African Journal of Biotechnology Vol. 9(37), pp.

6091-6095, 13 September, 2010

Available online at http://www.academicjournals.org/AJB
DOI: 10.5897/AJB10.133
ISSN 16845315 2010 Academic Journals

Full Length Research Paper

Inter simple sequence repeat (ISSR) markers as

reproducible and specific tools for genetic diversity
analysis of rose species
Z. Jabbarzadeh1*, M. Khosh-khui2, H. Salehi2 and A. Saberivand3
1

Institute of Science and Biotechnology, Urmia University, Orumieh, Iran and Department of Horticultural Science,
College of Agriculture, Shiraz University, Shiraz, Iran.
2
Department of Horticultural Science, College of Agriculture, Shiraz University, Shiraz, Iran.
3
Department of Clinical Science, College of Veterinary Medicine, Urmia University, Orumieh, Iran.
Accepted 30 April, 2010

Rose is one of the most important cultivated ornamental plants in the world. A molecular approach
using inter-simple sequence repeat (ISSR) markers was applied to seven species of Rosa. To obtain
clear and reproducible bands on 2% agarose gels, 9 ISSR primers and 5 parameters (annealing
temperature, DNA concentrations, primer concentrations, Taq DNA polymerase and MgCl2
concentrations) were screened. The resolution of six ISSR markers was performed, with optimal
annealing temperature (Ta) varying from 45 to 50C. A total of 66 DNA fragments were amplified, of
which 50 were polymorphic. The optimal conditions for ISSR system were determined as follows: MgCl 2
concentration was 2 mM, the quantity of Taq DNA polymerase 1 U, template DNA 30 ng and the
concentration of primer was 1 M and the reaction program was: initial denaturation for 5 min at 94C,
35 cycles of denaturation for 30 s at 94C, annealing for 45 s at specific annealing temperature for each
primer, extension for 2 min at 72C and a final 10 min extension at 72C.
Key words: Inter-simple sequence repeat marker, rose species, genetic diversity, optimization.
INTRODUCTION
The genus Rosa contains more than 150 species, but
only ten species have contributed to the modern commercial roses (Gudin, 2000). The genetic background of
modern roses is therefore narrow compared to the
available Rosa species (Gudin, 2000; Koopman et al.,
2008; Takeuchi et al., 2000). Genetic relationships within
the genus Rosa are confusing due to the variability of
species and the weak barriers to intraspecific hybridization

*Corresponding author. E-mail: [email protected].

Tel: +987116243978. Fax: +987112286133.
Abbreviations: ISSR, Inter-simple sequence repeat; Ta,
annealing temperature; RFLPs, restriction fragment length
polymorphism; PCR, polymerase chain reaction; RAPD,
random amplified polymorphic DNA; SSRs, simple sequence
repeats; AFLP, amplified fragment length polymorphism; Tm,
melting temperature.

(Koopman et al., 2008).

An understanding of species relationships is a
prerequisite for the effective utilization of the genetic
variation available to a breeder. The value of grouping into
sections all the known species and hybrids derived is
apparent, as the procedure simplifies the study of rose
development. There is a need to improve our understanding of the biological relationship between Rosa
species (Matsumoto et al., 1998).
The genus Rosa has been classified into four subgenera:
Hulthemia, Platyrhodon, Hesperhodos, which are monotypic or include two species and Eurosa, which contains
all the remaining species grouped into 10 sections
(Wissemann and Ritz, 2005). The classification of the
genus Rosa has presented many problems to taxonomists, as gradation between many subdivisions are slight
and in many instances, segregation is a matter of opinion
(Takeuchi et al., 2000).
Recently, as an adjunct to the morphological and

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Afr. J. Biotechnol.

