Molecular characterisation of chilli leaf curl virus and identification of resistant sources in Indian chilli germplasm

Chilli is an important vegetable and spice, but production is severely hindered by chilli leaf curl virus (ChiLCV). A ChiLCV isolate from Bengaluru was maintained, comparative sequence analyses were conducted and Indian chilli germplasm was screened through whitefly-mediated inoculation. Viruliferous adult whiteflies, following acquisition from infected plants, were released onto healthy seedlings; infected and healthy leaf samples were tested for begomovirus presence using three overlapping primer sets (MK, GEMA, OY). Sequence analysis of the DNA-A component of the Bengaluru isolate showed > 98 % nucleotide identity with previously reported ChiLCV isolates, confirming that the isolate belongs to ChiLCV group and represents a distinct ChiLCV variant. Mitochondrial CO1 sequencing of the vector showed 99.38 % similarity to Bemisia tabaci (Asia II-5; KJ709449). During summer 2023, 135 chilli accessions were evaluated under controlled conditions using whitefly-transmitted challenge inoculation and monitored for characteristic symptoms, including vein clearing and leaf curling. Based on observed disease reactions, accessions were classified as 26 resistant, 29 moderately resistant, 24 susceptible, 25 moderately susceptible and 31 highly susceptible. Genotypic validation using a ChiLCV-associated simple sequence repeat (SSR) marker (PAU-LC-343-1) detected a 195 bp fragment in 55 accessions associated with resistance and a 175 bp fragment in 80 accessions associated with susceptibility, corroborating the phenotypic screening. These results identify valuable resistant germplasm and a linked molecular marker for breeding programs and provide a molecularly characterised Bengaluru ChiLCV isolate for use in future screening and management strategies. Integration of these resistant sources into cultivar development could enhance production, reduce reliance on chemicals and limit yield losses from ChiLCV.