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Molecular and morphological diversity of Rhizoctonia bataticola causing dry root rot disease from India.

Dry root rot of different agriculturally important crops viz. Black gram, Chick Pea, Cotton, Cowpea, Jute, Mungbean, Onion, Pea, Rice, Soybean, Spinach and Wheat etc. is caused by Rhizoctonia bataticola (Taub.) Butler in different parts of world including India 36. The perfect stage of R. bataticola is Thanatephorus cucumeris (Frank.) Donk. It also produces pycnidia and this stage is known as Macrophomina phaseolina (Maubl.) Ashby. R. bataticoa is very diversified and cosmopolitan soil borne fungus, producing different types of symptoms viz., blight, rot, wilt and decay (15). The hyphae are septate and 1.5-2.5 pm thick, and produce black and irregular sclerotia up to 100 [micro]m in diam. resembles charcoal powder.

A number of workers have carried out a series of comprehensive studies with reference to its incidence, etiology and genetic variability (41,42,2,27).They found that isolates of R. bataticola are very diverse in nature with high phenotypic, pathogenic and genetic variation and even differences may occur in the different isolates from a single host. A high level variation in the sclerotial morphology of R. bataticola was reported by no. of workers (32,39).

PCR based molecular marker techniques were used to determine and evaluate the genetic diversity among different isolates of M. phaseoliona (21). Genetic variability within the population was varied with the type of the marker (28). Restriction Fragment Length Polymorphism (RFLP) of rDNA-ITSregions (2). Random Amplified Polymorphic DNA (1,2,44), Amplified Fragment Length Polymorphism(AFLP) (9,35) Universal Rice Primer PCR (URP-PCR) (18) Inter simple sequence repeats (ISSR), (17,30,21) Repetitive Sequence-Based Polymerase Chain Reaction (Rep-PCR) (30) and Simple Sequence Repeats (SSR) (6) were explored extensively to determine the variation of different isolates of R. bataticola mostly from single host plant. Of these techniques, RAPD is simple, low cost and requires small amount of material. Inter simple sequence repeat (ISSR) markers are powerful tools to reveal the variation in genome microsatellite regions. Both RAPD and ISSR markers have been successfully used to differentiate and identify many fungi (44,21).

The objective of present investigation was to study the morphological and genetic variability among the different isolates of R. bataticola obtained from geographically distinct regions (10 states) over a range of 19 host plant species using RAPD and ISSR markers.


Collection of R. bataticola isolates

Twenty five isolates taken under consideration from different places and sources were collected from Indian Type Culture Collection (ITCC), Division of Plant Pathology, IARI, New Delhi (Table 1, Fig. 1). All the 25 isolates were taken for the morphological characterization and for variability studies using RAPD and ISSR markers.

Morphological Identification of R. bataticola

The phenotypic characteristics of Rhizoctonia isolates were investigated based on sclerotial morphology.

Genomic DNA Extraction

Genomic DNA was extracted from frozen mycelium of R. bataticola based on Cetyltrimethyl ammonium bromide (CTAB) mini extraction method. (12)

The DNA concentration and purity of the samples was determined with Nano Drop Spectrophotometer (Thermo Scientific).

Identification of R. bataticola isolates using species-specific primers:

The specific primers MpKFI (5'-CCGCCAGAGGACTATCAAAC-3') and MpKRI (5'-CGTCCGAAGCGAGGTGTATT-3') (4) were used during the course of this study for amplification of the isolates using PCR. Controls included DNA of isolates of Trichoderma harzianum, Colletotrichum gloeosporioides, Fusarium oxysporum and Chaetomium globosum.

PCR protocol was standardized varying the cycle number, annealing temperature and the concentration of target DNA. The optimized protocol is described here; PCR amplifications were performed in a total volume of 20pl by mixing 2 [micro]l of 10X Taq buffer, 0.5 [micro]ldNTPs (100Mm dNTPs Mix), 5 pmol of each primer(0.5 [micro]l), 1 U (0.3 [micro]l) of Taq DNA polymerase, 0.5 [micro]l of 50 mMMg[Cl.sub.2] and 35-50 ng of template DNA(2 [micro]l). The PCR reaction was carried out for 25 cycles of denaturation at 95[degrees]C for 30 s, followed by annealing at 56[degrees]C for 1 min, extension at 72[degrees]C for 2 min. and the final extension step of 72[degrees]C for 10 min.

