Biological Control 49 (2009) 207–213
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Biological Control
journal homepage: www.elsevier.com/locate/ybcon
Internal transcribed spacer-2 restriction fragment length polymorphism
(ITS-2-RFLP) tool to differentiate some exotic and indigenous trichogrammatid
egg parasitoids in India
G. Ashok Kumar a, Sushil K. Jalali a,*, T. Venkatesan a, Richard Stouthamer b, P. Niranjana a, Y. Lalitha a
a
b
Insect Biotechnology Laboratory, Post Bag No. 2491, H.A. Farm Post, Bellary Road, Hebbal, Bangalore 560024, Karnataka, India
Department of Entomology, University of California, Riverside, CA, USA
a r t i c l e
i n f o
Article history:
Received 27 March 2008
Accepted 6 February 2009
Available online 20 February 2009
Keywords:
Molecular identification
ITS-2-RFLP
Trichogrammatids
Restriction enzymes
a b s t r a c t
ITS-2-RFLP method was employed to distinguish 12 different trichogrammatids consisting of indigenous
and exotic species such as Trichogrammatoidea armigera and Tr. bactrae, Trichogramma achaeae, T. chilonis,
T. japonicum, T. embryophagum, T. pretiosum (Thelytokous Form—TF), T. brassicae, T. dendrolimi, T. evanescens and T. mwanzai. ITS-2 region was amplified; complete ITS-2 sequences of nine species were deposited in Genbank. The size of the amplified product ranged from 500 to 900 bp. Restriction enzyme
digestion of ITS-2 region showed different banding profiles for these 12 species. Dichotomous keys using
the size of the ITS-2 product and the restriction fragment length polymorphism for the enzymes (EcoRI,
MseI, MvaI, and TaqI) allowed quick species identification of these trichogrammatids.
Ó 2009 Elsevier Inc. All rights reserved.
1. Introduction
The family Trichogrammatidae consists of about 650 species
(Grissel and Schauff, 1990) and is the most widely used taxon of natural enemies in various biocontrol programs worldwide. Although
about 210 species of Trichogramma are known to attack the eggs of
various crop pests (Pinto, 1998), at least 12 species are used in biological control programs. With the increasing preference for sustainable agriculture and awareness about side effects from
indiscriminate use of insecticides, biological control agents are
attracting more attention. However, with so many species, ecotypes
and strains available and very frequent exchange of culture material,
correct identification is the first step for a successful biological control program. Morphological identification of trichogrammatids remains difficult because of their minute size (<1 mm long), is time
consuming and requires specialized skills (Pinto and Stouthamer,
1994). Morphological identification of most species is based on subtle differences in male genitalia (Nagarkatti and Nagaraja, 1971,
1977). Many important species share similar genital structures, forcing workers to rely on less dependable characters that often are intra-specifically variable (Pinto et al., 1989). Given the economic
importance of trichogrammatids in biological control programs,
species identification must be quick, simple and widely applicable.
Novel approaches that used DNA sequences of the internal transcribed spacer 2 (ITS-2) helped to solve this difficulty (Stouthamer
* Corresponding author. Fax: +91 080 23411961.
E-mail address:
[email protected] (S.K. Jalali).
1049-9644/$ - see front matter Ó 2009 Elsevier Inc. All rights reserved.
doi:10.1016/j.biocontrol.2009.02.010
et al., 1999). Ribosomal RNA (rDNA) comprises of three genes 18S,
5.8S and 28S separated by internal transcribed spacers (ITS-1 and
ITS-2). ITS regions evolve faster than the regions coding for the ribosomal RNA (Hoy, 1994). The ITS region is widely used in identification studies (Hillis and Dixon, 1991). Sequence and restriction
analysis of ITS-2 region has been used to distinguish Trichogramma
species collected from tomato fields in Portugal (Silva et al., 1999).
