Jiban Kumar Kundu

• Ph.D.
• Group Leader at Czech Agrifood Research Center (Crop Research Institute)

Background Celosia argentea is a widely recognized plant for its ornamental qualities and therapeutic uses in traditional medicine. As demand for such multipurpose plants grows, enhancing its phenotypic and physiological traits could further expand its commercial potential. Polyploidization, particularly through chemical treatments like oryzalin, o...

Autophagy, an intracellular degradation process, has emerged as a crucial innate immune response against various plant pathogens, including viruses. Tomato spotted wilt orthotospovirus (TSWV) is a highly destructive plant pathogen that infects over 1000 plant species and poses a significant threat to global food security. However, the role of autop...

Myzus persicae and Brevicoryne brassicae are the main aphid pests and vectors of viruses that attack many crops, including oilseed rape, the most commonly grown dicotyledonous crop in the Czech Republic. In this study, we analysed the flight activity of both aphids from five suction traps over 20 years (2004–2023). We focussed on (i) the influence...

RNA silencing is an innate immune mechanism of plants against invasion by viral pathogens. Artificial microRNA (amiRNA) can be engineered to specifically induce RNA silencing against viruses in transgenic plants and has great potential for disease control. Here, we describe the development and application of amiRNA-based technology to induce resist...

To properly assess promoter activity, which is critical for understanding biosynthetic pathways in different plant species, we use agroinfiltration-based transient gene expression assay. We compare the activity of several known promoters in Nicotiana benthamiana with their activity in Cannabis sativa (both hemp and medicinal cannabis), which has at...

Turnip yellows virus (TuYV), is one of the most important pathogens of oilseed rape, which has caused enormous yield losses in all growing regions of the world in recent years. Therefore, there is a need for resistant varieties for sustainable crop protection. We have investigated the resistance of known varieties and newly developed advanced-breed...

Barley yellow dwarf viruses (BYDVs) are one of the most widespread and economically important plant viruses affecting many cereal crops. Growing resistant varieties remains the most promising approach to reduce the impact of BYDVs. A Recent RNA sequencing analysis has revealed potential genes that respond to BYDV infection in resistant barley genot...

Wheat dwarf virus (WDV) is one of the most important pathogens of cereal crops worldwide. To understand the molecular mechanism of resistance, here we investigated the comparative transcriptome of wheat genotypes with different levels of resistance (Svitava and Fengyou 3) and susceptibility (Akteur) to WDV. We found a significantly higher number of...

The emergence of brassica yellow virus (BrYV) has increasingly damaged crucifer crops in China in recent years. In 2020, a large number of oilseed rape in Jiangsu showed aberrant leaf color. A combined RNA-seq and RT-PCR analysis identified BrYV as the major viral pathogen. A subsequent field survey showed that the average incidence of BrYV was 32....

Accurate phenotypic identification is the basis of research for resistance genetics and rice breeding for resistance to RBSDV disease. Obtaining rice black-streaked dwarf virus (RBSDV) viruliferous small brown planthoppers (SBPHs) with high transmission efficiency is an essential part of accurate phenotypic identification. Here, through quantifying...

Turnip yellows virus (TuYV) is one of the most important pathogens of oilseed rape worldwide. The virus has a large host range including many crop species (e.g., oilseed rape, pea, chickpea) and weeds from more than twenty plant families. Other than oilseed rape, we detected TuYV in many commonly grown weed species that share the fields and vegetat...

We have developed a Potato virus X (PVX)-based vector system compatible with the GoldenBraid 2.0 (GB) cloning strategy to transiently express heterologous proteins or peptides in plants for biotechnological purposes. This vector system consists of three domestication vectors carrying three GB parts—the cauliflower mosaic virus (CaMV) 35S promoter w...

The calcium (Ca²⁺) signaling is a crucial event during plant-herbivore interaction, which involves a transient change in cytosolic Ca²⁺ concentration, which is sensed by Ca²⁺-sensors, and the received message is transduced to downstream target proteins leading to appropriate defense response. Calmodulin-like proteins (CMLs) are calcium-sensing plan...

Reverse transcription PCR (RT-PCR) is a popular method for detecting RNA viruses in plants. RT-PCR is usually performed in a classical two-step procedure: in the first step, cDNA is synthesized by reverse transcriptase (RT), followed by PCR amplification by a thermostable polymerase in a separate tube in the second step. However, one-step kits cont...