physiological methods, identification tests based on

isozyme patterns have been introduced to fingerprint Rosa
species (Grossi et al., 1997; Kim and Byrne, 1996; Kuhns
and fretz, 1978), but the information derived from
isozyme markers has been limited by the number of loci
for which assays are available. Conventional detection of
restriction fragment length polymorphism (RFLPs) is
expensive, time consuming and demand probes, radiochemical and qualified personnel (Rajapakse et al.,
1995).
The commonly used polymerase chain reaction (PCR)based DNA marker systems are random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP) and more recently, simple sequence
repeats (SSRs) or microsatellites (Reddy et al., 2002).
The major limitations of these methods are low reproducibility of RAPD, high cost of amplified fragment length
polymorphism (AFLP) and the need to know the flanking
sequences to develop species specific primers for SSR
polymorphism (Belaj et al., 2003). ISSR-PCR is a
technique that overcomes most of these limitations (Wu
et al., 1994). It is rapidly being used by the research
community in various fields of plant improvement (Reddy
et al., 2002). The technique is useful in areas of genetic
diversity, phylogenetic studies, gene tagging, genome
mapping and evolutionary biology in a wide range of plant
species. ISSR markers are DNA sequences delimited by
two inverted SSR composed of the same units which are
amplified by a single PCR primer; composed of few SSR
units with or without anchored end. ISSR-PCR gives
multilocus patterns which are very reproducible, abundant
and polymorphic in plant genomes (Bornet and Branchard,
2001, 2004). The technique combines most of the
benefits of AFLP and microsatellite analysis with the
universality of RAPD (Bornet and Branchard, 2001,
2004). As a result of these advantages and their universality
and easiness of development (no need to sequence
data), ISSR markers are more and more requested.
Most of previous procedure established for ISSR-PCR
analysis in plants involved the use of radioisotope and
polyacrylamide sequencing gels (Blair et al., 1999;
Shahsavar et al., 2007). The merit of ISSR analysis
applied to this research project was its simplicity; however
the technique was applied with minimum inexpensive
agarose gels and non-radioactive detection, a deviation
from the normal practice of most studies that employ
microsatellite-based markers. In the present study,
experimental conditions for the use of ISSR in genetic
diversity analysis of rose species were explored.

DNA extraction

MATERIALS AND METHODS

Among the 9 tested primers, 3 [ISSR-3 (5 -CCA(CT)8-3 ),

ISSR-5 (5 -CCA(AG)8T-3 ) and ISSR-6 (5 -(CT)8AC-3 )]
gave no or few amplified bands between the tested species
and the rest of the primers gave rich and highly polymorphic fingerprints of which only the latter ones were
used. Consequently, a total of 66 clear and reproducible
bands were amplified from seven species using the 6

Plant materials
For this study, seven species of Rosa including: Rosa banksiae Ait.,
Rosa canina L., Rosa chinensis Jacq. Var. minima, Rosa damascena
Mill., Rosa foetida Herm, Rosa hybrida L. and Rosa moschata
Herm. were used.

Samples (fresh mature leaves 4 g) were rinsed in tap water

followed by sterilized distilled water. They were then air-dried and
stored at -80C if not used immediately. The leaves were ground in
liquid nitrogen in a sterile prechilled mortar and pestle. Extraction
buffer (120 mM Tris-HCl, pH 8.0; 80 mM EDTA pH 8.0; 4% mercaptoethanol; 2% CTAB) (at a ratio of 5 ml per gram of fresh
sample) was added to each tube, the tubes were incubated at 60C
water bath for 40 min and vortexed vigorously at 5 min interval. The
tubes were centrifuged at 8000 g for 5 min and the supernatant
discarded. 20 ml clean up buffer (120 mM Tris-HCl pH 8.0; 10 mM
EDTA pH 8.0; 2% -mercaptoethanol; 2% PVP; 1.5 M NaCl; 0.2%
CTAB) was added to each pellet and after resuspension, were
incubated at 60C water bath for 30 min with occasional inversion.
After the tubes were cooled to room temperature, 20 ml of
chloroform-isoamyl alcohol (24: 1 v/v) and 2 ml of 5 M potassium
acetate was added and the tubes were shaken vigorously to form
an emulsion. Tubes were centrifuged at 8000 g at room temperature for 20 min. After centrifugation, the aqueous phase was
transferred to a new tube and 20 ml of chloroform-isoamyl alcohol
(24: 1 v/v) were added and centrifuged. The aqueous phase
obtained after centrifugation was transferred to a new tube and 20
ml cold isopropanol with 2 ml of 3 M sodium acetate were added,
mixed and incubated at 20C for 30 min. The DNA was precipitated
by centrifuging at 8000 g at room temperature for 10 min.
Resulting pellets were washed 3 times with an equal volume of
70% ethanol and the pellets were dried and resuspended in 2 ml of
TE (Tris + ethylenediaminetetraacetic acid (EDTA)) buffer with 10 l
of RNAase and incubated at 37C for 4 h.