Variability among the different isolates of R. bataticola using different RAPD Markers

DNA from 25 isolates was subjected to genetic diversity analysis by the RAPD method using 10 randomly chosen 10-base random primers. Among them six primers were chosen for further studies (Table 3). PCR reactions were carried out in 0.2 ml thin-walled PCR tubes with a total reaction volume of 25 [micro]l containing 2.5 1/Al of 10X buffer, 2.5mM of each dNTPs (0.5 1/4l), 11/Al of primer, 0.5 1/4 l MgCl2 (25mM) and 1U (0.21/4l) of Taq polymerase (Bangalore, Genei). The PCR amplification conditions were initial denaturation at 94[degrees]C for 3 min followed by 40 cycles of denaturation at 94[degrees]C for 1 min, primer annealing at 35[degrees]C for 1 min, primer extension at 72[degrees]C for 2 min, and a final primer extension at 72[degrees]C for 5 min. Six primers of RAPD were selected for final analysis based on informative banding patterns, clarity, and repeatability.

Variability among the different isolates of R. bataticola using different ISSR Markers

ISSR analysis was carried out amplifying the genomic DNA using six ISSR primers. Among them five primers were chosen for further studies (Table 3).The PCR amplification conditions were: Initial denaturation at 95[degrees]C for 5 min followed by 40 cycles of denaturation at 94[degrees]C for 1 min, primer annealing at 34[degrees]C for 1 min, primer extension at 72[degrees]C for 1 min, and a final primer extension at 72[degrees]C for 5 min. A total of six primers were screened initially. Five primers were selected for final analysis based on informative banding patterns, clarity, and repeatability.

Statistical analysis

RAPD and ISSR reproducible fragments were scored as present (1) or absent (0), and bands were entered in a computer file as a binary matrix, one for each molecular marker. The binary matrix was analyzed using the NTSYS-pc (Numerical Taxonomy and Multivariate Analysis System) package, version 2.0 to calculate the similarity values. After obtaining the similarity matrix, clustering was performed by sequential agglomerative hierarchical nested clustering (SAHN). The graphical representation of the cluster was obtained by using the unweighted pair group method of mathematical averages (UPGMA). Bootstrap analysis of the data was performed with 1000 replications using the WINBOOT program to estimate structural stability of clusters. Polymorphic information content (PIC) or average heterozygosity was calculated as per the formula of. (34) Average heterozygosity (Hav) is obtained by taking the average of PIC values obtained for all the markers. Multiplex ratio (MR) for each assay was estimated by dividing the total number of bands (monomorphic and polymorphic) amplified by the total number of assays. Marker index (MI) was obtained by multiplying the average heterozygosity (Hav) with MR. (28) A principal coordinate analysis (PCO) was performed EIGEN procedure in the NTSYSpc in order to highlight the resolving power of the ordination. To estimate the congruence among dendrograms, cophenetic matrices for each marker type were computed and compared using the Mantel matrix correspondence test. This test was performed using the MXCOMP procedure in the NTSYSpc.


The present research was undertaken to study the sclerotial and genetic variability among the different isolates of R. bataticola obtained from geographically distinct regions (10 states) infecting 19 different crop plants. All the isolates were divided into four different groups based on their high level variation in sclerotial shape, size and arrangement. RAPD and ISSR markers were used to estimate the genetic variability. ISSR markers were found more efficient than RAPD markers to correlate the genetic diversity with the grouping of isolates according to the geographical regions.But RAPD markers were found efficient to differentiate R. bataticola isolates into different clusters according to their sclerotial morphology.

Morphological Identification

Morphological features of 25 isolates of R. bataticola were observed by growing the isolates on PDA medium. Sclerotial morphology was considered to assess the possible variation among different isolates.

Variability in Sclerotial morphology

Among the isolates, the size of sclerotia ranged from 29.4-100 X 21.1-52.9 1/4 m. Based on sclerotial shape, size and arrangements, the isolates were divided into four different groups (Table 2). The observations were made under the compound microscope and pictures were taken for further documentation (Fig. 2).

Molecular identification of R. bataticola based on species specific marker

Molecular characters of 25 isolates of R. bataticola were analyzed in order to resolve their identification based on species specific marker. The primers used yielded single amplified product of 350 bp with all the R. bataticola isolates tested (Fig. 3). The specificity of the primers was tested on representative species of common soil borne microbes like Trichoderma harzianum, Colletotrichum gloeosporioides, Fusarium oxysporum and Chaetomium globosum. The primer pair was found to be specific for R. bataticola as none of the other soil microbes tested could yield any amplification product under identical conditions of amplification.

