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Research Project: CHARACTERIZING, DETECTING, AND ELIMINATING PATHOGENS TO ENABLE THE SAFE INTRODUCTION OF PLANT GENETIC RESOURCES

Location: National Germplasm Resources Laboratory

Title: Viral metagenomics and sugarcane pathogens

Author
item Roumagnac, Philippe - Cirad, France
item Mollov, Dimitre
item Daugrois, Jean-heinrich - Cirad, France
item Filloux, Denis - Cirad, France

Submitted to: Book Chapter
Publication Type: Book / Chapter
Publication Acceptance Date: 4/21/2017
Publication Date: 3/5/2018
Citation: Roumagnac, P., Mollov, D.S., Daugrois, J., Filloux, D. 2018. Viral metagenomics and sugarcane pathogens. In: Rott, P., editor. In Achieving Sustainable Cultivation of Sugarcane Volume 2: Breeding, pests and diseases. Cambridge, UK: Burleigh Dodds Science Publishing. p.183-200. http://dx.doi.org/10.19103/AS.2017.0035.20.

Interpretive Summary: Sugarcane (Saccharum species) was domesticated in Southeast Asia and is now grown in more than 90 counties with about 26 million hectares under production in tropical and sub-tropical areas. Sugarcane is the source of 80% of the global sugar supply, which is traditionally used for consumption. The entire plant has also recently been used as a source of ethanol and biomass for renewable energy production. Sugarcane production faces numerous challenges and average yields have not increased significantly in several decades. This is partially due to the abundance of pests and pathogens than damage sugarcane, including viruses. In this book chapter, we describe the most up-to-date technology for detecting sugarcane viruses. The highly sensitive next generation sequencing and metagenomics methods help detect known sugarcane viruses and discover new ones, study their diversity, and investigate the etiology of unknown sugarcane diseases that are probably caused by viruses. These advances will help to implement better diagnostic and management strategies for sugarcane viruses

Technical Abstract: Plant viral metagenomics has recently proved effective for studying the collection of viruses associated with plant. Consequently, the advent of metagenomics-based approaches has led to the discovery and characterization of novel plant viruses and helped solving etiologic enigmas. In this chapter, we first describe the plant virus metagenomics methods that were developed during the last decade and then focus on the use and application of these approaches in the sugarcane pathology field. Hence, we present three recent studies that have used viral metagenomics-based approaches aiming at (i) solving long-standing etiologic enigmas, (ii) identifying known and potentially new sugarcane viruses in a sugarcane quarantine context and (iii) assessing the diversity of a known sugarcane virus (Sugarcane yellow leaf virus). Finally we discuss challenges and opportunities of using such approaches to address plant pathology modern issues.