RT-PCR/PCR analysis detected mixed infection of DNA and RNA viruses infecting sugarcane crops in different states of India

Abstract

A sensitive assay based on the polymerase chain reaction detected mixed infection of four viruses, viz. Sugarcane mosaic virus (SCMV), Sugarcane streak mosaic virus (SCSMV), Sugarcane yellow leaf virus (SCYLV) and Sugarcane bacilliform virus (SCBV) on sugarcane crops of India. Thirteen sugarcane varieties exhibiting mosaic, chlorotic streaks, mid-rib yellowing and without symptoms (from the vicinity of symptomatic fields) that originated from Uttar Pradesh, Andhra Pradesh, Tamil Nadu, Madhya Pradesh, Kerala, Bihar and Haryana states of India were evaluated for virus association through PCR and RT-PCR assays with specific designed primers for SCMV (SCMV-F3 and SCMVR3), SCSMV (SCSMV-ST2 and SCSMV-P1), SCYLV (SCYLV-615F and SCYLV-615R) and SCBV (SCBV-F and SCBV-R).The expected 0.9 kb SCMV fragment was amplified by RT-PCR with the SCMV-F3 and SCMV-R3 primers from sugarcane varieties of Kerala and Uttar Pradesh. The expected 0.5 kb SCSMV fragment was amplified by RT-PCR with the SCSMV-ST2 and SCSMV-P1 from sugarcane varieties of Uttar Pradesh, Kerala, Andhra Pradesh and Tamil Nadu. However, a 610 bp SCYLV fragment (by RT-PCR with the SCYLV-615F and SCYLV-615R primers) and 580 bp SCBV fragment (by SCBV-F and SCBV-R) was respectively amplified from all the 13 symptomatic and non-symptomatic sugarcane varieties in the study. Interestingly, mixed infection of all the four viruses SCMV, SCSMV, SCBV and SCYLV was detected in two sugarcane varieties of Uttar Pradesh and Kerala and mixed infection of three viruses (SCSMV+SCYLV+SCBV) was detected in the four states (Uttar Pradesh, Kerala, Andhra Pradesh and Tamil Nadu). However, mixed infection of SCYLV and SCBV was reported in all the seven surveyed states.