Virome profiling of pigeonpea using high-throughput sequencing and development of LAMP assay for PPSMV detection

Pigeonpea (Cajanus cajan (L.) Millsp) is a major pulse crop vulnerable to various biotic stresses including viral diseases. In addition to known viruses, novel and emerging viruses further threaten its production. In the current study, a survey was conducted in pigeonpea fields of Karnataka, India during 2023-24. The incidence of pigeonpea viral diseases in the surveyed areas ranged from 2 to 34 %. During the survey thirty virus infected pigeonpea samples were collected for virome analysis. Total RNA extracted from fifteen samples each from Northern and Southern Karnataka was pooled separately into two equimolar RNA samples and subjected to virome profiling. The rRNA-depleted RNA was used to prepare mRNA libraries, which were sequenced on the Illumina NovaSeq 6000 platform. Virome analyses revealed the presence of three different viruses: pigeonpea sterility mosaic virus 1 (PPSMV 1), pigeonpea sterility mosaic virus 2 (PPSMV 2) and horsegram yellow mosaic virus (HgYMV) from Northern Karnataka and only PPSMV 1 from Southern Karnataka. Sequencing was validated by reverse transcription polymerase chain reaction (RT-PCR) in individual samples, which revealed the prevalence of PPMSV 1, PPMSV 2 and HgYMV in Karnataka, India. Further, a reverse transcription loop-mediated isothermal amplification (RT-LAMP) diagnostic assay was developed to detect PPMSV, which can be used for routine detection. Among the identified viruses in pigeonpea, HgYMV is reported for the first time from Karnataka, India.