The book describes the system of integrated pest management of vegetable crops in accordance with the rules of the Directive 2009/128/ES and requirements of national legislation. It takes into consideration also the challenges and new conditions, including the strategic documents of the EU as the “Green Deal” and “Farm to Fork Strategy”. It is a so...

Interfering RNA technology has been established as an effective strategy to protect plants against viral infection. Despite this success, interfering RNA (RNAi) has rarely been applied due to the regulatory barriers that confront genetically engineered plants and concerns over possible environmental and health risks posed by non-endogenous small RN...

Our goal was to target silencing of the Plum pox virus coat protein (PPV CP) gene independently expressed in plants. Clone C-2 is a transgenic plum expressing CP. We introduced and verified, in planta, the effects of the inverse repeat of CP sequence split by a hairpin (IRSH) that was characterized in the HoneySweet plum. The IRSH construct was dri...

Plant viruses are important pathogens that cause significant crop losses. A plant protein extraction protocol that combines crushing the tissue by a pestle in liquid nitrogen with subsequent crushing by a roller-ball crusher in urea solution, followed by RuBisCO depletion, reduction, alkylation, protein digestion, and ZipTip purification allowed us...

Wheat yellow dwarf disease (BYD), caused by different species of barley/cereal yellow dwarf viruses (B/CYDVs), is one of the most serious cereal diseases in China and the Czech Republic. Because genetic diversity of the virus directly influences disease epidemiology, the molecular diversity and population structure of 24 Chinese isolates and 16 the...

The plant genome can produce long non-coding RNAs (lncRNAs), some of which have been identified as important regulators of gene expression. To better understand the response mechanism of rice plants to Rice black-streaked dwarf virus (RBSDV) infection, we performed a comparative transcriptome analysis between the RBSDV-infected and non-infected ric...

High-throughput deep-sequencing technology and bioinformatics analysis of the small RNA (sRNA) population isolated from plants allows universal virus detection and complete virome reconstruction for a given sample. In the present sRNA deep-sequencing analysis of virus-infected wheat samples in the Czech Republic, samples were firstly tested for bar...

The two contrasting cultivars, the very susceptible Ludwig and moderately susceptible Svitava, previously evaluated in field trials to determine their resistance levels to Wheat dwarf virus (WDV), were analysed by four different test methods to allow for the comparison of the methods and to consider whether the resistance level of cv. Svitava can b...

Barley yellow dwarf virus (BYDV) causes an often-devastating disease of cereals that is most effectively controlled by using plant genotypes that are resistant or tolerant to the virus. New barley lines Vir8:3 and Vir13:8, with pyramided resistance genes against different pathogens and resistance gene Ryd2 against BYDV, are currently being tested....

The PAV strain of barley yellow dwarf virus (BYDV) is one of the causal agents of yellow dwarf disease in cereals. The use of germplasm resistant to BYDV is generally regarded as the most effective means of controlling damage caused by this pathogen. In field trials, response to infection with a barley yellow dwarf virus of selected wheat cultivars...

High throughput sequencing technologies were used to identify plant viruses in cereal samples surveyed from 2012 to 2017. Fifteen genome sequences of a tenuivirus infecting wheat, oats and spelt in Estonia, Norway and Sweden were identified and characterized. Like most tenuiviruses, the genome of this tenuivirus contains four genomic segments. The...

Stone fruits are an important crop in most parts of the world and are heavily challenged by several viruses including Plum pox virus (PPV), Prune dwarf virus (PDV), Prunus necrotic ringspot virus (PNRSV), and Apple chlorotic leaf spot virus (ACLSV). We validated the PPV resistance in C5 plum plants (commercially known as HoneySweet) grown in the Cz...

Small RNAs (sRNAs) are 20–30-nucleotide-long, regulatory, noncoding RNAs that induce silencing of target genes at the transcriptional and posttranscriptional levels. They are key components for cellular functions during plant development, hormone signaling, and stress responses. Generated from the cleavage of double-stranded RNAs (dsRNAs) or RNAs w...

The bacterial communities in the gut of an insect have important ecological and functional effects on the insect. However, the community composition and diversity of the gut microbiota in insects that vector plant viruses are poorly understood. As an important insect vector, Psammotettix alienus transmits various viruses including wheat dwarf virus...