RAPD Analysis of R. bataticola

A total of 238 bands were produced for Rhizoctonia isolates and all of them were found to be polymorphic. Maximum number (59) bands were obtained with OPA-11, followed by OPE-14 (45 bands), OPO-4 (41), OPN-4 (35), OPN-20 (30), OPS-18 (26) and all of them were polymorphic (Table 3). The size of the fragments varied from 0.4 to 2.5kb. The data obtained from RAPD analysis of 25 isolates of Rhizoctonia species with six primers was subjected to UPGMA analysis. A dendrogram was prepared using the similarity coefficient of RAPD marker. The dendrogram showed the presence of differences among R. bataticola isolates.

As per Fig. 4, one isolate (No. 1) of R. bataticola was not grouped. Rest all the isolates were grouped into four clusters.

The dendrogram obtained separated R. bataticola isolates (No. 2 and 15) completely from all other isolates and revealed more than 75 percent similarity among themselves. These isolates were characterized based on their sclerotial morphology which were large and highly connected. Isolate (Nos.14,16,17,18,20,21,22,23,24,25) were having large, round to irregular and free sclerotia separated from all other isolates and show 72-94% similarity.

Similarly isolate 8 and 13 were characterized as the isolates having small, round and free sclerotia and also clustered together with 73% similarity. Isolates nos. 3,4,5,6,7,10,11 and 12 were clearly visualized in the same cluster with almost 63-84% similarity as these isolates having large, irregular and loosely connected sclerotia. Isolate 1 was not grouped with any other cluster based on RAPD analyses even though it has similar sclerotia later isolates.

This dendrogram revealed the presence of the variability among the different isolates by separating based on their sclerotial morphology.

ISSR Analysis of R. bataticola

A total of 250 bands were produced for Rhizoctonia isolates and all of them were found to be polymorphic. Maximum number (53) of bands were obtained with ISSR-1 and ISSR-2, followed by ISSR-3 (49 bands), ISSR-4 (46), ISSR-6 (49) and allof them were polymorphic (Table 3). The size of the fragments varied from 0.7 to 2.5kb. The data obtained from RAPD analysis of 25 isolates of R. bataticola with five primers was subjected to UPGMA analysis. A dendrogram was prepared using the similarity coefficient of ISSR marker. The dendrogram showed the presence of differences among R. bataticola isolates.

Isolates formed two main clusters with all the five primers tested (Fig. 5). ISSR primers were able to separate the R. bataticola isolates into 8 clusters (Table 4) on the basis from where they were collected. Cluster I consists the isolates of Kalyani (1, 12, 23) and Tezpur (22); Cluster II consists the isolates of Hyderabad(2), New Delhi (5) and Coimbatore (15); Cluster III consists the isolates of Agra (3), Aligarh (8) and New Delhi (7, 10, 16); Cluster IV consists the isolates of New Delhi (13, 14, 19); Cluster V consists the isolates of Navasari (4), Junagadh (6) and Jaipur (9); Cluster VI consists the isolates of Jobner (11), Junagadh (18) and Bikaner (20); Cluster VII consists the isolates of Jammu (17, 21); Cluster VIII consists the isolates of Almora (24) and Lucknow (25) and only Delhi Isolate (No. 5) was not cluster with other isolates of same origin. ISSR markers were found a much more efficient tool to differentiate variability among the different isolates of Rhizoctonia.


Rhizoctonia bataticola is a non-host specific fungus causing dry root rot disease in a wide range of hosts and is responsible for causing losses in many number of cultivated and wild plant species. (22,20) R. bataticola was reported on highly economic hosts viz., cotton, rice, maize, cucurbits, okra, and wheat (24,36) Physiological specialization of the fungus is not well demonstrated (14) and reported a high level of variation in morphology, physiology and pathogenesis among different isolates obtained from different parts of the same plant.

Therefore, morphological and molecular variability were assessed in the present study. Twenty five isolates were collected from different host plants growing in different parts of the country. These isolates were characterized and grouped by their sclerotial morphology. All the isolates from Jute, Pea, Soybean, Chick Pea, Cotton, Balsam, Onion, black gram, Cowpea, Spinach, Wheat, Rice, Castor, Anola, Strawberry, Mungbean, burning bush and Sarpgandha were found variable in the shape and size of sclerotia. The size of the sclerotia was 29.4-100 X 21.1-52.9 [micro]m in the present study. The biggest sclerotia reported was 101.51 [micro]m in Gliri-cidia isolate ofR. bataticola while cowpea isolate produced the smallest sclerotia (66.88 [micro]m) (10) whereas (25) reported the size varied from 58.83 [micro]m to 126.63 [micro]m. (29) also reported the morphological variability in R. bataticola collected from different pulse crops. Therefore, it is clear that variability exists in sclerotial morphology.

