I. Mycology

DNA Barcoding

Potential DNA barcode regions for the identification of Fusarium spp. (tef-1+ND6; 540bp)) and Trichoderma spp.(β-tubulin; 500bp), Phoma spp. (SSU), Bipolarisspp. (ITS) have been identified.


Technique for production of Silver Nano particles by T. harzianum, T. virens, T. asperellumand T. longibrachiatum was developed.

Trichodermawere screened fortheproductionof extracellular silvernanoparticles. The fungal filtrates were subjected to 1 mMsilver nitrate solution.  After incubation of 120 hours, showed   brown colour in the culture filtrate which is an indication ofsilver nanoparticle production.Further, these two isolates were analyzed by Transmission Electron Microscopy (TEM) and the silver nanoparticles were in the range of 1-70 nm. 


New Fungi described and new records
Five new genera and 11 new species were described from ITCC. 



New Genera Described

Botryodeorsum indicum

Prameela, Nita Mathur,

Fecundostilbum sacchari       

Prameela and Chowdhry

Polyrostrata indica

Prameela and Nita Mathur

Proliferosphaera capsici        

Prameela and Nita Mathur 

Capillosclerotium indicum

Prameela, Deeba and Nita Mathur


New Species Described

 Phomopsis vateria

Prameela and Chowdhry sp.nov.


Chowdhry  and  Prameela sp.nov.

Meliola leuceii

Prameela and Chowdhry sp.nov.


Prameela and Chowdhry sp.nov.


Chowdhry  and  Prameela sp.nov.

Appendiculella anacardii

Prameela and Chowdhry sp.nov.


Prameela and Chowdhry sp.nov.


Prameela and Chowdhry sp.nov.

Xylochia oryzae

Prameela and Chowdhry sp.nov.

Pestalotiopsis anacardii

Deeba and prameela sp. nov

Pestalotiopsis termitarii

Deeba and prameela sp. nov                 


I. Bacteriology

Race scenario

  • Determined the recent race status of Xoo from north-west and eastern parts of India; identified that race 4 is the most virulent and predominant among the six races.
  • Biovar grouping of 154 isolates of R. solanacearum: 95% isolates belonged to biovar 3 and only 4.5% were biovar  4. All the isolates from potato, tomato, chilli, capsicum and brinjal belong to race 1 and phylotype 1.
  • Determined the presence of 3 races of X. campestris pv. campestris, race 1, race 4 and race 6 in India.





Host-pathogen interaction

  • First time demonstrated the total composition of type III effectors of Xop family in Indian strains of Xanthomonas oryzae pv. oryzae race 4 and in X. axonopodis pv. punicae infecting rice and pomegranate, respectively.
  • Elucidated the possible role of XopN-T3SS effector secreted by Xap in suppressing PTI- response to induce blight in pomegranate.


  • Studies on gene expression changes in Arabidopsis thaliana upon bacterial colonization by microarray analysis :Many defense related genes like AtRLP22, WRKY33, AtRLP19, anac036, TIR, PDF1.4, ATL2, ATEXO70B2, pEARLI, AtMC2, RPS2, LUG, NHL3, CBP60G,PLA2A,WAKL2 were found to be up regulated upon plant colonization by Pseudomonas putida BP25R. Many of the genes participating in the developmental processes, transport of nutrient thru transmembranes, transcription, cell organization and biogenesis, protein metabolism, growth regulating factors were found to be down regulated. Some of these are ACO1 (participate in ethylene biosynthesis); AtGRF5, MEE23, MEE3, OFP2, iqd21 (involved in developmental processes); AtbZIP3, HAT3, HSFB4, MYB28, NRPB6A, ZFHD1, ZFP3 (transcription related genes); GDU1, NRT1.5, SLAH1 (play role in transport mechanisms). Bacillus megaterium triggered up-regulated genes included genes related to nutrient uptake, growth, development (like NIR1; involved in nitrite assimilation, AMT 1; 3 involved in ammonium transport, SULTR1; 2 involved in sulfate uptake, SHV3; involved in root hair cell differentiation and root hair elongation) and also stress tolerance genes (like SRO5, ANNAt7, DDF1) which enhance tolerance to some abiotic stresses like salt stress, water deprivation etc. some genes involved in response to salicylic acid and jasmonic acid were also up regulated.

