Chlorotic curly stunt: a severe begomovirus disease of bottle gourd in northern India

Bottle gourd IC-0262269, a super-susceptible genotype to tomato leaf curl Palampur virus

While conducting field trial of 82 genotypes of bottle gourd at Delhi during 2020-2021, a particular genotype, IC-0262269 was found to be affected by chlorotic curly stunt disease (CCSD). The affected plants were severely stunted and bearing very small chlorotic and crinkle leaves. The disease incidence in the said genotype was as high as 80% among different replicated trial blocks. The application of PCR using a generic primers specific to begomoviruses, as well as species-specific PCR diagnostics to six tomato-infecting begomoviruses: tomato leaf curl New Delhi virus (ToLCNDV), tomato leaf curl Palampur virus (ToLCPalV), tomato leaf curl Joydebpur virus (ToLCJoV), tomato leaf curl Gujrat virus (ToLCGuV), tomato leaf curl Bangalore virus (ToLCBV), and chilli leaf curl virus (ChiLCV) showed that, only ToLCPalV could be detected in the genotype IC-0262269. Following, rolling circle amplification, cloning and sequencing of full-length DNA-A and DNA-B genome of an isolate BoG1-ND from the genotype IC-0262269 revealed association of ToLCPalV with the disease. The successful agro-infection of the cloned genome of BoG1-ND (DNA-A and DNA-B) in the plants of Nicotiana benthamiana and bottle gourd demonstrated that ToLCPalV is the causal begomovirus of CCSD. The study provides the first evidence of the natural occurrence of ToLCPalV in bottle gourd crop and also showed that the bottle gourd genotype IC-0262269 is super-susceptible to ToLCPalV.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03838-y.

The selection and validation of reference genes for quantitative real-time PCR studies in near-isogenic susceptible and resistant tomato lines, infected with the geminivirus tomato curly stunt virus

Quantitative real-time PCR (qPCR) is a sensitive and commonly used technique for gene expression profiling and provides insight into biological systems. Successful qPCR requires the use of appropriate reference genes for the normalization of data. In the present study, we aimed to identify and assess the best-suited reference genes in near-isogenic resistant (R) and susceptible (S) tomato lines infected with begomovirus Tomato curly stunt virus (ToCSV). Ten candidate reference genes namely, Actin7 (ACT), β-6 Tubulin (TUB), Ubiquitin 3 (UBI), Clathrin adaptor complexes medium subunit (CAC), Phytoene desaturase (PDS), Expressed protein (EXP), Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), Adenine phosphoribosyl transferase-like protein (APT1), TAP42-interacting protein (TIP41) and Elongation factor 1-alpha (EF1α) were selected and evaluated for their expression stability in resistant and susceptible tomato leaves using the analytical tools geNorm, NormFinder, BestKeeper, and RefFinder. After ranking the reference genes from most to least stable, the results suggested that a combination of ACT, EXP, and EF1α in the S lines and a combination of TIP41, APT1, and ACT in the R line is appropriate for qPCR normalization. Furthermore, to validate the identified reference genes, iron superoxide dismutase (SOD), heat shock protein 70 (HSP70) and Glutathione-S-transferase (GST) were selected as targets for normalization. The relative expression of the target genes varied when normalized against the most stable reference genes in comparison to the least stable genes. These results highlight the importance of careful selection of reference genes for accurate normalization in qPCR studies.