Primers
Primers were purchased in lyophilized form from Cinnagen Co
(Iran). 9 ISSR primers were tested in this research (Table 1).

PCR conditions and gel electrophoresis

To optimize the reaction conditions, several PCR parameters,
including DNA concentration (10, 20, 30, 40, 50 ng/reaction), primer
concentration (0.5, 1.0, 1.5, 2.0 M), MgCl2 concentration (0.5, 1.0,
1.5, 2.0, 2.5 mM) and Taq DNA polymerase (0.5, 1.0, 1.5, 2.0
unit/reaction) were tested. The optimum annealing temperature was
determined for each primer. Amplification were carried out by using
a DNA thermal cycler (Eppendorf, mastercycler gradient) programmed
as: 94C for 5 min, 35 cycles at 94C for 30 s, specific annealing
temperature for 45 s and 72C for 2 min and a final extension at
72C for 10 min. PCR products were separated using 2% agarose
gel and stained by 0.5 g/ml ethidium bromide and observed under
UV light and photographed using gel documentation unit.

RESULTS AND DISCUSSION

Influences of annealing temperatures

Jabbarzadeh et al.

6093

Table 1. The ISSR primers used to assess genetic variation among seven rose species.

No.
1
2
3
4
5
6
7
8
9

Primer
ISSR-1
ISSR-2
ISSR-3
ISSR-4
ISSR-5
ISSR-6
ISSR-7
HB11
HB15

Sequences (5-3)
5 -(AG)8YT-3
5 -(GA)8C-3
5 -CCA(CT)8-3
5 -(AC)8YT-3
5 -CCA(AG)8T-3
5 -(CT)8AC-3
5 -(GA)8ACC-3
5 -(GT)6CC-3
5 -(GTG)3GC-3

Sequences (5-3)
5 -AGAGAGAGAGAGAGAGYT-3
5 -GAGAGAGAGAGAGAGAC-3
5 -CCACTCTCTCTCTCTCTCT-3
5 -ACACACACACACACACYT-3
5 -CCAAGAGAGAGAGAGAGAGT-3
5 -CTCTCTCTCTCTCTCTAC-3
5 -GAGAGAGAGAGAGAGAACC-3
5 -GTGTGTGTGTGTCC-3
5 -GTGGTGGTGGC-3

Y = Pyrimidine.

Table 2. List of primers, their sequence motifs, melting temperatures, annealing temperatures, number of the
amplified fragments generated by ISSR primers in seven rose species.

No.

Primers

1
2
3
4
5
6
Total

ISSR-1
ISSR-2
ISSR-4
ISSR-7
HB11
HB15

5-3
motif
AG)8YT
(GA)8C
(AC)8YT
GA)8ACC
(GT)6CC
(GTG)3GC

Melting
temperature
42.3
43.3
48.3
51.5
42.6
43.5

Annealing
temperature
45
45
50
50
45
45

Number of
polymorphic bands
6
8
8
11
10
7
66

Total number of
bands amplified
8
11
10
12
15
10
50

Y = Pyrimidine.

