Genetically Diverse Variants of Sugarcane bacilliform virus Infecting Sugarcane in India and Evidence of a Novel Recombinant Badnavirus Variant

Abstract

AbstractSugarcane bacilliform viruses (SCBV; genus Badnavirus) cause leaf fleck disease in sugarcane worldwide. SCBV was detected in 28 sugarcane cultivars originating from eight states of India. Eight representative SCBV isolates from five different states showed sequence variability up to 27% in the reverse transcriptase and RNase H (RT/RNase H) genetic region. Five isolates [SCBV‐AP (Co693077): HQ324248, SCBV‐Assam (CoBIN94063): HQ324246, SCBV‐Bihar (Bo141): HQ324245, SCBV‐UP (Co1424): KC013276 and SCBV‐UP (CoSe6460): KC013277] showed sequence identity of 86–88% with Sugarcane bacilliform IM virus (SCBIMV), but the other three isolates [SCBV‐Kerala (Co7219): HQ324249, SCBV‐TN (Co86032): GQ385038 and SCBV‐UP (CoSe92423): HQ324247] showed maximum sequence identity of 75–79% with Sugarcane bacilliform MO virus (SCBMOV). In phylogenetic analysis, the SCBV isolates segregated into two new subclades and were distinct from the known SCBV genotypes. The rates of non‐synonymous and synonymous (dN/dS) substitution indicated the signs of purifying selection with strong functional constraints for RT/RNase H region in SCBV population. A variant (SCBV‐UP, CoSe92423) was identified to be a recombinant isolate having two other Indian SCBV isolates as parents. Although RT/RNase H region is a recombination cold spot, a strong recombination might have played a key role in the evolution of this new variant of SCBV. Our study provides an insight into the diverse genetic structure of SCBV population and presence of a novel recombinant SCBV species/variant infecting sugarcane cultivars in India. Our results will be helpful in devising a robust detection procedure for quarantine and field testing of sugarcane germplasm.