Genome-wide transcriptome analysis of cassava challenged with Ugandan cassava brown streak virus (UCBSV)

Abstract

Cassava is staple to millions in Africa, yet cassava brown streak disease (CBSD) greatly threatens cassava production. This study reports the mechanism of cassava’s resistance to CBSD using Ugandan cassava brown streak virus (UCBSV), one of the two CBSD-causal virus species. In a green house, five varieties: Albert, Kiroba, Mkombozi, Namikonga and NDL06/132 were analysed for response to UCBSV at 20 time points. In the first experiment, Albert and Namikonga were compared. In the second experiment, all five varieties were studied. Plants were phentyped for foliar and root symptoms of CBSD, virus titre was measured using qRT-PCR while RNAseq and QuantStudio were used to determine gene expression. Virus infected plants of susceptible variety (Albert) developed clear leaf symptoms and necrotic storage roots. UCBSV-infected plants of Namikonga (resistant) showed minimal leaf symptoms and storage roots were non-necrotic. UCBSV titre was highest in susceptible variety (Albert), and very low in the resistant variety (Namikonga). More genes were differentially expressed in Namikonga (10,028) compared to Albert (688). In Namikonga, highest expression was recorded at 2 dag and 5 dag, when only two genes were differentially expressed in Albert. GO terms for phosphorelay signal transduction, ribosome and elongation factors were enriched in Namikonga and none in Albert. In another experiment, UCBSV-infected storage roots from Kiroba were non-necrotic. Defence genes identified in Kiroba were similar to Namikonga’s, except that in Kiroba, genes were highly expressed at 1 dag and 51 dag. One storage root of Mkombozi developed a necrotic spot. Mkombozi had no distinct pattern of defence-gene expression as seen in Kiroba and Namikonga. Varieties NDL06/132 and Albert were susceptible, and showed limited numbers of differentially expressed genes. Therefore, Kiroba and Namikonga are resistant to CBSD. The resistance mechanism involves up regulation of known defence proteins, and restricted multiplication of UCBSV in infected plants.