Many plant viruses are vectored by insects in a persistent circulative manner. The insect gut and salivary gland are important barriers limiting virus spread, but the mechanisms by which viruses are able to cross the gut escape barriers of the insect remain largely unknown. Wheat dwarf virus (WDV), transmitted by Psammotettix alienus in a persisten...

Background Although many genetic manipulations of crops providing biofortified or safer food have been done, the acceptance of biotechnology crops still remains limited. We report on a transgenic barley expressing the multi-functional protein osmotin that improves plant defense under stress conditions. Methods An Agrobacterium–mediated technique w...

Scheme of the expression vector pBRACT214 containing the osmotin gene. (TIF)

Regeneration of transgenic barley var. Golden Promise after transformation with osmotin gene. a) Regenerating plantlets from calluses after 6 wk on selection medium. b) Putative transgenic plants on regenerating medium. c) Transgenic plants T0 generation in greenhouse. (TIF)

Detection of osmotin transgene in the genomic DNA of T0 regenerants. Lane 1–11: samples; lane 12: negative control (DNA/RNA free water); lane 13: positive control (plasmid pBRACT214::osm); lane 14: negative control (genomic DNA of WT plants); lane 15: DNA standard (50 bp DNA ladder, Bioline). Size of PCR product is 222 bp. (TIF)

Detection of transgene encoding the marker for selection (hpt gene) in the genomic DNA of T0 regenerants. Lane 1–3: samples; lane 4: negative control (DNA/RNA free water); lane 5: negative control (genomic DNA of WT plants); lane 6: positive control (hpt positive plant), lane 7: DNA standard (2-kb DNA ladder, Bioline). Size of PCR product is 275 bp...

Exposition of transgenic and control barley to fungi infection. left: Non-transgenic barley (left) versus transgenic barley bearing tobacco osmotin gene (right) after biotic stress (15 days after first spraying of Fusarium oxysporum spores). Right: symptoms recognized on non-transgenic barley leaves after stress (chlorosis, necrosis, premature leaf...

The bird cherry-oat aphid (Rhopalosiphum padi (L.)) is one of the most detrimental pests of cereals, causing harm mainly by transmitting Barley yellow dwarf virus (BYDV). R. padi migration has been monitored since 1992 using suction traps at five sites in the Czech Republic. The count data were subjected to the following different analyses: (i) the...

Although many genetic manipulations of crops providing biofortified or safer food have been prepared, the acceptance of biotechnology crops still remains limited. We report on a transgenic barley expressing the multi-functional protein osmotin that improves plant defense under stress conditions. An Agrobacterium–mediated technique was used to trans...

We constructed Wheat dwarf virus (WDV) infectious clones in the bacterial plasmids pUC18 and pIPKb002 and tested their ability to inoculate plants using Bio-Rad Helios Gene Gun biolistic inoculation method and Agrobacterium tumefaciens agroinoculation method, and we then compared them with the natural inoculation method via viruliferous P. alienus....

Wheat dwarf virus (WDV), an important cereal pathogen, is closely related to Maize streak virus (MSV), a model virus of the Mastrevirus genus. Based on its similarity to known MSV resistance strategies, a truncated part of the WDV replication-associated (RepA) gene (WDVRepA215) and the WDV RepA gene with a mutated retinoblastoma-related protein (RB...

In the Czech Republic, Barley yellow dwarf virus (BYDV) and Wheat dwarf virus (WDV) are the prevailing viral species that can cause significant yield losses in cereal stands. Another virus, which has been on the increase in the Czech Republic and whose impact is expected to increase, is Wheat streak mosaic virus (WSMV). In this study, a TaqMan Mult...

Resistance to Plum pox virus (PPV) in transgenic Prunus domestica L., clone C5 (cv. HoneySweet) was evaluated in a regulated field in the Czech Republic for fifteen years (2002–2016). PPV mild symptoms appeared in C5 trees only in several leaves situated close to the point of inoculum grafting up to 2010. No symptoms of PPV were observed in the yea...

Wheat streak mosaic virus (WSMV) causes wheat streak mosaic, a disease of cereals and grasses that threatens wheat production worldwide. It is a monopartite, positive‐sense single stranded RNA virus and the type member of the genus Tritimovirus in the family Potyviridae. The only known vector is the wheat curl mite (WCM, Aceria tosichella), recentl...

