Genetic Diversity, Evolution, and Diagnosis of Sugarcane Yellow Leaf Virus from 19 Sugarcane-Producing Locations

Authors: ROTT, PHILIPPE - Cirad, France; Grinstead, Sam; DALLOT, SYLVIE - Cirad, France; Foster, Zachary; DAUGROIS, JEAN HEINRICH - Cirad, France; FERNANDEZ, EMMANUEL - Cirad, France; KAYE, CLAUDIA - Us Sugar Corporation; HENDRICKSON, LETICIA - Animal And Plant Health Inspection Service (APHIS); HU, XIAOJUN - Animal And Plant Health Inspection Service (APHIS); Adhikari, Bishwo; MALAPI-WIGHT, MARTHA - Animal And Plant Health Inspection Service (APHIS); Grunwald, Niklaus - Nik; ROUMAGNAC, PHILIPPE - Cirad, France; Mollov, Dimitre

Submitted to: Plant Disease
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/14/2023
Publication Date: 4/20/2023
Citation: Rott, P., Grinstead, S.C., Dallot, S., Foster, Z.S., Daugrois, J., Fernandez, E., Kaye, C., Hendrickson, L., Hu, X., Adhikari, B.N., Malapi-Wight, M., Grunwald, N.J., Roumagnac, P., Mollov, D.S. 2023. Genetic Diversity, Evolution, and Diagnosis of Sugarcane Yellow Leaf Virus from 19 Sugarcane-Producing Locations. Plant Disease. https://doi.org/10.1094/PDIS-10-22-2405-RE.
DOI: https://doi.org/10.1094/PDIS-10-22-2405-RE

Interpretive Summary: Sugarcane is an important crop cultivated worldwide. Sugarcane viruses hinder crop quality and reduce yield. Sugarcane yellow leaf virus (SCYLV) could reduce yield between 10 and 60% depending on sugarcane variety susceptibility level and growth conditions. In this research we completed 65 genomic sequences of SCYLV. Combined with the publicly available 44 genomes we used all 109 SCYLV genomic sequences to study virus diversity. Additionally with this robust genomic dataset we explored virus evolution and identified three distinct lineages. This work allowed us to compare 14 previously available diagnostic methods and to evaluate the reliability of SCYLV detection. We identified primer sets that can detect isolates belonging to all lineages. These findings will help the regulatory entities and industry to facilitate better control strategies of this viral disease.

Technical Abstract: Sugarcane yellow leaf virus (SCYLV), the causal agent of yellow leaf, has been reported in an increasing number of sugarcane growing locations since its first report in the late 1980s in Brazil and Hawaii. In this study, the genetic diversity of SCYLV was investigated using the genome coding sequence (5561-5612 nt) of 109 virus isolates from 19 geographical locations, including 65 newly obtained sequences. These isolates were distributed in three phylogenetic clades representing three major virus lineages (BRA, CUB, and REU). Twenty-two recombination events were identified among the 109 isolates of SCYLV, thus confirming that recombination was a significant driving force in genetic diversity and evolution of this virus. No temporal signal was found in the genomic sequence data set, most likely because of the short temporal window of the 109 SCYLV isolates (1998-2020). Among 27 primers reported in the literature for the detection of the virus by RT-PCR, none matched 100% with all the 109 SCYLV sequences, suggesting that use of some primer pairs may not result in detection of all virus isolates. Primers YLS111/YLS462, which were the first primer pair used by numerous research organizations to detect the virus by RT-PCR, failed to detect isolates belonging to the CUB lineage. In contrast, primer pair ScYLVf1/ScYLVr1 efficiently detected isolates of all three lineages. Continuous pursuit of knowledge of SCYLV genetic variability is therefore critical for effective diagnosis of yellow leaf, especially in virus-infected and mainly asymptomatic sugarcane plants.