Identifying Genes That Underlie Whitefly Resistance in Cassava

The yields and quality of cassava (Manihot esculenta), a major food staple in developing countries, are strongly impacted by phloem-feeding whiteflies, such as Bemisia tabaci and Aleurotrachelus socialis. Whiteflies are responsible not only for direct damage due to feeding, but also for the transmission of plant viruses. To date, little is known about cassava’s resistance mechanism to whiteflies. Our goal, as part of the multidisciplinary Cassava-Whitefly project (http://cassavawhitefly.org), is to identify the genes underlying whitefly resistance in South American and African cassava. We have employed a unique source of natural resistance to whiteflies in the South American genotype Ecu72, which is resistant to both the South American whitefly A. socialis and the B. tabaci species attacking cassava in Africa. Ecu72 expresses a strong, phloem-mediated resistance that kills whitefly nymphs. To identify candidate whitefly resistance genes, the Ecu72 and whitefly-susceptible Col2246 were infested with A. socialis for 0, 12 hr, 24 hr, 7 d, 14 d and 22 d. Time-course infestations were performed in triplicate. RNAs were isolated, mRNA was purified with oligodT beads and RNA-seq libraries were constructed with a home-made protocol. Six libraries per lane were multiplexed and single-end sequenced using Illumina’s HiSEQ2500 platform. The systemPipeRNASeq pipeline (www.bioconductor.org) was used to analyze these sequences. We routinely obtained 25-30 million reads per library, and ~89% of these reads were mapped to the cassava genome.  Using 2-fold change and a 10% FDR, transcripts that were temporally regulated in both Ecu72 and Col2246 were identified. In addition, a number of differentially expressed transcripts that were positively or negatively correlated with resistance were identified. We will report the analyses of these time-course studies. Differentially regulated transcripts have been mapped to the cassava genome and are being correlated with the segregation of whitefly resistance loci in a mapping population. At the present time, time-course infestations of other whitefly-resistant genotypes from South America are being characterized to determine if resistance mechanisms are conserved or if novel strategies are deployed in these genotypes.