Table 2.
Confirmation of the RNA-Seq expression profiles with qRT-PCR
| Transcript | RNA-Seq(CS) | RNA-Seq(DS) | RNA-Seq(SS) | qRT-PCR(CS) | qRT-PCR(DS) | qRT-PCR(SS) | Annotation |
|---|---|---|---|---|---|---|---|
| Mf53179 | 5.93 | 0.69 | 0.05 | 9.28 | 5.01 | 2.43 | DREB protein |
| Mf40807 | 3.81 | 1.30 | 0.91 | 4.27 | 4.06 | 1.71 | GH3 |
| Mf52262 | 2.79 | 3.45 | 2.16 | 7.24 | 8.87 | 5.47 | NFR5 |
| Mf44686 | 2.55 | 6.14 | 2.35 | 7.62 | 7.03 | 3.19 | ERF |
| Mf24843 | 2.45 | 5.53 | 3.08 | 7.28 | 9.46 | 5.09 | ERF |
| Mf94524 | 2.22 | 3.83 | 0.66 | 4.43 | 3.25 | 0.45 | CYP707A |
| Mf21376 | 2.18 | 1.70 | 0.40 | 2.13 | 1.57 | 0.33 | NCED |
| Mf89827 | 2.17 | 4.92 | 5.37 | 1.74 | 6.17 | 5.14 | Stress-induced receptor |
| Mf26361 | 2.11 | 2.72 | 1.95 | 1.84 | 4.19 | 0.43 | OPCL1 |
| Mf20359 | 2.04 | 0.58 | 1.34 | 0.15 | 4.39 | 2.06 | ACS |
| Mf40505 | 1.93 | 3.50 | 2.66 | 2.01 | 5.98 | 1.40 | OPR |
| Mf51793 | 1.88 | 6.03 | 3.99 | 5.03 | 6.35 | 4.40 | Calmodulin binding |
| Mf23563 | 1.86 | 1.12 | 2.39 | 1.86 | 1.12 | 2.40 | CrtZ |
| Mf84393 | 1.49 | 3.81 | 2.09 | 3.76 | 4.96 | 3.95 | JMT |
| Mf42223 | 1.48 | 3.83 | 1.88 | 4.74 | 4.71 | 1.66 | AOS |
| Mf34249 | 1.40 | 1.88 | 1.29 | 3.81 | 1.02 | 1.43 | ACS |
| Mf84453 | 1.28 | 1.53 | 1.31 | −0.16 | 1.05 | −2.60 | LOX |
| Mf31223 | 1.26 | 1.52 | 1.24 | 1.74 | 3.19 | 0.05 | AOC |
| Mf37052 | 1.24 | 3.75 | 3.10 | 2.81 | 2.83 | 1.09 | NFR1 |
| Mf19438 | 1.21 | 2.24 | 1.65 | 5.07 | 3.66 | 1.07 | SAMS |
| Mf21208 | 1.16 | 1.68 | 1.12 | 0.70 | 3.28 | 1.34 | 2-beta-dioxygenase |
| Mf37096 | 1.15 | 4.29 | 2.69 | 1.03 | 3.22 | 0.23 | DMI3 |
| Mf46196 | 1.09 | 4.29 | 5.05 | 3.56 | 10.67 | 9.19 | NCED |
| Mf41585 | 1.08 | 1.51 | 1.14 | 0.10 | 1.95 | −1.19 | SNF1 |
| Mf84582 | 0.96 | −1.01 | 0.29 | −0.52 | −2.24 | −2.72 | cytochrome P450 |
| Mf19924 | 0.96 | 3.13 | 1.70 | 1.18 | 0.89 | 0.64 | SAMS |
| Mf35541 | 0.83 | 2.21 | 1.65 | 0.26 | 1.46 | −1.00 | SNF1 |
| Mf53098 | 0.75 | 1.69 | 1.60 | 0.32 | 1.67 | 0.43 | JAR1 |
| Mf52729 | 0.70 | −0.38 | 0.46 | 5.19 | −0.63 | 3.87 | Cysteine-rich receptor |
| Mf29322 | 0.65 | 0.91 | 1.75 | 1.69 | 1.25 | 1.20 | ACO |
| Mf32232 | 0.59 | 1.13 | 3.02 | −0.04 | 1.13 | 3.01 | ZEP |
| Mf46161 | 0.49 | 3.69 | 1.20 | 2.24 | 3.79 | 0.46 | ACS |
| Mf33973 | 0.42 | 1.21 | 0.25 | 2.01 | 1.73 | 0.69 | DMI1 |
