Identification of genes that have undergone adaptive evolution in cassava (Manihot esculenta) and that may confer resistance to cassava brown streak disease

Abstract

Cassava (Manihot esculenta) is a vital food security crop and staple in Africa, yet cassava brown streak disease (CBSD) and cassava mosaic disease result in substantial yield losses. The aim of this study was to identify genes that have undergone positive selection during adaptive evolution, from CBSD resistant, tolerant and susceptible M. esculenta varieties and inter-specific hybrids, as well as a wild cassava species. Transcriptomes of 13 genotypes were sequenced and three genes with strong positive selection were detected (designated as EG2771, EG964 and EG5651). Sequence variation for candidate genes in 18 different cassava genotypes was 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.