Development of a severity scale and an RT‐qPCR assay for screening resistance levels in rice genotypes against rice stripe necrosis virus and its vector

Abstract

AbstractRice stripe necrosis virus (RSNV) is the causal agent of the disease ‘rice crinkling’ and is transmitted by the protozoan Polymyxa graminis. Although genetic resistance has been explored, no resistant commercial cultivars are currently available. Oryza glaberrima has been identified as a promising source of resistance. However, it remains unclear whether this resistance is effective against the virus, the vector, or both, as well as whether it can be transferred to Oryza sativa cultivars. Disease‐resistant genotypes are primarily selected through visual observations of symptom expression. The absence of a severity scale for RSNV makes this process difficult, and relying solely on visual assessments can introduce subjectivity. We developed a severity scale and a reverse transcripiton‐quantitative PCR (RT‐qPCR) assay for screening resistance levels in rice genotypes against RSNV and its vector and to analyse the genetic variability of RSNV isolates. To achieve absolute quantification, experiments were conducted using O. glaberrima and three O. sativa cultivars. Inoculation occurred naturally using soil from an area with a history of the disease. Visual symptoms were recorded and disease intensity was evaluated. Subsequently, total nucleic acid extraction was performed on the samples and viral and vector loads were quantified through RT‐qPCR and qPCR, respectively. To characterize the virus variability, symptomatic rice samples were collected in the 2021/2022 crop season. RT‐PCR was conducted to amplify the coat protein gene of RSNV, and molecular variability descriptors were analysed.