Comparative mapping of 18 equine type I genes assigned by somatic
cell hybrid analysis
Alexandre R. Caetano,
James D. Murray,
Ann T. Bowling
University of California-Davis, Veterinary Genetics Laboratory, Davis, California 95616-8744, USA
University of Nebraska-Lincoln, Department of Animal Science, Lincoln, Nebraska 68583-0908, USA
University of California-Davis, Animal Science Department, Davis, California 95616-8744, USA
University of California-Davis, Department of Population Health and Reproduction, Davis, California 95616-8744, USA
Received: 24 July 1998 / Accepted: 29 October 1998
Abstract. Polymerase chain reaction primers designed from horse
cDNA sequences and from consensus sequences highly conserved
in mammalian species were used to amplify markers for synteny
mapping 18 equine type I genes. These markers were used to
screen a horse–mouse somatic cell hybrid panel (UCDavis SCH).
Fourteen primer sets amplified horse-specific fragments, while re-
striction enzyme digests of PCR products were used to distinguish
the fragments amplified from horse and mouse with four primer
sets. Synteny assignments were made based on correlation values
between each marker tested and other markers in the UCDavis
SCH panel database. The 18 horse genes were assigned to previ-
ously established synteny groups. Synteny mapping of two genes
previously mapped in the horse by FISH was used to anchor two
UCD synteny groups to horse chromosomes. Previous chromo-
some assignments of three equine loci by FISH were confirmed.
Comparative mapping analysis based on published human–horse
Zoo-FISH data and the synteny mapping of 14 horse genes con-
firmed the physical assignment of 12 synteny groups to the re-
spective horse chromosomes and was used to infer the physical
location of one synteny group.
Technical and conceptual innovations made in recent years have
opened new frontiers and potential applications for plant and ani-
mal genomic research. Great progress has been made in the de-
velopment of gene maps of species directly or indirectly important
to agriculture and animal husbandry (Archibald et al. 1995; Bishop
et al. 1994; Echard et al. 1994; Postlethwait et al. 1998). This work
has led to the identification of genome regions containing genes
responsible for genetic diseases and genes involved in the expres-
sion of quantitative traits in humans and in other organisms
(Andersson et al. 1994).
The identification of chromosomal regions containing genes of
interest is, however, far from being the ultimate step in under-
standing the actions and control mechanisms of specific genes.
These goals can be fully accomplished only with gene transfer and
expression studies. The current strategies elaborated to identify
and isolate desired genes (that is, ‘positional cloning’ and the
‘candidate gene approach’) demand highly developed genome
maps, densely packed with type I and II loci (O’Brien et al. 1993),
which are presently available for only a few model organisms.
These circumstances leave economically important agricultural
species on the search for alternative strategies for finding and
isolating genes that may impact each particular industry.
The idea that orthologous genes show linkage conservation in
related species is not new, dating to Haldane (1927). By compiling
mapping information from different species, comparative maps are
being constructed to help unveil reorganizations accumulated dur-
ing the independent evolution of related genomes (Wakefield and
Graves 1996; O’Brien et al. 1997). In addition, heterologous chro-
mosome painting studies (Zoo-FISH) are being used to reveal
synteny blocks conserved across species (Chowdhary et al. 1996;
Fronicke et al. 1996). Comparative mapping information ulti-
mately provides a means for the use of data from densely mapped
genomes in genetic studies of species with underdeveloped maps.
The lack of mapping information in a species can, therefore, be
partially overcome by the identification of conserved candidate
genome regions containing genes that have been well character-
ized in more thoroughly studied species (humans and mice, in the
case of mammals).
The genome map of the domestic horse (Equus caballus)is
poorly developed in comparison with other domestic livestock
species, such as cattle, pig, and sheep. The majority of the current
mapping data for the horse was attained by establishing syntenic
relationships between molecular markers with the use of somatic
cell hybrid (SCH) panels, with Williams et al. (1993) and Bailey et
al. (1995) identifying three and five synteny groups, respectively.
Shiue and co-workers (1999) identified 33 horse synteny groups
by characterizing a horse-mouse SCH panel (UCDavis SCH) with
240 PCR-based molecular markers (182 microsatellites and 58
RAPDs). Recently, considerable effort has been made to physi-
cally map markers to horse metaphase chromosomes with FISH
(for example, Breen et al. 1997; Godard et al. 1997, 1998) and the
first low-resolution, microsatellite-based linkage map of the horse
has been published (Lindgren et al. 1998). The first step toward
establishing a comprehensive comparative map of the horse ge-
nome was taken by Raudsepp et al. (1996), who performed human
whole chromosome paintings on the horse karyotype, revealing
that a minimum of 20 breaks, followed by the appropriate rear-
rangements, is sufficient to reconstruct the horse karyotype relative
to the human karyotype.
This report presents the assignment of 18 equine type I genes
by analysis of the UCDavis SCH panel. These data were used to
anchor previously established synteny groups onto horse chromo-
somes, test the synteny conservation between humans and horses
proposed by Zoo-FISH experiments, and increase the gene content
of the horse map.
Materials and methods
The sequences and references for the PCR prim-
ers used to amplify the loci mapped in this study are shown in Table 1.
Primer sets for ESR, DNAPK, DRA, GH, HYPP, and IGF2 were designed
based on horse cDNA sequences for these genes published in GenBank,
Correspondence to: A.T. Bowling
Mammalian Genome 10, 271–276 (1999).
© Springer-Verlag New York Inc. 1999