Genetic diversity

  • Determined the phylogeny of Xapstrains using multiple loci viz. 16S rRNA, gyrB, T3SS-effector genes and established its close linkage with X.  citri subsp. malvacearum.
  • Fingerprint analysis of 152 isolates of R. solanacearum using BOX and REP-PCR revealed 5 major and two minor clusters.
  • Multilocus sequence typing of 18 tomato isolates of R. solanacearum based on 4 housekeeping genes (gdhA, adk, gapA, ppsA) and 3 virulence genes (Flic, hrp, egl) indicated that isolates of Uttarakhand were grouped in all the clades whereas Jharkhand isolates clustered clade 1 only.
  • Rep PCR-based genetic diversity analysis involving 217 isolates of X. campestris pv. campestris revealed that all the isolates were grouped into 56 DNA types at 75 % similarity coefficient. However, there was no correlation found between races and genetic diversity.


  • Developed and commercialized a specific PCR based detection kit for pomegranate bacterial blight using gyrB gene.
  • Developed detection protocol for Ralstonia solanacearum from asymptomatic tomato, soil and irrigation water using hrp gene (323 bp).


Emerging disease scenario

  • Etiology of new bacterial diseases, bacterial panicle blight caused by Burkholderia glumae (Figure 3), leaf blight of rice caused by Pantoea ananatis, fruit blotch of mango and fruit rot of tinda caused by Pseudomonas aeruginosa were established.

Disease management

    • Minimum bacterial wilt (R. solanacearum) incidence was found in bleaching powder (0.01%) + Bacillustreatment in both cultivars Arka Abha (19.0%) and Pusa Rubi (29.6 %).
    • Investigated the antibacterial properties of nanocopper against Xap. A patent filed on“Nanocopper”-a novel formulation to combat bacterial blight of pomegranate, rice and bean.
    • Pseudomonas putida BP25R and Bacillus megaterium BP17R were found to colonize black pepper, ginger and model plant Arabidopsis thaliana. Pseudomonas putida BP25R caused a tuft root phenotype in plants whereas Bacillus megaterium BP17 enhanced the plant growth. The Volatile Organic Compounds (VOCs released during the growth of Pseudomonas putida BP25or Bacillus megaterium BP17 were found to inhibit broad range of pathogens such as Pythium myriotylum, Phytophthora capsici, Gibberella moniliformis, Rhizoctonia solani, Athelia rolfsii, and Colletotrichum gloeosporioides.GC-MS analysis of VOCs revealed several novel metabolites with diverse functions. The activity screening conducted in vitro clearly revealed that seven of them, Dimethyl trisulfide; 2-Ethyl-3, 6-dimethylpyrazine; 2-ethyl-3-methyl- Pyrazine; 2-ethyl-5-methyl- Pyrazine; 2-ethyl- Pyrazine; 2, 5-Dimethyl Pyrazine and 2-methyl- Pyrazine were highly effective in inhibiting Oomycete pathogen Phytopthora capsici, Ralstonia solanacearum and Magnaporthe oryzae

Fungal Pathology

The ‘Puccinia Path’ shows the dispersal route of stem, yellow and leaf rusts and plan for gene deployment

The strategic research for identification of different races of pathogens and deployment of rust resistant genotypes have saved wheat losses to extent of 6.8 mt worth Rs 104 billion annually.



Trichoderma and Chaetomium based bioformulations:

  • Pusa 5SD- a bio-formulation of Trichodermaharzianum (IARI P- 4; MTCC No. 5371) for seed treatment
  • PusaBiopellet 10G- a bio-formulation of Trichodermaharzianum (IARI P-4; MTCC No. 5371) for soil application.
  • Formulations are effective against chickpea wilt and dry and wet root rot of mungbean

Validation of Chaetomium based bioformulation
Aformulated product from C. globosum (Pusa Cg2WP), foundeffective against late blight of potato during 2009-10, tested again during 2010-11 at CPRI Regional Station, Modipuram. Three sprays of the  bioformulation were found effective in controlling the disease up to 30% and increasing the yield up to 10 per cent.

