Molecular Characterization and Genetic Diversity of Rice Stripe Necrosis Virus (RSNV) in Burkina Faso

Abstract

Rice stripe necrosis virus (RSNV) is a threat to rice cultivation in Burkina Faso causing huge crop losses. The objective of this study was to perform a molecular characterization of the diversity of RSNV viral isolates from Burkina Faso, in order to develop effective control strategies for the virus to producers. Samples of symptomatic rice leaves, characterized by stunted growth and the presence of chlorotic spots, were collected from rice fields in four locations of Sudanian zone and subjected to total RNA extraction using Trizol. Amplifications for virus characterization were performed using the capsid protein (CP). They have been retranscribed into cDNA before being amplified by Polymerase chain reaction (PCR). Thus, the RSNV diversity has been analyzed through the sequencing of the capsid protein. The results indicated a grouping of the isolates into three (03) distinct groups, regardless of their geographical origin. Inter-isolate nucleotide diversity ranged from 0.2% to 5.5%. The highest nucleotide divergence (5.1%) was observed between sequence from Banfora and Karfiguela. In contrast, lower divergent rates (0.2%) were recorded between the sequences from Bama and Banfora, as well as between those from Bagre and Bama. This represents the first study of RSNV diversity based on capsid protein sequences in Burkina Faso. This study provides essential information for the development of effective and sustainable control strategies against RSNV, particularly through the development and deployment of resistant/tolerant rice varieties.