The reverse transcription polymerace chain reaction (RT-PCR) assay was successfully used for the detection of Apple stem pitting virus (ASPV) and Apple stem grooving virus (ASGV) in four apple cultivars of a 25 years old orchard. These two main pome fruit viruses were detected frequently in all tested apple cultivars. ASGV and ASPV occurred in as m...

Wheat streak mosaic virus (WSMV) has become a re-emerging pathogen in recent years in the Czech Republic. Crop (e.g. wheat, barley, maize) and non-crop grasses from the Poaceae family are the natural hosts of the virus. Here, we report the results from coat protein (CP) gene-sequence analysis of WSMV isolates from wheat crops (four cultivars: Turon...

Wheat streak mosaic virus (WSMV) has become a re-emerging pathogen in cereal crops in the Czech Republic. WSMV was first reported in the former Czechoslovakia in the early 1980s, and then no record of the virus was documented until 2009. The incidence of the virus was recorded in recent years in several winter wheat field and many grass species. He...

Sharka caused by Plum pox virus (PPV) is the most harmful disease of stone fruits in Europe and elsewhere in the world. There is no highly PPV resistant cultivar of plum. Biotech approach has led to the development of resistance through genetic engineering. In this study, we evaluated a transgenic plum Prunus domestica L., clone C5 (cv. HoneySweet)...

A survey of Barley yellow dwarf virus (BYDV) incidence in cereal crops in the Czech Republic over 4 years showed, on average, 13.3% BYDV-positive, randomly tested wheat and barley samples. The cultivated wheat and barley cultivars had different levels of susceptibility to BYDV infection. Field trials were performed with different barley and wheat b...

The Barley yellow dwarf virus (BYDV) complex, belonging to the Luteovirus genus, is one of the most economically harmful plant viruses. Apart from fighting the aphid vectors by spraying cereal fields with insecticides, the only protection against this virus is to grow resistant cultivars. However, cereal plant resistance to BYDV is rare and complic...

A survey of Barley yellow dwarf virus (BYDV) incidence in cereal crops in the Czech Republic over 4 years showed, on average, 13.3% BYDV-positive, randomly tested wheat and barley samples. The cultivated wheat and barley cultivars had different levels of susceptibility to BYDV infection. Field trials were performed with different barley and wheat b...

Tobacco ringspot virus (TRSV) is a quarantine pathogen in Europe. During an official inspection in November 2011, Impatiens walleriana plants showing symptoms were found in a nursery in the Czech Republic. The causal agent of the disease was detected as Nepovirus group A by RT-PCR using specific primers of the Nepovirus group. Sequence analysis of...

Less prevalent viruses of family Poaceae are usually excluded from the focus of interest, even though they represent a possible threat to agricultural production. We designed and validated a set of primer pairs suitable for detection and quantification of five RNA viruses, Lolium latent virus (LoLV), Oat necrosis mottle virus (ONMV), Ryegrass mosai...

The Cydia pomonella granulovirus (CpGV) is an important agent for control of the codling moth C. pomonella (L.). Since 2004, cases of resistance to CpGV products have been found in codling moth populations of several apple plantations in Europe. Recently, the first codling moth population (Cp-VBII) with reduced susceptibility to CpGV was found in t...

This study investigated the distribution and characteristics of the Barley yellow dwarf virus (BYDV) species BYDV-PAS, which was recently separated from BYDV-PAV, the most commonly studied BYDV species. Throughout 3 years of experimental monitoring of BYDV incidence, PAS was the most frequently occurring species infecting cereals and grasses in the...

Transgenic, 'HoneySweet' plums inoculated with Plum pox virus, recombinant strain (PPV-Rec) alone, PPV-Rec + Apple chlorotic leafspot virus (ACLSV), PPV-Rec + Prune dwarf virus (PDV), and PPV-Rec + ACLSV + PDV were grown in an open field under high and permanent infection pressure both from graft inoculation and natural aphid vectors for 8 years. '...

"HoneySweet" is a plum variety developed through genetic engineering to be highly resistant to plum pox potyvirus (PPV) the causal agent of sharka disease that threatens stone-fruit industries world-wide, and most specifically in Europe. Field testing for over 15 years in Europe has demonstrated the stable and durable PPV resistance of “HoneySweet”...

