PRJNA211897
Manihot esculenta Transcriptome or Gene expression
Cassava (Manihot esculenta Crantz.) is a vital food security crop and staple in Africa, yet cassava brown streak disease (CBSD), cassava mosaic disease and the whitefly (Bemisia tabaci) vector of their causative viruses result in substantial yield losses. Here we aim to identify genes that have undergone positive selection during adaptive evolution, from CBSD resistant and susceptible M. esculenta varieties and inter-specific hybrids, as well as a wild cassava species. Whitefly resistant and susceptible genotypes were included. Transcriptomes of 13 genotypes were sequenced and three genes with strong positive selection were detected (EG2771, EG964 and EG5651). These had full coding sequence Ka/Ks ratios of 1.44, 2.1 and 4.1 respectively.  Amplicons of these three genes from a further five genotypes were sequenced and the sequence variation examined in relation to known response to CBSD and whitefly infection. Although, we cannot ascribe a selection pressure that was responsible for the observed positive selection with complete certainty at this stage, given the congruence of the pattern of particular alleles of our positively selected genes and the pattern of disease resistance of the cassava varieties we examined, it is likely that some protein variants coded by alleles of EG2771 and EG964 may be associated with CBSD and whitefly resistance responses. This warrants further investigation. Other alleles of our positively selected genes were likely influenced by domestication or some other unknown selective pressure.