The sugarcane quarantine of CIRAD in Montpellier, France : from disease diagnosis to fundamental research and vice versa

Accurate disease diagnosis tools are a major need for a plant quarantine process. Thanks to the development of serological and molecular biological techniques, significant improvements were obtained in disease control in sugarcane quarantine, although "old traditional" methods such as isolation on selective culture media also remain very useful (for instance for the detection of Xanthomonas albilineans, the sugarcane leaf scald pathogen). Most of the time, new techniques can be rather easily adapted to the specific needs of disease diagnosis in quarantine; however, specific research activities must be undertaken i/ when a new disease appears and no diagnostic tools are available, and ii// to make sure that all strains or variants of a pathogen can be detected. For the above reasons, as well as for routine disease testing, CIRAD's sugarcane quarantine has been involved in research activities regarding the characterisation of emerging diseases and in genetic diversity studies of several plant pathogens. Within the last decade, CIRAD's sugarcane quarantine had to face two emerging diseases, yellow leaf, caused by the Sugarcane yellow leaf virus (SCYLV), and streak mosaic, caused by the Sugarcane streak mosaic virus (SCSMV). Tissue culture methods were used to eliminate SCYLV and SCSMV from infected varieties in quarantine, and studies on genetic diversity and variability in pathogenicity showed that these viruses were not homogeneous pathogens. Additionally, studies on SCYLV disease progress in the field and impact of yellow leaf on yields were carried out in Reunion Island where an unusual lineage of the virus occurs. Mosaic is another important disease to be detected in sugarcane quarantine. The disease occurs in more than 70 countries and the causal agents of mosaic, the Sugarcane mosaic virus (SCMV) and the Sorghum mosaic virus (SrMV), have been known and studied for several decades. Additionally, several molecular assays were developed for diagnosis and detection of these two viruses. Numerous strains have been described for SCMV based on plant inoculation and serological data, but most genetic diversity studies included only strains from Australia and the USA. We therefore studied the genetic diversity of a collection of SCMV isolates from eight countries, and especially 50 isolates from Africa. Our results showed that SCMV isolates are distributed into two major phylogenetic groups (sugarcane group and maize group) and several subgroups that are closely related to the country of origin of the isolates. Additionally, all isolates from sugarcane belonged to the sugarcane group. More recent discoveries revealed, however, that Chinese SCMV isolates from sugarcane belong to the maize group. These latter isolates were not detected by most molecular assays developed for the detection of SCMV from sugarcane. Fortunately, a PCR-assay developed for diagnosis of Poaceae viruses proved to be very efficient in the diagnosis of sugarcane and maize isolates of SCMV. This assay is also efficient to simultaneously detect SCMV and SrMV. (Texte intégral)