1022-7954/05/4104- © 2005 Pleiades Publishing, Inc.
Russian Journal of Genetics, Vol. 41, No. 4, 2005, pp. 378–388. Translated from Genetika, Vol. 41, No. 4, 2005, pp. 480–492.
Original Russian Text Copyright © 2005 by Gostimsky, Kokaeva, Konovalov.
Genomes of higher plants are characterized by large
sizes and complex organization. The use of molecular
methods of DNA analysis is one of approaches to
studying these complex genomes. Molecular markers
are currently most often used for these purposes.
Molecular DNA markers are polymorphic nucleotide
sequences dispersed over the genome whose mutations
may be detected by PCR-based techniques.
The introduction of molecular markers into biologi-
cal studies offered new possibilities for studying
genetic diversity and determining genetic relationships
within and between species.
The use of molecular DNA markers is very promising
for detailed chromosome mapping, identifying and clon-
ing genes, and constructing new plant cultivars. Variants
of DNA ampliﬁcation with arbitrary and speciﬁc primers
allowing the rapid detection of numerous variable loci
throughout the plant genome are widely used.
METHODS OF DNA ANALYSIS
The random ampliﬁed polymorphic DNA (RAPD)
method [1, 2] is one of the most widely used
approaches for revealing genetic polymorphism in
plants. This method is based on polymerase chain reac-
tion (PCR) with arbitrary single primers nine to ten
nitrous bases in length with a predominantly G/C com-
position (60–80%) and relatively low annealing tem-
peratures. Usually, RAPD primers yield three to ﬁfteen
ampliﬁcation products . The DNA regions ampliﬁed
by the RAPD method are scattered over the genome;
most of them are repetitive nucleotide sequences .
This method has the advantage of technical simplic-
ity and rapidness. It requires neither information on the
DNA sequence nor large initial amounts of DNA [4, 5].
The method does not use radioactive substances, is
inexpensive, and can be automated .
Beginning from 1994, PCR-based inter simple
sequence repeat (ISSR) analysis  has been used in
molecular marking. Oligonucleotide primers used in
PCR consist of repetitive units and the so-called anchor
at the 3' or 5' end. The ampliﬁed DNA fragments are
located within a relatively small region between two
microsatellite sequences. The repetitive units comprise
one to ﬁve nucleotide pairs. The method does not
require preliminary information on the DNA sequence
analyzed [7, 8]. The PCR using ISSR primers yields a
set of intermicrosatellite DNA fragments of various
lengths. The ISSR analysis has as high a resolution as
the RAPD method while ensuring better reproducibility
of the spectrum (since the primer is longer and comple-
mentary to the microsatellite region). The method is
promising for genomic mapping and marking agricul-
turally important characters [9–11].
Sequence characterized ampliﬁed region (SCAR)
markers  are PCR-based molecular markers origi-
nating from individual RAPD fragments but identiﬁed
with the use of long, speciﬁc primers.
Studying Plant Genome Variation
Using Molecular Markers
S. A. Gostimsky, Z. G. Kokaeva, and F. A. Konovalov
Department of Genetics, Biological Faculty, Moscow State University, Moscow, 119899 Russia;
fax: (095) 939-43-09; e-mail: firstname.lastname@example.org; www.msu.pisumsativum.org
Received November 10, 2004
—The authors’ studies on the organization and variation of plant genome with the use of molecular
markers are brieﬂy reviewed with special emphasis on random ampliﬁed polymorphic DNA (RAPD), inter sim-
ple sequence repeat (ISSR), sequence characterized ampliﬁed region (SCAR), and cleaved ampliﬁed polymor-
phic sequence (CAPS) markers detected with the use of polymerase chain reaction (PCR). These markers have
been demonstrated to be promising for identifying cultivars and determining the purity of genetic strains of pea.
Genetic relationships between strains, cultivars, and mutants of pea have been studied. The role of molecular
markers in molecular genetic mapping and localizing the genes of commercially important characters of pea
has been shown. The possibility of the use of molecular markers for studying somaclonal variation and detect-
ing mutagenic factors in plants during long-term spaceﬂights is considered. The prospects of using DNA mark-
ers for understanding the organization and variability of higher plant genomes are discussed.