In India, twenty six species of trichogrammatids have been recorded and among them Trichogrammatoidea armigera, Tr. bactrae,
Trichogramma achaeae, T. chilonis and T. japonicum are widely distributed and used against lepidopteran pests in several crops
(Singh and Jalali, 1994; Jalali et al., 2003). Elsewhere in the world
T. evanescens, T. dendrolimi, T. pretiosum and T. brassicae are most
frequently used in the field (Smith, 1996). Trichogramma galloi is
now extensively used as biocontrol agent in sugar cane fields of
Brazil (Parra and Zucchi, 2004). In the past decade, several exotic
species have been introduced in India to target pests such as codling moth (Cydia pomonella Linnaeus), diamondback moth (Plutella
xylostella Linnaeus), corn borer [Chilo partellus (Swinhoe)] and
American bollworm (Helicoverpa armigera Hübner) (Jalali et al.,
2003). With the introduction of these non-native trichogrammatid
species in addition to the native ones, there is a need for a quick
and reliable identification technique to identify these parasitoids.
While the identification of males of these species could be done
using morphological features, many of the specimens collected
from the field are females that are not identifiable using morphology. In the present study we develop an identification method
based on the ITS-2 sequences of the 12 most commonly used spe-
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G. Ashok Kumar et al. / Biological Control 49 (2009) 207–213
Table 1
Trichogrammatids studied, analysis performed, identity and origin of the cultures.
Line
designate
Studies
Species
Origin
Collection
year
Tra1
1,2
India
1990
Trb1
Ta1
Tj1
Tem1
Tc1
Tp1
Tev1
Tm1
Tbra1
Td1
Tbrass1
1,2
1,2,3
1,2,3
1,2,3
1,2,3
1,2,3
1,2,3
1,2,3
1,2,3
1,2,3
1,2,3
Trichogrammatoidea
armigera
Trichogrammatoidea bactrae
Trichogramma achaeae
T. japonicum
T. embryophagum
T. chilonis
T. pretiosum
T. evanescens
T. mwanzai
T. pretiosum (TF)
T. dendrolimi
T. brassicae
India
India
India
Russia
India
USA
France
Kenya
USA
Germany
USA
1990
1990
1990
1993
1990
1993
2004
2003
1993
1994
2004
1, ITS-2; 2, sequencing; 3, restriction analysis.
cies in India: Trichogrammatoidea armigera Manjunath, Tr. bactrae
Nagraja, Trichogramma achaeae Nagaraja and Nagarkatti, T. chilonis
Ishii, T. japonicum Ashmead, T. embryophagum Hartig, T. pretiosum
Riley, T. pretiosum Riley (Thelytokous form-TF), T. brassicae Bezdenko, T. dendrolimi Matsumura, T. evanescens Westwood and T.
mwanzai Schulten and Feijen.
2. Materials and methods
2.1. Parasitoid culture
We studied 12 isofemale lines identified by Dr. H. Nagaraja
as Trichogrammatoidea armigera, and Tr. bactrae, Trichogramma
Fig. 1. PCR amplified ITS-2 plus flanking regions of 5.8s and 28s rDNA from
different trichogrammatids (Lanes: M, 50 bp DNA perfect ladder (Novagen); 1, Tr.
armigera; 2, Tr. bactrae; 3, T. achaeae; 4, T. embryophagum; 5, T. japonicum; 6, T.
chilonis; 7, T. dendrolimi; 8, T. evanescens; 9, T. mwanzai; 10, T. brassicae; 11, T.
pretiosum (TF); 12, T. pretiosum).
achaeae, T. chilonis, T. japonicum (all indigenous), T. embryophagum, T. pretiosum, T. pretiosum (TF) often mistakenly referred
to as T. brasiliense Ashmead (Pinto, 1997), T. brassicae, T. dendrolimi, T. evanescens and T. mwanzai (all exotic). Voucher specimens are kept by Dr. H. Nagaraja in PDBC (Bangalore, India).
All cultures were maintained on rice moth, Corcyra cephalonica
(Stainton) eggs (killed by ultraviolet irradiation) at 26 ± 1 °C,
RH 60 ± 5%, LD 14:10. The origin of each species studied is provided in Table 1.
Fig. 2. (a) Multiple sequence alignment of ITS-2 region of group II Trichogramma species. (b) ITS-2 sequences of group III Trichogramma species (A dash indicates that the
nucleotides are absent, indicates for similar nucleotides).