Genetic Diversity, Pathogenicity and Pseudorecombination of Cucurbit-Infecting Begomoviruses in Malaysia

Cucurbits are important crops in the world. However, leaf curl disease constrains their production. Here, begomovirus diversity and pathogenicity associated with the disease in Malaysia were studied based on 49 begomovirus-detected out of 69 symptomatic plants from seven cucurbit crops in 15 locations during 2016 and 2017. The presence of Squash leaf curl China virus (SLCCNV) and Tomato leaf curl New Delhi virus (ToLCNDV) were confirmed by virus detection by polymerase chain reaction, viral DNA sequence analysis and specific detection of the viral components. ToLCNDV Malaysian isolates were further distinguished into strains A, B, C and D. Virus co-infection was detected in bitter gourd, bottle gourd and squash. Among them, eight bitter gourd samples were detected without SLCCNV DNA-A. However, one bottle gourd and five squash samples were without ToLCNDV DNA-B. Pseudorecombination of ToLCNDV DNA-A and SLCCNV DNA-B was detected in two bitter gourd samples. The pathogenic viruses and pseudorecombinants were confirmed by agroinoculation. The viral DNA-B influencing on symptomology and host range was also confirmed. The results strengthen the epidemic of cucurbit-infecting begomovirus in Malaysia as well as Southeast Asia. Especially, the natural pseudorecombinant of begomovirus that extends host range and causes severe symptom implies a threat to crops.

A new seed-transmissible begomovirus in bitter gourd (Momordica charantia L.)

A begomovirus isolate collected from bitter gourd plants showing yellowing, puckering and stunting symptoms from Coimbatore district, Tamil Nadu, India was characterized. The full-length genome of the virus isolate was amplified by rolling circle amplification using phi29 DNA polymerase. The virus isolate exhibited 98% identity in the nucleotide sequence of DNA-A component with the Coccinia mosaic Virudhunagar virus (GenBank accession no. KY860899). The DNA-B component was very distinct and shared only 60% identity with the begomovirus, Coccinia mosaic Tamil Nadu virus (GenBank accession no. KM244719). The virus renamed as new species Bitter gourd yellow mosaic virus (BgYMV) was detected in seeds from infected plants and in the grow-out test seedlings by ELISA and virus-specific PCR. The seed infectivity was 79.16% and transmission rate to seedling was 32.05%. The virus titre as indicated by A₄₀₅ absorption value was high (0.854-0.280) in different seed parts. Results clearly indicated seed transmission of the begomovirus, BgYMV.

Survey, symptomatology, transmission, host range and characterization of begomovirus associated with yellow mosaic disease of ridge gourd in southern India

Ridge gourd is an important vegetable crop and is affected by several biotic and abiotic factors. Among the different biotic factors, ridge gourd yellow mosaic disease (RgYMD) is new emerging threat for the production of ridge gourd. The incidence of the RgYMD varied from 30 to 100% in southern India with highest disease incidence of 100% observed in Belagavi district of Karnataka state. The infected plants showed chlorosis, mosaic, cupping of leaves, blistering, reduction in leaf size and stunted growth. The varieties/hybrids grown in the farmer's fields were found to be susceptible to the disease. Begomovirus was detected in 61 out 64 samples collected from different areas of southern India. Further, all the samples failed to give amplification for beta and alpha satellites. The transmission studies revealed that single whitefly (Bemisia tabaci) is enough to transmit the virus, however, 100% transmission was observed with 10 whiteflies. The minimum acquisition access period and inoculation access period for transmission of virus by whitefly was 15 min. Among the 56 host plants belonging to diversified families tested for host range, sponge gourd, ash gourd, bottle gourd, pumpkin, cucumber, summer squash, cluster bean, tobacco and datura were shown to be susceptible. Seventy six varieties/hybrids evaluated for identifying the resistance source for RgYMD, all were found highly susceptible. Sequence analysis of DNA-A revealed that the causal virus shared highest nucleotide sequence identity (92.3%) with Tomato leaf curl New Delhi virus (ToLCNDV) infecting sponge gourd from northern India. Sequence and phylogenetic analysis of both DNA-A and DNA-B components showed that the begomovirus associated with RgYMD is found to be strain of ToLCNDV. This is first report of ToLCNDV association with RgYMD from southern India.

