitman et al. 1997). The genetic mechanisms
that mediate this clustering of risk factors remain poorly under-
DNA microarray studies implicated Cd36 as the gene under-
lying the SHR Chromosome (Chr) 4 QTL for insulin resistance
and identified over 200 other genes and ESTs that are apparently
differentially expressed between SHR and insulin-sensitive con-
trols (Aitman et al. 1999). Some of these genes may underlie other
QTLs previously identified in SHR for, amongst others, insulin
resistance, blood pressure, and cardiac mass.
In this study, RH mapping has been used to map 70 rat genes
and ESTs from a data set of differentially expressed genes in SHR.
These data will contribute to development of the rat gene map and
may also be used to prioritize candidate QTL genes in SHR and
other rat strains on the basis of their chromosomal locations.
Materials and methods
A set of genes, differentially expressed between SHR/
NCr1BR (Charles River, UK) and a normotensive Brown Norway (BN)
control strain, BN/SsNOlaHsd (Harlan, UK), was identified by DNA mi-
croarray analysis (Aitman et al. 1999).
The identity of the differentially expressed genes was
determined by sequencing and BLAST searches. 38% of clones were iden-
tified as known rat genes or rat ESTs, and 43% were similar to genes and
ESTs from other species. The remaining clones were either not signifi-
cantly homologous to any other sequence in the GenBank database or
remained unsequenced. Redundant GenBank entries were eliminated by
searching the UniGene database (http://www.ncbi.nlm.nih.gov/UniGene).
For clones that were identified as known rat genes or rat ESTs, primers
were generally designed to the 3Ј untranslated region (UTR) of the pub-
lished sequence, to increase the likelihood of differences between rat and
hamster PCR products; or to the coding region if there was limited se-
quence availability. For clone sequences that were homologous to known
genes or ESTs from other species or could not be identified, primers were
designed directly to the determined sequence, which for most clones was
at the 3Ј end of the gene. Primers were synthesized by Genset (Sunderland,
UK) and Sigma Genosys (Cambridge, UK). Primer sequences are available
on our website (http://www.csc.mrc.ac.uk/PhysGenMed/RHdata.html).
Correspondence to: C.A. Wallace; E-mail: caroline.wallace@
Mammalian Genome 13, 194–197 (2002).
© Springer-Verlag New York Inc. 2002
Incorporating Mouse Genome