Genetic variability of Sugarcane bacilliform virus causing leaf fleck of sugarcane in India

Abstract

Sugarcane bacilliform virus (SCBV) (Genus: Badnavirus, Family: Caulimoviridae), a plant pararetrovirus which causes leaf fleck in sugarcane considered as economically important pathogen, limiting the exchange of its germplasm worldwide. To explore the prevalence and genealogies of SCBV from germplasm and cultivated varieties, 358 leaf fleck affected samples from cultivars and germplasm were collected and subjected to PCR to amplify 726bp reverse transcriptase/ribonuclease H region of ORF3. 104 PCR amplicons were sequenced and the contigs derived from each fragment was assembled using CAP3 contig assembly and variability analysis was performed in MEGA X using the maximum likelihood method with tamura-Nei model. Phylogenetic analyses of the sequences revealed formation of three major groups, in which CBJ 46 alone formed a separate group with 40% similarity to the remaining isolates. The sequences had shown 85-99% similarity with other SCBV partial sequences (ORF 3 region) from NCBI genbank. Overall, SCBV-BT and SCBV-BRU genotypes are found to widely present in India and existence of newer genotypes viz. CHN 1, CHN 2 from China, SCBV-IM and SCBV MO from Australia were identified from India for the first time. Even though the isolate CBJ 46 showed >80% similarity to ORF 3 of SCBV YN –YZ 20602 from China, in phylogenetic analysis it has formed a clear distinct separate group which indicates the possible emergence of new SCBV variant. Huge phylogenetic diversity existing among the SCBV isolates throws light on the variation within the SCBV species in India and their variation from the other genera of Badna viruses. Thus the present study helps to understand the SCBV population structure in India and will address the spread of new genetic variants from other countries through germplasm exchange