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Background  The phenylalanine ammonia lyase genes play crucial role in plant response to biotic and abiotic stresses. In this study, we characterized the role of PAL genes in increasing resistance to the  Cassava brown streak virus  that causes the economically important cassava brown streak disease (CBSD) on cassava in Africa.    Methods  The whole transcriptomes of eight cassava varieties differing in resistance to CBSD were obtained at 1, 5 and 8 weeks after CBSV infection.    Results  Analysis of RNA-Seq data identified the overexpression of  PAL1, PAL2 , cinnamic acid and two chalcone synthase genes in CBSD-resistant cassava varieties, which was subsequently confirmed by RT-qPCR. The exogenous application of Acibenzolar-S-Methyl induced  PAL1  gene expression to enhance resistance in the susceptible var. Kalawe. In contrast, the silencing of  PAL1  by RNA interference led to increased susceptibility of the resistant var. Kaleso to CBSD.    Conclusions   PAL1  gene of the phenylpropanoid pathway has a major role in inducing resistance to CBSD in cassava plants and its early induction is key for CBSD resistance.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12985-021-01649-2.

PAL1 gene of the phenylpropanoid pathway increases resistance to the Cassava brown streak virus in cassava