selected ISSR primers, of which 50 were polymorphic

(Table 2).
Clear, intensive and thin bands were observed with
annealing temperatures (Ta) ranging from 45 to 50C
(Table 2). In this research, except for primer 7 whose Ta
was lower than melting temperature (Tm), in other
primers, using high stringency (Ta higher than Tm), clear
and reproducible bands were observed (Figures 1 and 2).
Modifications of annealing temperature are known to
have a great impact on the richness and legibility of
fingerprints. According to Bornet and Branchard (2001),
Ta is primer specific and always superior to Tm because
of the need of high stringency to facilitate annealing of
primers. These authors reported that Ta values for
optimal hybridization was 2 to 14C higher than Tm.
Similar results were also reported by Charters and
Wilkinson (2000). Although in many papers, unique and
low annealing temperatures have been used for ISSR
amplifications with different primers (Gilbert et al., 1999;
Sanchez de la Hoz et al., 1996), however, a low annealing
temperature may increase nonspecific amplification,
leading to artifact bands. The discrepancy in trends
toward optimal values of Ta in comparison with Tm
indicated the need of optimization. In our study, no
particular trends in optimal hybridization temperature were

found.
Influences of PCR conditions
We investigated several parameters that could affect
pattern quality and reproducibility of ISSR fingerprints.
The genomic DNA at 30 ng was found to be optimum for
PCR amplification. More spurious products were amplified
at lower concentration with low intensity and were difficult
to score. Some products that were amplified at 30 ng
were not amplified at higher concentration (50 ng). Many
studies showed that 5 500 ng template DNA could offer
an amplification result (Huang and Sun, 2000). The
optimal content of DNA used for ISSR-PCR mainly
depends on the kind of material and purity of template
DNA (Hua et al., 2006). Among the four concentration of
Taq DNA polymerase, 1 U yielded sharp and consistent
bands, whereas, other concentrations produced either
faint bands or smears. Sharpness of bands was improved
by increasing MgCl2 concentration to 2 mM. Mg2+ was an
important factor in stimulating Taq DNA polymerase,
opening double chains of prime and template DNA and
annealing temperature, so the appropriate Mg2+ concentration was essential to the ISSR (Bhatia et al., 2009; Dje

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Afr. J. Biotechnol.

3000

1000

500

100

Figure
1. ISSR-PCR
band profiles
by the primer
with the
sequence
Figure
1. ISSR-PCR
band generated
profiles generated
by ISSR-2
the primer
ISSR-2
with5 the

sequence (GA)
5 -(GA)
Lane 1:
8C-3 used in seven rose species included in this study.
8C-3 used in seven rose species included in this study.
Rosa banksiae, lane 2: Rosa canina, lane 3 Rosa chinensis, lane 4: Rosa
Lane 5:
1: Rosa
canina.,
lane 3:
Rosa
damascena, lane
Rosabanksiae,
foetida, lane
lane2:6:Rosa
Rosa
hybrida
and
lanechinensis,
7: Rosa
moschata; M: weight marker.
lane 4: Rosa damascena, lane 5: Rosa foetida, lane 6: Rosa hybrida and
lane 7: Rosa moschata and M: Weight marker.

3000

1000

500

100

Figure 2. ISSR-PCR band profiles generated by the primer ISSR-15 with the
Figure
band profiles
the primer
with
the sequence
Lane2.1:ISSR-PCR
Rosa banksiae,
lanegenerated
2: Rosa by
canina,
laneISSR-15
3: Rosa
chinensis,
lane5-4:

Rosa damascena, lane 5: Rosa foetida, lane 6: Rosa hybrida and lane 7:
(GTG)3GC -3 used in seven rose species included in this study.
Rosa moschata;
M: weight marker.
Lane 1: Rosa banksiae, lane 2: Rosa canina., lane 3: Rosa chinensis,
lane 4: Rosa damascena, lane 5: Rosa foetida, lane 6: Rosa hybrida and
lane 7:

Jabbarzadeh et al.

et al., 2006; Hua et al., 2006).

Our results show no modification of patterns when primer
concentrations were changed. Concentrations lower than
1 M per reaction produced complete fingerprints, but the
band intensity was low. The optimum concentration of
PCR components was standardized on the basis of
reproducibility of the bands after repeating the experiments
three times.
In conclusion, ISSR markers were chosen because the
technique is very simple, fast, cost effective, highly discriminative, reliable and require small quantity of sample
DNA. They also do not need any prior primer sequence
information and are non-radioactive.
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