Genetic diversity of Chilli veinal mottle virus infecting different chilli landraces in North East India indicates the possibility of transboundary movement of virus

Abstract

Diverse chilli genetic resources of North East India occupy a unique niche in the Nation's chilli gene pool. Widely cultivated chilli landraces (King chilli: , bird eye chilli: and ) of North East India in general and Manipur in particular suffer from decline complex due to high incidence of viral diseases. With this background and the known prominent distribution of (ChiVMV) in Asian region, we studied its prevalence and association with diverse symptoms of chilli landraces. Molecular indexing of samples from 40 chilli plantation groves of Manipur using reverse transcription (RT)-PCR targeting the coat protein (CP) region of ChiVMV genome revealed a high incidence and wide prevalence. Out of a total of 127 chilli samples collected from different groves of Manipur, 81 chilli samples (63.78%) were positive for ChiVMV. Interestingly, ChiVMV infection rate was comparatively higher in the hilly groves (69.23% samples positive) compared to the valley groves (60% samples positive). Present study through the extensive surveys and molecular indexing work, conclusively reported the association of ChiVMV with diverse symptoms like cupping of leaf lamina with mottling, vein banding and puckering in different chilli landraces. Further, five representative ChiVMV isolates sampled from different groves of Manipur upon mechanical inoculation showed significant variation in symptom expression, indicating wide pathogenic diversity among them. Partial coat protein (CP) sequence analysis of five ChiVMV isolates from Manipur although indicated genetic homogeneity among them, but distinctiveness from ChiVMV isolates reported from the other parts of India. Phylogenetic clustering of ChiVMV isolates from Manipur near Chinese isolates rather than other Indian isolates suggested the possibility of transboundary movement.

Molecular Characterization of Chilli Veinal Mottle Virus Infecting King Chilli (Capsicum Chinense Jacq.) of North East Indian State Assam

“…High incidence of viral infection as recorded through visual observations of symptoms and recent report of ChiVMV infection on Naga chilli from Meghalaya indicated the possibility of its association with chilli decline in the NE region (Banerjee et al 2014). Sanabam et al, 2018 reported that, NE region being contagious to the Eastern Asian region provided a strong base for the possible prevalence of pathogenically and genetically diverse ChiVMV isolates. Previous researches revealed genetic heterogeneity among the characterized ChiVMV isolates using CP gene fragment might be due to the strong selective constraint on CP protein (King et al, 2011).…”

“…Different researches have shown over time that the crop is susceptible to different viruses which include Cucumber mosaic virus (CMV), Potato virus Y (PVY) (Talukdar et al, 2015;Baruah et al, 2016), Tomato Spotted Wilt Virus (TSWV) (Talukdar et al, 2015), Chilli leaf curl virus (ChLCV) ( Talukdar et al, 2015;Baruah et al, 2016) and Groundnut Bud Necrosis Virus (GBNV) (Baruah et al, 2016). Bhut jolokia has also been found to be susceptible to Chilliveinal mottle virus as reported from Meghalaya (Sanabam et al, 2018;Banerjee et al, 2014). The plants are at times infected by a single virus or collectively by different viruses thereby forming a viral complex (Baruah et al, 2016) which reduces the production and productivity to greater extent.…”

A Simplified Multiplex PCR Assay for Simultaneous Detection of Six Viruses Infecting Diverse Chilli Species in India and Its Application in Field Diagnosis

“…Viral diseases have always been a major constraint to chilli production and productivity worldwide [ 7 , 8 , 9 , 10 ]. At least 65 viruses have been reported to infect the chilli worldwide [ 11 ]; 24 among them occur under natural infection, and the rest occur under experimental conditions [ 12 ].…”

“…in the Indian subcontinent [ 13 ]. The NER of India has recorded a widespread prevalence and high incidence of viral diseases on all the cultivated chilli landraces (King chilli and bird’s eye chilli) due to the favourable environmental conditions prevailing throughout the growing seasons [ 7 , 14 ]. A thorough identification through the accurate detection of these viral diseases is the only means of carving out effective management measures.…”

“…A thorough identification through the accurate detection of these viral diseases is the only means of carving out effective management measures. As such, the most widely prevalent viruses infecting different cultivars and landraces of chilli across India as well as in the NER of India are capsicum chlorosis orthotospovirus (CaCV) [ 15 , 16 ], pepper mild mottle virus (PMMoV) [ 17 ], chilli veinal mottle virus (ChiVMV) [ 7 , 14 ], cucumber mosaic virus (CMV) [ 18 , 19 ], chilli leaf curl virus (ChiLCV) [ 20 ], and newly reported large cardamom chirke virus (LCCV) [ 21 ].…”