1022-7954/01/3703- $25.00 © 2001
Russian Journal of Genetics, Vol. 37, No. 3, 2001, pp. 276–282. Translated from Genetika, Vol. 37, No. 3, 2001, pp. 358–364.
Original Russian Text Copyright © 2001 by Larkin, Kuznetsov, Astakhova, Zhdanova.
Using polymerase chain reaction (PCR) for map-
ping of mammalian genomes promoted saturation of
genomic maps by markers of various types. PCR mark-
ers signiﬁcantly exceed biochemical markers and
cloned genomic or cDNA sequences with regard to the
number of localized markers. This is explained by the
fact that technically PCR is much simpler than DNA–
DNA hybridization or protein analysis. Moreover,
development of consensus primers and partially degen-
erate primers made PCR an indispensable tool of com-
parative genome mapping.
Markers used for successful mapping with interspe-
ciﬁc somatic cell hybrids should be relatively con-
served, on one hand, and possessing interspeciﬁc poly-
morphism, on the other. This type of markers was pro-
posed for comparative mapping in different species of
mammals. According to O’Brien , they were termed
type 1 markers.
Hypervariable, repeated genomic sequences, e.g.,
microsatellites, were assigned to markers of type 2.
These markers are species-speciﬁc and used mainly for
genetic mapping. According to Sun and Kirkpatrick
, the efﬁciency of type 2 markers in comparative
mapping is about 7.5%.
To increase the efﬁciency of comparing maps of dif-
ferent species, a set of type 1 markers consisting of 321
evolutionary conserved genes was proposed [1, 3]. Cri-
teria of molecular homology and homology of biologi-
cal or biochemical functions were suggested to use for
conﬁrming gene homology.
It has been recently shown that PCR with primers
selected for gene ampliﬁcation in a particular species in
some cases can be used for ampliﬁcation of homeolo-
gous sequence in other species . This method of
detecting interspeciﬁc polymorphism is a convenient
and rapid technique for developing genomic maps in
insufﬁciently mapped species since theoretically it pro-
vides a possibility to map virtually in any species any
gene whose nucleotide sequence is known at least in
two remote species.
Consensus PCR primers for a number of conserved
loci were constructed. Different strategies were pro-
posed for optimal ampliﬁcation of homeologous
sequences using heterologous primers. This led to the
construction of several sets of heterologous primers.
Using them in various species should promote mapping
of homeologous sequences and facilitate comparisons
of genomic maps since it opens a possibility of map-
ping the same set of genes (including those belonging
to the type 1 markers) in different species.
CATS (Comparative Tagged Sequences).
primers are homologous to conserved exon sequences
but they can also amplify introns . Because of this, it
is possible to amplify required genes and detect inter-
speciﬁc polymorphism within the length of ampliﬁca-
Testing 321 pairs of CATS primers in 20 members
of 11 orders showed that 32 to 35% of these pairs
ampliﬁed a single product without additional optimiza-
tion of ampliﬁcation conditions. This indicates that in
the case of additional optimization, about 75% of
CATS may be successfully used in various species of
TOAST (Traced Orthologous Ampliﬁed Sequence
In this case, genes with sequences known in
more than two species were selected for creating prim-
ers. After aligning of sequences of several species,
primers amplifying either an exon or an intron with part
of ﬂanking exons were developed. If DNA sequences
completely homologous in several species could not be
found, several primer pairs accounting for nucleotide
replacements in each species were constructed. In all,
225 primer pairs for 146 genes were created. Out of
these, 68.9, 80.9, 56.0, and 36.4% produced a single
product in ampliﬁcation of genomic DNA of human,
pig, dog, and Chinese hamster, respectively .
EST (Expressed Tagged Sites).
These markers are
widely used for developing high-resolution maps of the
Using PCR Markers for Mapping Pig Chromosome 12
D. M. Larkin, S. B. Kuznetsov, N. M. Astakhova, N. S. Zhdanova
Institute of Cytology and Genetics, Russian Academy of Sciences, Novosibirsk, 630090 Russia;
fax: (3832) 33-12-78; e-mail: email@example.com
Received July 18, 2000
—Using PCR analysis of pig–mink and pig–Chinese hamster hybrid cell lines and heterologous and
homologous primers of various types, chromosomal and subchromosomal mapping of genes
BRCA1, GAS, HLR1, MYL4, LIS1, MCP1, ENO3, CRYB1, P4HB, STAT5B
to pig chromosome 12
was carried out. The efﬁciency of using different types of heterologous primers for pig chromosome mapping