Virulence analysis

Five pathotype of Bipolaris Sorokiniana have been identified in India. Melanin and toxin production is correlated with virulence.

F. fujikuroi, F. proliferatum and F. verticillioides were isolated and identified associated with bakane disease of rice. However F. fujikuroi only could produce typical elongation symptom of the disease. F. fujikuroi is the highly prevalent pathogen associated with bakanae disease of rice in India.

Rice genesPi54, Pita2, Pizt, Pi9, Piz, Piz5 and Pi12 (t) are effective against Magnaporthe oryzae isolates of Basmati rice growing regions.

Virulence of 70 isolates of Fusariumoxysporum f. sp. ciceriswas tested on a new set of 10 differential cultivars of chickpea, which categorized them in to eight races out of them race four was predominant. Eight races of F.O.C have been identified in India on a new set of differential hosts.



Molecular characterization
Bipolaris sorokiniana
Based on URP-PCR analysis, the isolates of Bipolarissorokiniana clustered according to the geographic origin.Interspecific variation in Bipolarisspp. obtained through ITS region was relatively low.

Wheat rust pathotypes
Seven predominant wheat rust pathotypes  pt- 77-5, 104-2 and 12-2 (leaf rust),  pgt 40A and 40-1 (stem rust) and pst-78S84 and 46S119 (stripe rust) were characterized using RAPD and URP markers showed 91.87 and 90.11% polymorphism resepectively. RAPD markers differentiated all the three rusts pathotypes, while URP markers differentiated Puccinia striiformispathotypes from pathotypes of P. triticina and P. graministritici.

Fusarium fujikuroi
Fusariumfujikuroiisolates characterized for variability using URP markers showed that isolatesfrom Haryana are more variable.

Fusarium oxysporum f.sp. ciceris (FOC)
Genetic diversity in FOC isolates originating from 13 locations assessed by comparing translation elongation factor-1α (TEF-IX, 720bp), β tubulin (500bp) and internal transcribed spacer (ITS) region (550bp), suggested that these regions are highly conserved showing 95-100% identity. 


Development and validation of specific markers for detection of pathogens
Bipolaris sorokiniana
A PCR based SCAR marker RABS600was developed and validated for detection of Bipolarissorokiniana. The marker was able to detect the fungus at 50pg pure fungal genomic DNA concentration. The marker could detect the pathogen in planta at pre-symptomatic stage and also in infested soil.

Puccinia striiformis
A specific PCR-based marker developed for detection of Pucciniastriiformistriticiwhich can detect Pstupto 10pg by conventional PCR and10fg by qPCR.

Rhizoctonia solani
Specific primers have been designed for R. solani which can detect the fungus at 24 h and 6 h post-inoculation under field and in vitro condition respectively. The detection limit for R. solani 0.025 ng by conventional PCR and 1 pg by qPCR analysis.

Fusariumoxysporum f. sp. ciceris
Two sets of sequence characterized amplified region (SCAR) markers are developed for detection of F. oxysporumf. sp. ciceris. Real time PCR assay based on β-tubulin gene (B125 F1 & R1) and IGS region (ISR 52 F1& R1) has been developed for detection of F. oxysporum f. sp. ciceris.

Alternaria brassicicola
A PCR based assay has been developed for the identification of A. brassicicola infected seeds using primers derived from conserved ITS regions. The sensitivity limist for detection (100pg).

Trichoderma spp.
Genus specific marker for Trichoderma, species specific markers were developed for T. harzianum, T. virens, T. asperellum and T. longibrachiatum for individual and simultaneous detection using multiplex PCR. SCAR marker for the identification of Aspergillus flavus was developed.

Multiplex PCR  developed for simultaneous detection of different Trichoderma spp.


