Molecular characterization and phylogentic analysis of isolates of sugarcane yellow leaf virus infecting sugarcane from Andhra Pradesh
TM Hemalatha, BV Bhaskara Reddy, R Sarada Jayalakshmi, SR Koteswara Rao, M Hemanth Kumar and G Mohan Naidu
Sugarcane Yellow Leaf Disease caused by Sugarcane yellow leaf virus (ScYLV) is an emerging disease affecting the production and productivity in many ruling sugarcane varieties in India. The losses due to the disease range from 60% in the main crop to 100% in the ratoon crop. Infected plants shows typical symptoms of midrib yellowing on adaxial surface with lateral spread of yellow discolouration to the leaf lamina. Later followed by tissue necrosis from the leaf tip spreading downwards along the midrib and a bushy appearance of the top of the plant due to internode shortening in maturing plants. In the present study, twenty five SCYLV infected leaf samples were collected from major sugarcane growing regions and amplified the ORF 3& 4 regions of the genome of the virus coding for coat protein and movement protein. RT-PCR was performed using specific primers (ScYLV-613F & ScYLV 613R) amplifying the coat protein and movement protein of the virus. Amplification of band of size 613 bp was observed in twelve of the samples. These amplicons were sequenced and were analyzed to determine the sequence identities, sequence variations and phylogenetic relationships with the SCYLV isolates reported earlier from India and abroad with the view to determine the variability among the SCYLV isolates reported from india and abroad. 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. The analysis of the nucleotide sequence data of 12 isolates under study revealed 95–100% identities among them and also with isolates of CUB ans COL isolates. The identities were 94-97% with other SCYLV isolates reported. 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 There was greater similarity in aminoacid sequence ie., upto 94.2 - 99.2% between the Indian isolates and the CUB, COL isolates while the similarity was about 90.0-96.1% with other genotypes. This was further confirmed from the phylogenetic analysis where the CUB and COL isolates clustered with the isolates reported from India while the other genotypes (HAW, CHN, REU, PER, BRA) clustered into a separate group. The Indian isolates showed close relationship with the CUB and COL isolates. Hence it was confirmed from the study that SCYLV isolates collected from major sugarcane growing regions of Andhra Pradesh closely related to SCYLV-CUB and SCYLV-COL genotypes.
How to cite this article:
TM Hemalatha, BV Bhaskara Reddy, R Sarada Jayalakshmi, SR Koteswara Rao, M Hemanth Kumar, G Mohan Naidu. Molecular characterization and phylogentic analysis of isolates of sugarcane yellow leaf virus infecting sugarcane from Andhra Pradesh. Pharma Innovation 2021;10(4):115-123.