Molecular detection of resistance‐breaking strain Cucumber mosaic virus (rbCMV) (Cucumovirus; Bromoviridae) on resistant commercial pepper cultivars in Turkey

Abstract

AbstractThe cultivation of pepper (Capsicum annuum), a significant crop worldwide, is severely affected by a number of viral agents. In Antalya province, it was observed that pepper varieties possessing the cmr1 allele that provides resistance against CMV‐P0 isolate of CMV were affected in 2019 and 2020. Typical symptoms of CMV are emerging at an alarming rate in resistant pepper plants. Afterward, virus mechanical inoculation was carried out under controlled conditions on the five commercial resistant and susceptible varieties. The success of the inoculation studies was determined by RT‐PCR using CMV CPG‐specific primers. All commercial varieties carrying the resistance cmr1 gene showed disease symptoms. For complete genome analysis, RNA from a pepper plant carrying the cmr1 gene was sequenced using Illumina‐HiSeq 2000. BLAST analyses of the obtained complete genome sequence were carried out. The breaking (CMV‐P1) and non‐breaking isolates (CMV‐P0), which were previously described in conducted studies, were analysed and aligned for SNPs. SNP mutations in these nucleotide regions were similar to resistance‐breaking and completely different from non‐breaking isolates. Our study results revealed that the CMV‐P1 isolate obtained from pepper samples carrying cmr1 resistance has been shown to be able to overcome both field and laboratory conditions. To our knowledge, this is the first report of resistance‐breaking CMV‐P1 strain on pepper varieties in Turkey.