Prevalence and RT/RNase H Genealogy of Sugarcane Bacilliform Virus Isolates from China

Abstract Sugarcane bacilliform viruses ( SCBV ; genus Badnavirus ; family Caulimoviridae ) are a threat to the global exchange of sugarcane germplasm. To investigate the prevalence and genetic diversity of SCBV across major Chinese sugarcane‐growing areas, a total of 280 sugarcane leaf tissue samples collected from six provinces in China, 25 from three states in the USA and five from Queensland, Australia, were tested for the presence of SCBV by polymerase chain reaction ( PCR ) using newly designed degenerate primers targeting a 720‐base pair (bp) fragment of the reverse transcriptase/ribonuclease H ( RT / RN ase H) genomic region. PCR ‐amplified fragments from 94 SCBV ‐positive samples were then cloned, sequenced and analysed for their genetic diversity. The results revealed a considerable haplotype diversity within individual SCBV isolates. Recombination analyses showed weak signatures of recombination among some of the SCBV sequences. Phylogenetic analysis revealed the segregation of global SCBV isolates into three major monophyletic clades encompassing 18 subgroups, including five previously undescribed subgroups named as SCBV ‐N to ‐R. Population genetic analysis data indicated that relatively low levels of genetic exchange have occurred between SCBV populations from different sugarcane production regions of the world. Together with the new set of degenerate SCBV ‐specific primers designed in this study, our results will advance the understanding of SCBV population structure in a semi‐perennial host plant and aid the screening of global sugarcane germplasm to minimize the spread of genetic variants of the virus via contaminated plant materials.