SCAR marker developed for identification of Aspergillus flavus



Host pathogen interaction
A cDNA library prepared fifteen significant defense related genes identified in Chiriya-7 in response to Bipolarissorokiniana infection and four mitogen activated protein kinases (TaMAPK2, TaMAPK1, TaFLRS and TaDSPK) characterized by cloning, sequencing and RT-PCR analysis. The gene sequences submitted in NCBI database.

Complete genome characterization of eleven viruses and partial genome characterization of seven viruses were done.

Complete genomes characterized


Name of the virus


Genome size


Citrus trizteza virus




Indian citrus ring spot virus




Banana streak MY virus, Banana streak OL virus


 7.8 kb, 6.9 kb


Large cardamom foorkey virus


9 components (~ 1kb)


Potato virus X


6.5 kb


Potato virus Y


10 kb


Cucumber mosaic virus


 8 kb


Sweet potato leaf curl virus


2.7 kb


Cotton leaf curl virus


2.7 kb ( 4 isolates)


Frangipani mosaic virus


6.6 kb


Unfolded the aetiology of Chirke and Foorkey diseases of large cardamom

Foorkey disease
Polymerase chain reaction (PCR) and rolling circle amplification (RCA) were employed and six distinct full-length DNA components encoding putative master-Rep (M-Rep), satellite-Rep (sRep) and coat protein (CP), three DNAs of unknown function (FU1, FU2 and FU3) and a partial DNA component encoding putative nuclear shuttle protein (NSP) were cloned and sequenced. Rep, sRep and CP components shared maximum sequence similarities (58.7-78.3 %) and phylogenetic affinity with that of Banana bunchy top virus and Abaca bunchy top virus in the genus Babuvirus and a distant relationship with the members in the genus Nanovirus under family Nanoviridae. This provides evidence of a new member, large cardamom foorkey virus under the genus Babuvirus and family Nanoviridae

Chirke disease
The 3¢ terminal genome sequence containing partial NIb, complete capsid protein gene and 3¢ untranslated region of the virus associated with the chirke disease of large cardamom revealed identity of a new virus species named, Large cardamom chirke virus (LCCV) under the genus  Macluravirus, family Potyviridae. The virus is most closely related  to Cardamom mosaic virus causing katte disease of small cardamom cultivated in the southern India, while the other close relatives were Alpinia mosaic virus andChinese yam necrotic mosaic virus. Chirke disease was known to affect large cardamom for over 50 years, the partial genome sequence helped determine the etiology of the chirke disease.

Identification of viruses associated with leaf roll disease of grapevine in India

More than fourty viruses are known to infect grapevine worldwide compromising the quality of fruits and wine.There was no report of viruses infecting grapevine in India. During the period of 2012-13 grapevine samples collected from Nasik, Maharashtra were analysed for the presence of viruses. Based on ELISA and RT-PCR Grapevine leaf roll associated virus -1, Grapevine leaf roll associated virus -3,Grapevine leaf roll associated virus - 4-9 and GFkV were identified in the samples.





Antiserum production by bacterial expressed viral coat protein

In many cases it is difficult to obtain a purified virus preparation which is required for antiserum production by traditional methods. Instead the antigenic protein, most often the virus coat protein expressed  in-vitro can be used for antiserum production. Antiserum was produced against  nine plant viruses using recombinant approaches – Large cardamom chirke virus, Cardamom bushy dwarf virus, Grapevine leaf roll associated virus 3, Banan streak MY virus, Bean common mosaic virus, Garlic common latent virus, Lettuce mosaic virus, Rice tungro spherical virus, Peanut mottle virus.  The specificity of the antisera was tested using SDS-PAGE and western blot. Protocols for detection of specific viruses by ELISA and DIBA were standardized.

Cocktail antisera for the detection of three different viruses

Core coat protein of   three viruses Cucumber mosaic vi rus, Papaya ring spot virus, andGroundnut bud necrosis virus were expressed as fusion protein. Rabbits were immunized with the fusion protein. Antisera generates can detect all three viruses in a single assay. This will help in multiple virus detection and overcome the limitation of individual protein expression, purification and use of multiple rabbits.  Useful for field samples where mixed infections are common.