These morphologically characterized 25 isolates of R. bataticola were also assessed at their molecular level. PCR-RAPD analysis is one of the simplest tools available for the analysis of genetic differences at DNA level without demanding any prior information about the genomic sequences.

Molecular markers are useful tools for assessing variation rapidly within and among species (11) In this study, we have compared two different molecular marker systems, RAPD and ISSR, to define genetic relationships among isolates of R. bataticola, and to investigate which marker system can be more effectively used. In RAPD, a total of 238 bands were produced for R. bataticola isolates and all of them were found to be polymorphic. Maximum number (59) of bands were obtained with OPA-11 and all of them were polymorphic. The size of the fragments varied from 0.4 to 2.5kb. The higher level of polymorphism detected by RAPD markers revealed the selective capacity of this marker among R. bataticola isolates. (40) In the present study, the variability based on PCR-RAPD was coinciding with the groups made based on sclerotial morphology.

The ISSR markers were successfully used to identify genetic differences in R. bataticola (17). The results of the present study clearly demonstrated that R. bataticola from different parts of the country were highly variable and ISSR markers are suitable to reflect the genetic diversity among the isolates. A high level of polymorphism in R. bataticola was found in the isolates collected from different hosts and regions using different molecular tools (3,19,23,43) Many number of workers demonstrated the genetic diversity among M. phaseolina isolates (1,2,5,6,7,17,18,26,30,31,33,35). The high genetic diversity was observed not only in isolates from distinct hosts and geographical origins but also in isolates collected from a single host or single region.

The number of alleles at a locus and their frequency of distribution are responsible for Polymorphism thereby genetic variation in a population (28). RAPD and ISSR markers target different portions of the genome resulted the difference in discrimination among the isolates. (21) The genetic variation usually depends on the number of polymorphic bands obtained with each marker. (8)

It was the first study that investigated genetic relationships among different isolates of R. bataticola from different host plants from India and also that compared two PCR-markers to define genetic relationships among isolates of R. bataticola.


The authors thank the Head. Division of Plant Pathology. Indian Agricultural Research Institute. New Delhi for the help in various aspects of this study. Financial support from Indian Council of Agricultural Research. Govt. of India. is gratefully acknowledged.


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T. Prameela Devi [1], Deeba Kamil [1], Ravi Mehndiratta [2], N. Prabhakaran [1] and R. Sudeep Toppo [1]

[1] Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi--110 012, India.

[2] Amity Institute of Biotechnology, Amity University Haryana, Amity Education Valley, Gurgaon--122 413, Haryana, India.

(Received: 16 July 2016; accepted: 20 September 2016)

* To whom all correspondence should be addressed. E-mail:

Caption: Fig. 1. Map * of India showing sampling regions of Rhizoctoniabataticola isolates

Caption: Fig. 2. Grouping of R. bataticolaisolates based on their sclerotial morphology

Caption: Fig. 3. Identification of R. bataticola with species specific primers. 1-25: R. bataticola isolates; 26: Trichodermaharzianum; 27:Colletotrichumgloeosporioides; 28: Fusariumoxysporum; 29: Chaetomiumglobosum.

Caption: Fig. 4. Dendrogram constructed with UPGMA clustering method based on Random Amplified Polymorphic DNA (RAPD)-PCR for 25 isolates of R. bataticolafrom different geographical areas of India.

Caption: Fig. 5. Dendrogram constructed with UPGMA clustering method based on Inter-Simple Sequence Repeat (ISSR) markers for 25 isolates of R. bataticola from different geographical areas of India
Table 1. Sources and location of different R.
bataticola isolates