A recombinant Tobacco curly shoot virus causes leaf curl disease in tomato in a north-eastern state of India and has potentiality to trans-replicate a non-cognate betasatellite

Leaf curl disease is a serious constraint in tomato production throughout India. Several begomoviruses were reported from different parts of the country; however, identity of begomovirus associated with leaf curl disease in tomato in north-eastern states of India was obscured. In the present study, the complete genome of an isolate (To-Ag-1) of begomovirus was generated from a leaf curl sample collected from Tripura state. However, no DNA-B and betasatellite were detected in the field samples. The genome of To-Ag-1 isolate contained 2,755 nucleotides that shared 94.7 % sequence identity with Tobacco curly shoot virus (TbCSV) and 71.3-90.1 % sequence identity with the other tomato-infecting begomoviruses occurring in the Indian subcontinent. Several inter-specific recombination events among different tomato-infecting begomoviruses from India and intra-specific recombination among different isolates of TbCSV reported from China were observed in the genome of To-Ag-1 isolate. Agroinoculation of the virus alone produced leaf curl symptoms in tomato and Nicotiana benthamiana. However, co-inoculation with a non-cognate betasatellite, Croton yellow vein mosaic betasatellite (CroYVMB) with the TbCSV resulted in increased severity of the symptoms both in tomato and N. benthamiana. Systemic distribution of the TbCSV and CroYVMB was detected in the newly developed leaves of tobacco and tomato, which showed ability of TbCSV to trans-replicate CroYVMB. The present study for the first time provides evidence of occurrence of TbCSV in tomato in north-eastern region of India and showed increased virulence of TbCSV with a non-cognate betasatellite.

Molecular Evidence for Occurrence of Tomato leaf curl New Delhi virus in Ash Gourd (Benincasa hispida) Germplasm Showing a Severe Yellow Stunt Disease in India

An evaluation of 70 accessions of ash gourd germplasm grown at National Bureau of Plant Genetic Resources, New Delhi, India during Kharif season (2010) showed natural occurrence of a yellow stunt disease in three accessions (IC554690, IC036330 and Pusa Ujjwal). A set of begomovirus specific primers used in PCR gave expected amplicon from all the symptomatic plants; however no betasatellite was detected. Complete genome of the begomovirus (DNA-A and DNA-B), amplified through rolling circle amplification, was cloned and sequenced. The begomovirus under study shared high sequence identities to different isolates of Tomato leaf curl New Delhi virus (ToLCNDV) and clustered with them. Among those isolates, the DNA-A and DNA-B of the present begomovirus isolate showed highest 99.6 and 96.8 % sequence identities, respectively with an isolate reported on pumpkin from India (DNA-A: AM286433, DNA-B: AM286435). Based on the sequence analysis, the begomovirus obtained from ash gourd was considered as an isolate of ToLCNDV. Thus, the present findings constitute the first report of occurrence of a new yellow stunt disease in ash gourd from India and demonstrated the association of ToLCNDV with the symptomatic samples. Occurrence of ToLCNDV in ash gourd germplasm not only adds up a new cucurbitaceous host of this virus but also raises the concern about the perpetuation of this virus in absence of its main host tomato and thus has an epidemiological relevance for understanding the rapid spread of this virus in tomato and other hosts in Indian sub-continent.

Tomato leaf curl New Delhi virus is Associated With Pumpkin Leaf Curl: A New Disease in Northern India

During 2006, pumpkin leaf curl-a new disease was observed in the experimental field at Indian Agricultural Research Institute. The disease was characterized by upward leaf curl with chlorotic patches and stunting of plant. Polymerase chain reaction (PCR) with coat protein specific primers to Tomato leaf curl New Delhi virus (ToLCNDV) indicated association of a begomovirus with the disease. The sequence comparison and phylogenetic analysis of the complete DNA genome further revealed the identity of the virus as ToLCNDV. The study provides evidence that ToLCNDV is associated with the leaf curl of pumpkin (Cucurbita moschata) in northern India.