Lateral flow assay based dipsticks for on-farm detection of plant viruses

Plant virus diagnostics generally involves multiple steps and specialized laboratory processes, which do not allow on-the-spot diagnosis and make it difficult for a common man to use it. One step lateral flow assays have been developed for on-farm detection and identificationfor four virusesvizLarge cardamom chirke virus, Cardamom bushy dwarf virus, Potato virus Y and Papya ring spot virus. These can detect the presence of viruses within fifteen minutes.


Multiplex PCR for detection of plant viruses

Multiplex PCR is a variant of PCR in which two or more viruses can be simultaneously detected in the same.Multiplex PCR was standardized for detection of six RNA viruses infecting potato namely PVX, PVY, PVS, PVM, PLRV and PVA. Multiplex PCR was also standardized for the detection of Poty, Carla a nd Alexiviruses in Garlic.


Plant virus detection Microarray

A microarray was developed for detection of all plant viruses and viroidsfor which sequences were available. 1572 probe sets for detection of viruses&viroids totaling to 17292 unique probes on chip. Each probe set is highly specific for virus or viroid and contain 7-11 probes. Both RNA & DNA viruses can be detected. Several viruses and viroids were detected using this chip from different crops like grapevine, chilli, tomato, sugarcane etc. Some of these viruses were already known to occur in India while some were not recorded earlier in the country.


New viruses and viroids detected


Grapevine virus F, Grapevine leafroll-associated virus 3, Grapevine rupestris stem pitting-associated virus, Hop stunt viroid , Australian grapevine viroid, Grapevine yellow speckle viroid 1, and Grapevine yellow speckle viroid 2


Pepper cryptic virus and a fabavirus  were detected along with  other 5 viruses




Infectious clones developed
Tomato leaf curl New Delhi virus, Tomato leaf curl Palampur virus, Croton yellow mosaic virus, Banana streak virus, Potato virus X etc
Virus based vectors developed
Potato virus X, Cucumber green mottle mosaic virus
Engineering resistance against biotic stresses affecting horticultural and field crops

  1. Attempt made to develop resistance to Tomato leaf curl New Delhi virus using microRNA derived construct
  2.  Ascertained the role of NSs (Non structural protein) as a suppressor of RNA silencing from Groundnutbudnecrosisvirus (GBNV)
  3.  Attempted Agrobacterium mediated transformation of Citrus using Coat protein gene construct
  4.  Identified pathogenesis related genes (effector genes, 5) of Xanthomonasoryzaepv. Oryzae
  5.  Cloned and sequenced endopolygalactourinase gene (1058 bp) from Rhizoctoniasolani causing sheath blight in rice

Attempts at IARI for transgenic resistance against viruses


Resistance against

Research Centre

Horticultural crops
1. Banana
2. Citrus
3. Cucurbits
4. Potato
5. Tomato


BBTV, wilt
PVY, PALCV, late blight


IARI, NRC Banana
IARI, South campus (DU)

Field Crops
1. Groundnut
2.  Soybean




Artificial micro RNA induced resistance against leaf curl
Artificial micro RNA based construct amiRAV1 exhibited transformation efficiencies of 68% and 62% in tobacco and tomato (Pusa Early Dwarf), respectively. 63% of amiRAV1 derived tomato transformants showed no symptoms, suggesting that the transgenic plants were resistant.

 Technologies Commercialized

Technology commercialized


Viral gene construct ( truncatedreplicase gene of Tomato leaf curl virus ) for developing transgenic tomato resistant to Tomato leaf curl virus.

M/s BejoSheetal Seeds Pvt. Ltd., Jalna,

Primary transgenic tomato resistant to leaf curl and Groundnut bud necrosis virus.

Advanta India Ltd. Hyderabad

RNAi based viral gene construct (artificial micro RNA based) for developing transgenic tomato for leaf curl resistance.

M/s BejoSheetal Seeds Pvt. Ltd., Jalna,