S. No   ITCC * Number      Source              Location

1           1568            Jute         Kalyani, West Bengal
2           2474            Soil       Hyderabad, Andhra Pradesh
3           5196          Pea Seed        Agra, Uttar Pradesh
4           6037          Soybean          Navasari, Gujarat
5           6375         Chick Pea         New Delhi, Delhi
6           5519        Cotton root        Junagadh, Gujarat
7            249          Soybean          New Delhi, Delhi
8           5510           Balsam       Aligarh, Uttar Pradesh
9           5128           Onion           Jaipur, Rajasthan
10           250         black gram            New Delhi
11          4253        Cowpea Seed        Jobner, Rajasthan
12          1567          Soybean        Kalyani, West Bengal
13          6184          Spinach          New Delhi, Delhi
14          2204           Wheat           New Delhi, Delhi
15           652            Rice        Coimbatore, Tamil Nadu
16          5141            Soil           New Delhi, Delhi
17           481            Rice         Jammu, Jammu &Kashmir
18          5521        Castor root        Junagadh, Gujarat
19          2577           Balsam          New Delhi, Delhi
20          6267           Anola          Bikaner, Rajasthan
21          6256         Strawberry      Jammu, Jammu &Kashmir
22          3546          Mungbean           Tezpur, Assam
23          1569        Burning bush     Kalyani, West Bengal
24          5467            Rice          Almora, Uttarakhand
25          5499         Sarpgandha     Lucknow, Uttar Pradesh

* Indian Type Culture Collection

Table 2. Variability in Sclerotial morphology in
different R. bataticolaisolates

Groups   Isolates                   Description of Sclerotia

I        2 and 15                   Highly irregular and are
                                    connected by thick walled
                                    mycelium, 52.2 -73.6 X
                                    42.1-52.6 [micro]m in size

II       14, 16, 17, 18, 19, 20,    Round to irregular and free,
         21,22, 23, 24 and 25       36.2-99.8 X 21.1- 47.4 [micro]m in

III      8 and 13                   Round and free, 29.4-52.9 [micro]m
                                    in size

IV       1, 3, 4, 5, 6, 7, 9, 10,   Round to irregular and
         11 and 12                  are connected by thin
                                    mycelium, 42.1-100 X 31.6-
                                    52.6 [micro]m in size

Table 3. List of Random Amplified Polymorphic DNA (RAPD)
and Inter-Simple Sequence Repeat (ISSR) primers and the
resulted DNA polymorphisms applied to differentiate isolates
of R. bataticola

Primers   Primer sequence (5'-3')      Total   Polymorphic
                                       Bands      Bands

Selected RAPD primers

OPA-11    5'-CAATCGCCGT-3'              59         59
OPN-20    5'-GGTGCTCCGT-3'              32         32
OPE-14    5'-TGCGGCTGAG-3'              45         45
OPO-4     5'-AAGTCCGCTC-3'              41         41
OPN-4     5'-GACCGACCCA-3'              35         35
OPS-18    5'-CTGGCGAACT-3'              26         26
Total     238                           238        --

Selected ISSR primers

ISSR-1    5'-GAGAGAGAGAGAGAGAGAT-3'     53         53
ISSR-2    5'-ACTGACTGACTGACTG-3'        53         53
ISSR-3    5'-GAGAGAGAGAGAGAGAGAAT-3'    49         49
ISSR-4    5'-ACCACCACCACCY-3'           46         46
ISSR-6    5'-GATAGATAGATAGATA-3'        49         49
Total     250                           250        --

Primers   Polymorphic   Monomorphic
          Percentage       Bands

Selected RAPD primers

OPA-11        100            0
OPN-20        100            0
OPE-14        100            0
OPO-4         100            0
OPN-4         100            0
OPS-18        100            0
Total          0

Selected ISSR primers

ISSR-1        100            0
ISSR-2        100            0
ISSR-3        100            0
ISSR-4        100            0
ISSR-6        100            0
Total          0

OPA--Operon Series A primer, OPN--Operon Series N
primer, OPE--Operon Series E primer, OPO--Operon Series O
primer, OPS--Operon Series S primer

Table 4. Different groups of R. bataticola
isolates based on Inter-Simple Sequence Repeat
(ISSR)-PCR analysis was found to coincided with
their place of origin

Group     Source of Collection        Isolate       Similarity
Numbers                               Numbers       Coefficient

I         Kalyani and Tezpur          1,12,22,23    0.5-06
II        Hyderabad, New Delhi        2,5,15        0.55
            and Coimbatore
III       Agra, New Delhi, Aligarh,   3,7,8,10,16   0.65
IV        New Delhi                   13,19,14      0.55
V         Navasari, Junagadh,Jaipur   4,6,9         0.55
VI        Jobner, Bikaner, Junagadh   11,20,18      0.55
VII       Jammu                       17,21         0.5-0.6
VIII      Almora, Lucknow             24,25         0.5-0.6
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Author:Devi, T. Prameela; Kamil, Deeba; Mehndiratta, Ravi; Prabhakaran, N.; Toppo, R. Sudeep
Publication:Journal of Pure and Applied Microbiology
Article Type:Report
Date:Dec 1, 2016
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