Table 3. Up-regulated photosynthesis and flavonoid biosynthesis related genes in JA-CMS at the SS and/or MS stages.
| Category | Function | Gene ID | SS stage | MS stage | ||||
| Fold | P value | Q value | Fold | P value | Q value | |||
| Photosynthesis | Photosystem I subunit X | comp53760_c0 | 2.53 | 2.23E-08 | 2.32E-06 | 2.56 | 1.23E-07 | 1.23E-05 |
| Plastocyanin | comp65386_c0 | 3.02 | 1.48E-30 | 7.37E-28 | 2.61 | 6.19E-24 | 2.34E-21 | |
| Photosystem I subunit PsaO | comp65579_c0 | 3.77 | 8.58E-17 | 1.99E-14 | 3.61 | 4.29E-14 | 8.67E-12 | |
| Photosystem II PsbW protein | comp65639_c0 | 2.34 | 5.34E-07 | 4.77E-05 | 2.35 | 1.28E-06 | 1.14E-04 | |
| Photosystem II 10kDa protein | comp68020_c0 | 1.17 | 3.48E-10 | 4.54E-08 | Not significant | |||
| Photosystem II PsbY protein | comp68793_c0 | 1.72 | 4.38E-07 | 3.96E-05 | Not significant | |||
| Photosystem I subunit XI | comp70643_c0 | 1.83 | 3.25E-15 | 6.79E-13 | 1.60 | 9.63E-11 | 1.44E-08 | |
| Ferredoxin | comp71277_c0 | 3.11 | 4.21E-18 | 1.07E-15 | 2.68 | 9.12E-15 | 1.94E-12 | |
| Photosystem I subunit IV | comp72189_c0 | 1.36 | 1.59E-08 | 1.70E-06 | 1.07 | 1.35E-05 | 1.01E-03 | |
| Photosystem II oxygen-evolving enhancer protein 1 | comp73151_c0 | 2.96 | 7.52E-57 | 9.24E-54 | 2.74 | 1.66E-45 | 1.70E-42 | |
| Photosystem II 22kDa protein | comp73229_c0 | 2.28 | 2.04E-14 | 4.05E-12 | 2.14 | 4.45E-12 | 7.67E-10 | |
| Photosystem II oxygen-evolving enhancer protein 2 | comp73376_c0 | 1.18 | 2.53E-10 | 3.38E-08 | Not significant | |||
| Photosystem I subunit III | comp73879_c0 | 1.83 | 2.89E-20 | 8.55E-18 | 1.65 | 1.73E-14 | 3.61E-12 | |
| Photosystem II oxygen-evolving enhancer protein 3 | comp84774_c2 | 1.83 | 4.26E-10 | 5.51E-08 | 1.55 | 2.13E-07 | 2.10E-05 | |
| Flavonoid biosynthesis | Chalcone synthase | comp72843_c0 | 2.23 | 2.61E-41 | 2.07E-38 | 1.63 | 1.96E-29 | 1.03E-26 |
| comp72843_c1 | 2.11 | 6.78E-13 | 1.18E-10 | 1.48 | 4.46E-09 | 5.49E-07 | ||
| comp84628_c1 | 2.06 | 5.90E-62 | 8.22E-59 | 1.56 | 2.09E-43 | 2.00E-40 | ||
| comp84628_c0 | 1.88 | 2.55E-78 | 5.51E-75 | 1.56 | 2.23E-68 | 4.13E-65 | ||
| Anthocyanidin reductase | comp73018_c0 | 1.27 | 1.48E-39 | 1.09E-36 | Not significant | |||
| Leucoanthocyanidin dioxygenase | comp75804_c0 | 2.17 | 1.28E-94 | 4.02E-91 | 1.89 | 3.33E-81 | 8.49E-78 | |
| Bifunctional dihydroflavonol 4-reductase/flavanone 4-reductase | comp75884_c0 | 1.75 | 2.37E-69 | 3.81E-66 | 1.54 | 8.80E-60 | 1.35E-56 | |
| Trans-cinnamate 4-monooxygenase | comp80855_c0 | 1.47 | 1.42E-71 | 2.54E-68 | 1.09 | 7.25E-44 | 7.05E-41 | |
| Flavonoid 3′,5′-hydroxylase | comp81439_c0 | 2.50 | 1.74E-93 | 4.97E-90 | 1.86 | 3.08E-57 | 4.39E-54 | |
| Naringenin 3-dioxygenase | comp82651_c1 | 1.67 | 5.00E-94 | 1.49E-90 | 1.25 | 6.40E-67 | 1.12E-63 | |
Note: Fold = log2(fold change). Significant DE genes were determined based on |log2(fold change)|>1 and FDR q value<0.005.