Table 4.

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).

Gene	Expression (fold difference in baseline expression levels, DT vs. DS)	SE	95 % CI	Probability (P = 0.05)	Relative significant difference (DT vs. DS)
MeALDH	1.379	0.598–2.832	0.370–4.163	0.319	NS
MeATTF	1.679	0.531–4.431	0.384–6.376	0.211	NS
MeGBF3	1.094	0.570–1.789	0.272–2.591	0.746	NS
MeGE3	1.959	0.501–6.700	0.270–10.729	0.221	NS
MeGF14	2.332	1.202–5.717	0.824–17.293	0.013	Up-regulation
MeMYC2	1.924	1.118–3.617	0.741–4.594	0.019	Up-regulation
MeMSD	0.584	0.429–0.837	0.366–1.282	0.014	Down-regulation
MeRD28	1.120	0.990–1.297	0.867–1.409	0.075	NS
MeP5CS	1.934	0.746–3.786	0.657–6.197	0.054	NS
MeZFP	0.858	0.504–1.471	0.317–2.258	0.539	NS