POLAK J., KUMAR J., KRSKA B., RAVELONANDRO M. (2012): Biotech/GM crops in horticulture: Plum cv. HoneySweet resistant to Plum pox virus. Plant Protect. Sci., 48 (Special Issue): S43-S48. Commercialisation of Biotech/GM (Biotech) crops started in 1995. Not only field crops, but also horticultural transgenic crops are under development and are beginn...

A SYBR Green(®)-based one step RT-qPCR assay was developed for the detection and quantification of Apple stem grooving virus (ASGV) and Apple mosaic virus (ApMV). The RT-qPCR assay employed seven plant-expressed genes-glyceraldehyde 3-phosphate dehydrogenase (GAPDH), 18S ribosomal RNA, ubiquitin, ribosomal protein S19, Rubisco, RNA polymerase subun...

A rapid method for detection, discrimination and quantification of wheat and barley strains of wheat dwarf virus (WDV) was successfully developed. The sensitivity of quantification of the wheat and barley strains of WDV ranged from an average of 1.2 × 10(7)-1.2 × 10(2) and from an average of 1.4 × 10(7)-1.4 × 10(4) copies of viral genome, respectiv...

Transgenic, 'HoneySweet' plums inoculated with Plum pox virus, recombinant strain (PPV-Rec) alone, PPV-Rec + Apple chlorotic leafspot virus (ACLSV), PPV-Rec + Prune dwarf virus (PDV), and PPV-Rec + ACLSV + PDV were grown in an open field under high and permanent infection pressure both from graft inoculation and natural aphid vectors for 8 years. '...

Seeds of three blackgrass populations from Southern Bohemia were collected in 2007-2008. Biological tests with chlorsulfuron were performed at the 2-3 leaf stage. Some plants survived after treatment with the highest dose 37.5 g/ha. Biological tests showed a resistant phenotype to chlorsulfuron. Leaves of these plants were analysed by dCAPS assay....

An isolate of Brome mosaic virus (BMV) was originally isolated from Agropyron repens and maintained in Hordeum vulgare. The full-length genome of this isolate (BMV-CZ) was sequenced. Phylogenetic analysis revealed that BMV-CZ shared a minimum of 95.6% sequence identity, localized in the 5′-UTR of RNA-1 with the other BMV isolates from the database,...

A quantitative PCR, real-time RT-PCR, and one-step real-time RT-PCR using SYBR Green-based tools for reliable detection and relative quantitation of Prune dwarf virus (PDV) in stone fruits are described. The assay reliability was tested on 55 samples from different hosts and regions. The sensitivity of the assay was also compared with other assays...

Real-time PCR assays aiming at quantifying the level of plant infection by pathogens are becoming more and important. Within microbiology, the application of Real-time PCR has had the biggest impact upon the field of virology. However, Real-time PCR application in fundamental plant virology studies is still lagging behind. The use of relative and a...

Reference genes are commonly used as the endogenous normalisation measure for the relative quantification of target genes. The appropriate application of quantitative real-time PCR (RT-qPCR), however, requires the use of reference genes whose level of expression is not affected by the test, by general physiological conditions or by inter-individual...

An isolate of Hydrangea ringspot virus (HdRSV) was obtained in 2008 from infected Hydrangea spp. in the Czech Republic. The isolate (HydCZ) induced chlorotic to mildly necrotic local lesions or chlorotic systemic symptoms, respectively, in Chenopodium quinoa and Nicotiana benthamiana. The genome of HydCZ (6185 nt) was fully sequenced. Phylogenetic...

A protocol of multiplex RT-PCR in a one-tube system for the detection of the most common stone fruit trees viruses [e.g., plum pox virus (PPV), prune dwarf virus (PDV), and Prunus necrotic ringspot virus (PNRSV)], including the internal control of NADH dehydrogenase subunit 5 (nad5) gene are described here. The method specificity was tested on more...

Three amplicons corresponding to the variable genome regions of Apple chlorotic leaf spot virus (ACLSV), Apple stem grooving virus (ASGV) and Apple stem pitting virus (ASPV) were sequenced from different apple cultivars and geographic areas in Europe and Asia. Multiple alignments of nucleotide sequence of these isolates with those from databases sh...