| Mf22267 | 0.18 | 0.45 | −0.53 | 0.43 | 0.40 | −0.87 | CrtZ |
| Mf37546 | 0.15 | 1.34 | 0.78 | 0.30 | 0.25 | −0.61 | JAR1 |
| Mf24274 | 0.14 | −0.68 | −0.40 | 0.07 | −1.38 | −0.26 | 20-oxidase |
| Mf58069 | 0.11 | 0.48 | 1.82 | 1.03 | 0.17 | 1.15 | ACO |
| Mf88132 | −0.21 | 1.26 | 2.37 | −0.66 | 2.33 | 2.90 | ABF 1 |
| Mf46174 | −0.25 | −1.17 | −0.25 | −1.11 | −0.95 | −0.41 | ZEP |
| Mf23784 | −0.77 | −0.72 | −1.00 | −1.93 | −0.06 | −0.42 | NSP11 |
| Mf49154 | −0.95 | 0.58 | 1.87 | −0.56 | 2.59 | 3.75 | Importin |
| Mf50824 | −0.96 | 3.51 | 1.26 | −0.79 | 1.20 | 0.70 | DMI2 |
| Mf54137 | −1.11 | 1.41 | 0.18 | −3.07 | 5.33 | 3.96 | Nodule receptor kinase |
| Mf22751 | −1.33 | −1.76 | −0.74 | −0.46 | −0.73 | −1.25 | PYR/PYL |
| Mf11674 | −1.36 | −2.59 | −0.26 | −0.68 | −1.45 | −2.58 | Leghemoglobin |
| Mf24497 | −1.49 | −0.88 | −1.62 | −3.93 | −0.23 | −2.52 | ENOD |
| Mf34644 | −1.54 | 0.43 | 0.14 | −0.55 | 0.99 | 0.60 | GID1 |
| Mf20666 | −1.76 | 1.26 | 0.37 | −0.16 | 0.92 | 0.20 | GID1 |
| Mf56011 | −1.77 | −1.09 | −0.47 | −2.17 | −2.48 | −1.62 | AAO |
| Mf38812 | −2.21 | 2.13 | 2.99 | 0.52 | 0.68 | 0.72 | DMI3 |
| Mf17441 | −2.26 | −1.66 | −2.11 | −1.45 | −0.71 | −1.14 | AAO |
| Mf87623 | −2.45 | −1.08 | −1.48 | −1.04 | −0.35 | −2.13 | PYR/PYL |
| Mf49788 | −3.16 | −2.17 | −2.18 | −0.70 | −0.57 | −2.60 | NSP2 |
| Mf20500 | −3.78 | 3.32 | −0.57 | −1.98 | 5.88 | −2.94 | ERN2 |
| Mf21830 | −4.11 | −1.75 | −2.31 | −1.84 | −0.73 | −4.88 | ENOD |
| Mf29128 | −5.20 | 1.10 | −0.12 | −0.46 | −0.05 | −1.69 | 3-beta-hydroxylase |
The expression levels of CS, DS, SS, and SC were calculated, and pairwise comparisons (CS versus SC, DS versus SC, and SS versus SC) were calculated. Expression ratios for the RNA-Seq data, shown as the fold change, were calculated for cold [RNA-Seq (CS)], dehydration [RNA-Seq (DS)], and high salinity [RNA-Seq (SS)] using the DESeq programme. Ratios for qPCR analyses were calculated for cold [qRT-PCR (CS)], dehydration [qRT-PCR (DS)], and high salinity [qRT-PCR (SS)] using a previously described method [114]. All expression ratios are presented as log2(treatment/standard). Negative values indicate that the standard has a higher expression level than the treatment, and expression ratios of 0 indicate no difference in expression between the treatment and standard