G. Ashok Kumar et al. / Biological Control 49 (2009) 207–213
209
Fig. 2 (continued)
2.2. Isolation of DNA
2.3. ITS-2 PCR
DNA was extracted using chelating agent Chelex100 (5%) (Biorad). One or two wasp previously frozen at 80 °C were crushed
with a micro pestle in 20 ll of chelex. The homogenate was incubated at 56 °C for 3 h followed by 10 min at 100 °C. The supernatant was stored at 20 °C until used.
The PCR reaction was performed in 50 ll reaction volumes
using Biorad icycler, 2 ll DNA template, 5 ll (10) Taq assay
buffer, 1 ll dNTP’s (each in 10 mM concentration), 1 ll
forward and reverse primers (10 picomoles/ll), 0.25 ll taq polymerase (1 U). The primers used to amplify the ITS-2 region were
210
G. Ashok Kumar et al. / Biological Control 49 (2009) 207–213
Fig. 2 (continued)
50 -TGTGAACTGCAGGACACATG-30 (forward) and 50 -GTCTTGCCTG
CTCTGAG-30 (reverse) (Stouthamer et al., 1999). The thermal cycling condition for PCR consisted of 30 cycles (Den: 94 °C for
1 min, Ann: 55 °C for 1 min, Ext: 72 °C for 2 min, with an initial
denaturation: 95 °C for 5 min and final extension at 72 °C for
10 min). PCR products were electrophoresed on 1.8% agarose gel
(ACROS). Gels were stained using ethidium bromide. Molecular
standards were run along with the samples for reference.
2.4. Sequencing
The PCR products were gel eluted using Qiagen gel clean up kit
and direct sequenced using an Applied Prism 310. The resulting sequences were blasted against sequences in GenBank to confirm
that the sequence was indeed ITS-2.
2.5. Restriction enzyme analysis
Restriction digestion of the PCR product was performed in a 20 ll
volume (10 ll PCR product, 2 ll (10) reaction buffer, 1 ll reaction
enzyme and 7 ll distilled water). The mixture was incubated overnight at appropriate temperatures as per manufacturer’s specifications. RFLP products were analyzed by electrophoresis in 1.8%
agarose gel. 50 bp DNA perfect ladder (Novagen) was included to
estimate the size of restriction fragment. Four restriction enzymes
used were EcoRI, MseI, MvaI and TaqI (MBI Fermentos). EcoRI was
common enzyme selected for all the species and MseI to differentiate
between T. chilonis, T. dendrolimi, T. evansecens, T. mwanzai, T. brassicae and T. pretiosum. These restriction enzymes were selected using
Bioedit (Hall, 1999) restriction fragment analysis, as these were
indicative for trichogrammatids used in the study.
Table 2
Restriction sizes following digestion of PCR amplified ITS-2 plus flanking regions of 5.8s and 28s rDNA of 12 trichogrammatids with various restriction enzymes.
Species
Accession No.
Group I (800–850 bp)
Tr. armigera
Tr. bactrae
ITS-2 size
EU251072
EU251071
900 bp
800 bp
T. achaeae
T. embryophagum
EU251070
DQ344044
ITS-2 size
627 bp
592 bp
T. japonicum
DQ471294
565 bp
T. chilonis
DQ220703
ITS-2 size
538 bp
EcoRI
233 bp
305 bp
MseI
MvaI
470 bp
68 bp
T. dendrolimi
DQ344045
515 bp
T. evanescens
DQ381280
546 bp
T. mwanzai
DQ381279
500 bp
T. brassicae
DQ314611
522 bp
263 bp
252 bp
268 bp
278 bp
243 bp
257 bp
300 bp
222 bp
447 bp
68 bp
478 bp
68 bp
432 bp
68 bp
454 bp
68 bp
T. pretiosum (thelytokous form)
DQ381281
525 bp
434 bp
87 bp
454 bp
92 bp
447 bp
53 bp
412 bp
32 bp
68 bp
T. pretiosum
DQ525178
528 bp
Group II (570–620 bp)
EcoRI
229 bp
363 bp
Group III (500–550 bp)
Note: denotes no site present.
a
Only bands larger than 100 bp are listed.
