Improvements in virus detection at CIRAD's sugarcane quarantine using both viral metagenomics and PCR-Based approaches

Visacane, CIRAD's sugarcane quarantine program (http://visacane.cirad.fr/en/), covers three main quarantine procedures: detection of pests and pathogens, elimination of pests and pathogens, and transfer of pest- and pathogen-free planting material. While we aim at improving sugarcane adaptability, stability, and sustainability through Visacane, sugarcane clones and related wild species with high levels of genetic diversity and originating from multiple sources are quarantined at Montpellier (France) to be sent to Visacane's partners. From 2013 to 2017, 2,830 batches of disease-free cuttings from 435 sugarcane clones were transferred to 42 partners of Visacane. Our main goal was to foster worldwide distribution of pest- and pathogen-free planting material and to guarantee breeder's rights. The virome of sugarcane was recently investigated using viral metagenomics, and the genetic diversity of three uncharacterized sugarcane viruses (sugarcane white streak virus, sugarcane striate virus, and sugarcane mild mosaic virus) was assessed for improved diagnosis. Hence, new protocols to detect these three viruses were developed and validated. An additional detection protocol targeting sugarcane bacilliform virus, a virus that was up to now not considered as a quarantine organism by many countries and undiagnosed in quarantine, was also developed. These issues are essential to guarantee the health status of the planting material and to increase the reliability of Visacane's sugarcane germplasm