Table 3.
Effect of water stress on mRNA levels, comparing stressed to control plants within a genotype. Quantitative RT-PCR was performed for each identified gene on three biological replicates for each treatment (stress and control) for 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. For each genotype, the control plants were used as a calibrator. 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 % significance 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).
| Genotype | Gene | Expression | SE | 95 % CI | Probability | Result |
|---|---|---|---|---|---|---|
| MH96/0686 Stressed against well watered | MeALDH | 2.815 | 1.818–4.183 | 1.327–6.112 | 0.000 | Up-regulated |
| MeATTF | 3.245 | 1.444–9.582 | 1.069–11.530 | 0.000 | Up-regulated | |
| MeGBF3 | 3.241 | 2.221–5.467 | 1.688–9.982 | 0.000 | Up-regulated | |
| MeGE3 | 0.317 | 0.181–0.647 | 0.097–0.988 | 0.006 | Down-regulated | |
| MeGF14 | 1.303 | 0.963–1.768 | 0.844–2.344 | 0.095 | NS | |
| MeMYC2 | 1.350 | 0.718–2.196 | 0.608–3.336 | 0.204 | NS | |
| MeMSD | 3.148 | 2.316–4.431 | 1.897-6.394 | 0.001 | Up-regulated | |
| MeRD28 | 1.511 | 1.062–1.998 | 0.852–2.153 | 0.013 | Up-regulated | |
| MeP5CS | 1.425 | 0.686–3.784 | 0.384–4.745 | 0.301 | NS | |
| MeZFP | 4.043 | 2.869–5.828 | 2.164–8.014 | 0.000 | Up-regulated | |
| NYALANDA Stressed against well watered | MeALDH | 2.160 | 1.003–5.120 | 0.464–7.983 | 0.056 | NS |
| MeATTF | 2.671 | 1.902–3.812 | 1.393–4.954 | 0.001 | Up-regulated | |
| MeGBF3 | 1.875 | 1.161–3.028 | 0.733–3.979 | 0.018 | Up-regulated | |
| MeGE3 | 0.205 | 0.057–0.671 | 0.034–0.941 | 0.000 | Down-regulated | |
| MeGF14 | 2.285 | 1.094–6.336 | 0.826–18.602 | 0.031 | Up-regulated | |
| MeMYC2 | 2.201 | 1.391–3.371 | 0.976–4.183 | 0.006 | Up-regulated | |
| MeMSD | 1.506 | 0.983–2.255 | 0.815–4.129 | 0.063 | NS | |
| MeRD28 | 1.128 | 0.994–1.286 | 0.875–1.381 | 0.059 | NS | |
| MeP5CS | 1.662 | 1.125–2.414 | 0.977–3.496 | 0.007 | Up-regulated | |
| MeZFP | 1.578 | 0.806–3.368 | 0.525–5.198 | 0.159 | NS |
CI, confidence interval at 95 %; expression, fold change in the expression of a gene in water stress relative to control treatment (P = 0.05).