Molecular detection and identification of thirteen isolates of Sugarcane yellow leaf virus associated with sugarcane yellow leaf disease in nine sugarcane growing states of India

Abstract

Thirty sugarcane leaf samples exhibiting midrib yellowing symptoms from nine sugarcane growing states of India were collected. The total RNA was isolated from infected samples and RT-PCR assays were performed using Sugarcane yellow leaf virus (SCYLV) specific primers. The infection of SCYLV was detected in 27 out of 30 samples, which showed the expected size (~610 bp) amplicon during RT-PCR. The amplicons from 13 samples were cloned, sequenced and sequence data of these isolates were analyzed to determine sequence identities, sequence variations and phylogenetic relationships with the SCYLV isolates reported earlier from India and abroad with the view to identify the virus isolates based on partial sequence of ORF5, and complete ORF3 (coat protein, CP) and ORF4 (movement protein, MP). The analysis of the complete sequence data (613 nucleotides) of 13 isolates under study revealed 96–100% identities among them and also with SCYLV-Cuban isolate. The identities were 90–94% with other isolates of SCYLV reported from other countries. The nucleotide (nt) and amino acid (aa) sequence comparison in the CP and MP coding regions showed a significant variation between Indian isolates (SCYLV-IND) and other SCYLV isolates reported worldwide. Phylogenetic analyses of the 13 SCYLV isolates under study showed that they clustered together along with most other SCYLV-Indian isolates and a SCYLV-Cuba isolate. The remaining isolates from other regions of the world and a single isolate from India characterized in a previous study clustered into separate groups. Therefore, the isolates under study were identified as isolates of SCYLV which are closely related to SCYLV-Cuba, the member of ‘CUB’ genotype.