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Background  Cassava is an important crop for food security and industry in the least-developed and developing countries. The completion of the cassava genome sequence and identification of large numbers of candidate genes by next-generation sequencing provide extensive resources for cassava molecular breeding and increase the need for rapid and efficient gene function analysis systems in cassava. Several plant virus-induced gene silencing (VIGS) systems have been developed as reverse genetic tools for rapid gene function analysis in cassava. However, these VIGS vectors could cause severe viral symptoms or inefficient gene silencing.    Results  In this study, we constructed agroinfection-compatible infectious cDNA clones of cassava common mosaic virus isolate CM (CsCMV-CM, genus  Potexvirus , family Alphaflexiviridae) that causes systemic infection with mild symptoms in cassava. CsCMV-CM was then modified to a viral vector carrying the Nimble cloning frame, which facilitates the rapid and high-throughput cloning of silencing fragments into the viral genome. The CsCMV-based vector successfully silenced  phytoene desaturase  ( PDS ) and  magnesium chelatase subunit I  ( ChlI ) in different cassava varieties and  Nicotiana benthamiana . The silencing of the  ChlI  gene could persist for more than two months.    Conclusions  This CsCMV-based VIGS system provides a new tool for rapid and efficient gene function studies in cassava.    Supplementary Information  The online version contains supplementary material available at 10.1186/s13007-021-00775-w.

A cassava common mosaic virus vector for virus-induced gene silencing in cassava