457 bp
68 bp
393 bp
68 bp
63 bp
TaqIa
141 bp
129 bp
143 bp
144 bp
129 bp
305 bp
323 bp
138 bp
135 bp
129 bp
307 bp
309 bp
G. Ashok Kumar et al. / Biological Control 49 (2009) 207–213
Fig. 3. PCR amplified ITS-2 region from different trichogrammatids belonging to
Group II digested with EcoRI (lanes1–3), (Lanes: M, 50 bp DNA ladder; 1, T. achaeae;
2, T. embryophagum; 3, T. japonicum).
3. Results
3.1. ITS-2 PCR and sequencing
Based on the size of the ITS-2 rDNA PCR products, base pairs
varied from 500 to 900 bp in the 12 trichogrammatid species used
in the study (Fig. 1). Based on this size variation, three groups could
be distinguished: Group I included Tr. armigera and Tr. bactrae, in
which the size of ITS-2 product varied from 800 to 900 bp; Group
II included T. achaeae, T. embryophagum and T. japonicum in which
Fig. 4. PCR amplified ITS-2 plus flanking regions of 5.8s and 28s rDNA from
different trichogrammatids belonging to Group III digested with EcoRI (Lanes: M,
50 bp DNA ladder; 1, T. chilonis; 2, T. dendrolimi; 3, T. evanescens; 4, T. mwanzai; 5, T.
brassicae; 6, T. pretiosum (TF); 7, T. pretiosum.
211
Fig. 5. PCR amplified ITS-2 plus flanking regions of 5.8s and 28s rDNA from
different trichogrammatids belonging to Group III digested with MvaI (Lanes: M,
50 bp DNA ladder; 1, T. chilonis; 2, T. dendrolimi; 3, T. evanescens; 4, T. mwanzai; 5, T.
brassicae; 6, T. pretiosum (TF); 7, T. pretiosum.
the size of ITS-2 product varied from 570 to 630 bp and Group III
included T. brassicae, T. chilonis, T. dendrolimi, T. evanescens, T.
mwanzai, T. pretiosum, and T. pretiosum (TF), in which the size of
ITS-2 PCR products varied from 500 to 560 bp. These groups could
be easily recognized after gel electrophoresis. Complete ITS-2 sequences of different species (Fig. 2a and b) have been deposited
with NCBI Genbank (Table 2).
3.2. Restriction enzyme analysis
Restriction digestion with PCR product obtained from two wasp
for each species (Table 2) gave reproducible profiles. EcoRI showed
no sites for T. achaeae, T. japonicum, T. pretiosum (TF) and T. pretiosum (Figs. 3 and 4). MseI showed no sites for T. chilonis, T. mwanzai,
T. pretiosum (TF) and T. pretiosum (Fig. 6). Trichogrammatoidea
Fig. 6. PCR amplified ITS-2 plus flanking regions of 5.8s and 28s rDNA from
different trichogrammatids belonging to Group III digested with MseI (Lanes: M,
50 bp DNA ladder; 1, T. chilonis; 2, T. dendrolimi; 3, T. evanescens; 4, T. mwanzai; 5, T.
brassicae; 6, T. pretiosum (TF); 7, T. pretiosum).
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G. Ashok Kumar et al. / Biological Control 49 (2009) 207–213
4. Discussion
Fig. 7. PCR amplified ITS-2 plus flanking regions of 5.8s and 28s rDNA from
different trichogrammatids belonging to Group III digested with TaqI (Lanes: M,
50 bp DNA ladder; 1, T. chilonis; 2, T. dendrolimi; 3, T. evanescens; 4, T. mwanzai;
5, T. brassicae; 6, T. pretiosum (TF); 7, T. pretiosum).
Table 3
Dichotomous key to differentiate the 12 Trichogramma species based on PCR product
of the ITS-2 region plus flanking regions of the 5.8S and 28S rDNA and restriction
analysis with various restriction enzymes.
