A century of diagnostic improvements in a sugarcane pathology changing context: from symptom observation to molecular assays

Sugarcane germplasm has been moved between geographical ragions of the world for numerous centuries, but the first record of a sugarcane disease in the literature dates only to 1869 when symptoms and signs of gumming were described in Brazil. At the end of the 19th century and the first hait of the 20th century, diagnosis of sugarcane diseases was solely based on symptom observation (including cytology and microscopy investigations), isolation and characterization of the pathogens (fungi and bacteria) isolated on culture media, and inoculation assays (including for viruses). Application of these methods resulted in the identification of pathogens that caused important disease outbreaks such as leaf scald, mosaic, orange rust, red rot, smut, etc. A first major breakthrough in disease diagnosis occurred du ring the second hait of the 20th century when serological assays were developed. This allowed better and faster detection of pathogens, especially viruses such as sugarcane mosaic viruses and bacteria such as Xanthomonas a/bilineans and Leifsonia xyli subsp. xyli. At the end of the 20th century, the advent of nucleic acid sequencing resulted in the development of molecular diagnostic methods based on DNA/RNA probing and amplification assays. Ali these molecular methods targeted specific genome sequences of a pathogen and were developed for most diseases threatening sugarcane production. A new and transformative breakthrough occurred at the beginning of the 21 st century with the development of high-throughput sequencing (HTS) technologies that permitted the detection of known but also unknown pathogens. HTS was used to investigate the virome of sugarcane and to discover new viruses but also to solve a ninety years mystery regarding the causal agent of sugarcane chlorotic streak. Numerous and powerful diagnostic methods are currently available to detect and identify sugarcane pathogens, as well as to ensure safe movement of germplasm among sugarcane producing locations.