Comparison of the baseline gene expressions of DT MH96/0686 and DS Nyalanda. Quantitative RT-PCR was performed for each identified gene on three biological replicates for well-watered plants (control) of each genotype (MH96/0686 and Nyalanda). Duplicate reactions were run for every biological replicate. The qRT-PCR reactions were normalized with the cassava actin gene as a reference for all comparisons. The ΔΔCT method of relative gene quantification was used to make the various comparisons of relative gene expression from the qRT-PCR data, using REST. During data collection, Nyalanda (DS landrace) was used as a calibrator. The DT genotype has several drought-tolerance genes whose levels are different from those in DS (under well-watered conditions). A gene is significantly up-regulated or down-regulated when its expression in a treatment is higher than or lower than that in a calibrator (standard/baseline), respectively, and when the t-test statistic is lower than 0.05 (at 95 % significant level). The expression in a calibrator is taken as unity (one), expression of more than one is up-regulation and expression less than one is down-regulation. The t-statistic will show whether the up-regulation or down-regulation is significant or non-significant (NS).