1
2
3
4
5
6
7
8
9
10
Size of the PCR product larger than 700 bp
Size of the PCR product smaller than 700 bp
Size of the PCR product 850 bp
Size of the PCR product 800 bp
Size of the PCR product larger than 560 bp
Size of the PCR product smaller than 560 bp
PCR product restricted with EcoRI results in two bands
PCR product restricted with EcoRI results in a single band
Size of PCR product larger than 600 bp
Size of the PCR product 600 bp
PCR product restricted with MseI results in a single band
>500 bp
PCR product restricted with MseI results at least one band
<500 bp
PCR product restricted with EcoRI results in two bands
(240, 300 bp)
PCR product restricted with EcoRI results in a single band
PCR product restricted with EcoRI results in two bands
clearly different in size
PCR product restricted with EcoRI results in two bands very
similar in size often only visible as a single band
Size of the band 275 bp
Size of the band 250 bp
PCR product restricted with TaqI results in largest band of
>300 bp
PCR product restricted with TaqI in largest product of
<150 bp
2
3
Tr. armigera
Tr. bactrae
4
6
T.
embryophagum
5
T. achaeae
T. japonicum
7
8
T. chilonis
T. pretiosum
T. brassicae
9
T. evanescens
10
T. mwanzai
T. dendrolimi
The ITS-2-RFLP tool was able to differentiate the 12 Trichogramma species used in this study. Length variation was observed in the
ITS-2 region and it clearly separated the two genera, i.e., Trichogramma and Trichogrammatoidea from each other. Such length variation in the ITS region has been reported before (Orrego and
Agudelo-Silva, 1993; Sappal et al., 1995). Using the length variation
and the RFLP patterns we were able to construct a dichotomous
key (Table 3). Studies on ITS-2-RFLP analysis to identify Trichogramma species have been limited to particular geographical regions (Silva et al., 1999; Ciociola et al., 2001; Thompson et al.,
2003) or particular crops over a wide area (Pinto et al., 2002). This
is one of the first attempts to differentiate some indigenous and
exotic species involved in various biological control programmes
in India. The intra-specific variability in both total ITS-2 length
and restriction fragments length appears to be low within the
two genera studied, as was found earlier in the analysis of ITS-2 sequences of some North American species (Stouthamer et al., 1999).
PCR–RFLP analysis is very simple, fast and reliable. PCR–RFLP tool
has been used in detection and species identification of fungal
pathogen and nematodes (Dendis et al., 2003; Roberta et al., 2003).
The restriction pattern shown for the MvaI digestion of the
arrhenotokous form shows that the ITS-2 for this species is polymorphic for the MvaI site, so within individuals of the arrhenotokous T. pretiosum two different ITS-2 families exist one with the
restriction site and one without that site. This is visible in the gel
because for the arrhenotokous population two bands are visible a
larger band of the same size as the thelytokous form and a smaller
band only found in the arrhenotokous form. Slight variation within
individuals is commonly found in Trichogramma wasps, for instance Trichogramma kaykai has a similar polymorphism for an
EcoRI site (Stouthamer et al., 1999). The differentiation using MvaI
between the arrhenotokous and thelytokous form of T. pretiosum
works for these particular populations that have been imported
to India. However, other arrhenotokous populations of T. pretiosum
originating from Brazil and some from Riverside, California also
show the same pattern as the arrhenotokous form shown here
(see for instance GenBank Accession Nos. AF082820, AY187261).
These methods are intended to replace the traditional morphological methods when large number of individuals need to be identified that belong to a known group of trichogrammatids. For
instance, for checking laboratory contamination or the fate of released species in the field. These DNA based methods are faster, because no mounting of the specimens is required, and allows
identification of both females and males. Application of the DNA
based methods should free up time for systematists to identify
and describe new species. From the present study it can be concluded that rDNA markers and restriction enzyme patterns can
be used for reliable differentiation between two genera and also
between various indigenous and exotic species to be field evaluated in India.
Acknowledgments
armigera and Tr. bactrae belonging to genus Trichogrammatoidea
could be easily differentiated after amplification of ITS-2 region.
Restriction digestion with EcoRI enzyme enabled differentiation
of 10 species, while restriction digestion with MseI enabled differentiation of six species. MvaI enzyme (Fig. 5) proved useful to differentiate T. pretiosum (TF) from T. pretiosum. Cleavage activity of
TaqI (Fig. 7) enzyme aided in discrimination of T. dendrolimi and
T. mwanzai. Based on restriction patterns, a dichotomous key was
constructed for easy differentiation of these 12 trichogrammatids
(Table 3).
We thank Dr. R.J. Rabindra, Project Director, Project Directorate
of Biological Control, Bangalore for his keen interest in the study
and Ms. R. Rajeshwari for valuable technical assistance.
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