Comprehensive Multiplex RT-PCR and PCR Assay for Simultaneous Detection of Mixed Infections of Major Sugarcane Viruses

Sugarcane is a globally important cash crop crucial for production of sucrose. The productivity of sugarcane is affected by several viral pathogens, including Sugarcane bacilliform virus (SCBV), Sugarcane mosaic virus (SCMV), Sugarcane streak mosaic virus (SCSMV), and Sugarcane yellow leaf virus (SCYLV). These viruses are known to primarily transmit through sugarcane planting seeds and germplasm exchange cause substantial economic yield losses worldwide. This study introduces an optimized multiplex PCR and conventional PCR assay for simultaneous detection of four major sugarcane viruses viz., SCBV, SCMV, SCSMV, and SCYLV. The proposed study developed and validated a multiplex PCR assay for early detection of major sugarcane viruses, supporting clean seed programs to enhance the productivity of sugarcane. In the present study, the sugarcane samples exhibiting characteristic disease symptoms were collected from six major sugarcane varieties of India. To assure the integrity and purity, overall genomic DNA and RNA were extracted. Based on the PCR results, the amplicons of approximately of 587 bp and 465 bp were detected for SCBV and SCMV, respectively in 3, 5, and 6 samples. However, amplicons of ~610 bp for SCYLV and ~599 bp for SCSMV have been seen in all six samples. The approach is very economical and demonstrated remarkable sensitivity, specificity, and robustness for the early and simultaneous detection of mixed viral infections in sugarcane. In order to promote sustainable sugarcane agricultural practices worldwide, the study fulfills a major gap in virus diagnostics by providing a strategic solution for early virus diagnosis, clean seed production, and enhanced sugarcane productivity.