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. 2013 Feb 7;5:plt007. doi: 10.1093/aobpla/plt007

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).