Variation of field symptoms and molecular diversity of the virus isolates associated with chilli leaf curl complex in different agroecological regions of Sri Lanka

G D N Menike,D M De Costa

doi:10.4038/tar.v28i2.8192

Abstract

The present study was conducted to detect and identify the virus isolates and to determine the molecular diversity associated with CLCC-infected chilli plants grown in a wide range of agroecological zones in Sri Lanka over two consecutive cultivation seasons. Randomly-selected chilli plants showing virus-like symptoms were collected from five experimental sites representing different agroecological zones and symptoms were recorded. DNA extracted from the above chilli leaf samples were subjected to PCR amplification using JS35 F and JS36 R primers, which are specific to Chili leaf curl Sri Lanka virus (ChiLCSLV). Amplified PCR products which targeted a region of DNA-A genome of begomovirus were subjected to DNA sequencing. Subsequent DNA homology search identified virus isolates associated with the CLCC-infected chilli plants which gave the highest homology to chilli leaf curl Salem virus-India, chilli leaf curl-Bhavansagar-India, Pepper Leaf curl Bangladesh virus, ChiLCSLV-isolate 14, ChiLCSLV-isolate 15 and Tomato leaf curl geminivirus, but having a variation of percentage identity. Phylogenetic analysis confirmed the genetic divergence of the CL-14 and CL-15 isolates, being them more genetically closer to chilli leaf curl-Bhavansagar-India and chilli leaf curl Salem virus- India, respectively. Eventhough single nucleotide differences were found in different clades of virus isolates, there was no strong relationship with clade separation and the location or season from which the samples were collected. Clade separation also did not show a relationship with a particular type of symptom. Findings of the study clearly revealed the presence of a diverse number of begomovirus isolates associated with the CLCC-infected plants and the genomic variations of them.

Highlights

Chilli (Capsicum annuum L.), an economically-important cash crop to Sri Lankan farmers, is grown in a range of agroecological regions of the country during the two major cultivation seasons (Maha and Yala)
The present study revealed the presence of chilli leaf curl virus isolates in Chilli leaf curl complex (CLCC)-infected chilli plants though they exhibited a wide variation of field symptoms
It was evident by the present study that majority of the virus isolates associated with CLCC-infected plants representing a range of locations of Sri Lanka showed the highest homology with begomovirus species (e.g. Chilli Leaf curl Salem virus-India, Chilli leaf curl virus[Bhavanisagar:India]) other than CL-14 and CL-15 of ChiLCSLV, indicating the potential association of diverse number of begomovirus species with CLCC-infected chilli in Sri Lanka

Summary

Introduction

Chilli (Capsicum annuum L.), an economically-important cash crop to Sri Lankan farmers, is grown in a range of agroecological regions of the country during the two major cultivation seasons (Maha and Yala). Chilli leaf curl complex (CLCC), one of the major biotic threats to the production of chilli in Sri Lanka, dates back to 1938 Chilli plants infected with CLCC shows virus-like symptoms including severe upward curling, stunted plant growth, leaf thickening, and vein clearing. Irregular scraping of epidermis could be seen (Johnpulle 1939).The wide range of virus-like symptoms could be due to either single or mixed infections by the above probable causes of CLCC. Mixed infections of chilli due to virus, mites and thrips are difficult to be distinguished purely by field symptoms. Association of begomoviurs in CLCC-infected plants in Sri Lanka has been confirmed by molecular methods (Senanayake et al, 2013)

Methods

Results

Conclusion