Molecular insights of pigeonpea sterility mosaic virus mixed infections and its variability in pigeonpea

Pigeonpea sterility mosaic virus-1 (PPSMV-1) and Pigeonpea sterility mosaic virus-2 (PPSMV-2) are the two distinct Emaraviruses causing Sterility Mosaic Disease (SMD), which is an emerging threat to the pigeonpea (Cajanus cajan L. Millspaugh) production in India. The dissemination of virus is progressing at an accelerated rate and existence of PPSMV-1 (Emaravirus cajani) and PPSMV-2 (Emaravirus toordali) exhibiting diversity across the ecosystems. A total of 34 symptomatic and healthy samples were collected from six districts covering Western, North-Eastern, Cauvery Delta Zone and North-Western agro-climatic zones of Tamil Nadu. The disease incidence ranged from 12.8% to 71.6% and the highest mean incidence of 52.67% was recorded in the North-Eastern agroclimatic zone of Tamil Nadu. The RT-PCR and multiplex RT-PCR analysis differentiated the presence of both PPSMV-1, PPSMV-2 and mixed infections. Sequence analysis of RNA1 and RNA3 segments of the virus genomes demonstrated significant genetic heterogeneity among isolates, while phylogenetic relatedness of PPSMV-1 and PPSMV-2 were grouped into distinct clusters. Intra-specific recombination events were observed in the RNA3 segments of both PPSMV-1 and PPSMV-2. There were no recombination events in RNA1 segments of the virus genomes. These results emphasise the widespread distribution and genetic diversity of PPSMV-1 and PPSMV-2 in Tamil Nadu and provide valuable insights for the development of rapid diagnostic tools for effective field management.