Table 4.
GO annotation of up- and down-regulated homoeologous copies of genes in the synthetic polyploid wheat
| GO term | Biological process | D genome (AT) | AB genome (TC) | ||
|---|---|---|---|---|---|
| suppression | activation | suppression | activation | ||
| GO:0009987 | cellular process | 264 | 512 | 145 | 1231 |
| GO:0008152 | metabolic process | 214 | 454 | 137 | 1039 |
| GO:0009058 | biosynthetic process | 127 | 170 | 53 | 494 |
| GO:0019538 | protein metabolic process | 115 | 199 | 78 | 545 |
| GO:0016043 | cellular component organization | 72 | 123 | 39 | 290 |
| GO:0006412 | translation | 64 | 54** | 29 | 232 |
| GO:0006810 | transport | 61 | 108 | 42 | 287 |
| GO:0006139 | nucleic acid metabolic process | 55 | 101 | 21 | 255 |
| GO:0006950 | response to stress | 53 | 65 | 24 | 201 |
| GO:0007275 | Multi-cellular organism development | 51 | 101 | 31 | 229 |
| GO:0008150 | Biological process | 45** | 118 | 45 | 295 |
| GO:0006464 | protein modification process | 42 | 95 | 30 | 205 |
| GO:0000003 | reproduction | 38 | 69 | 33 | 154 |
| GO:0009628 | response to abiotic stimulus | 30 | 32 | 15 | 88 |
| GO:0009790 | embryonic development | 29 | 52 | 24 | 121 |
| GO:0009791 | post-embryonic development | 27 | 41 | 19 | 102 |
| GO:0040007 | growth | 23 | 50 | 21 | 111 |
| GO:0007049 | cell cycle | 22 | 49 | 26* | 93 |
| GO:0006091 | precursor metabolites and energy | 21 | 62* | 4 | 97 |
| GO:0006350 | transcription | 19 | 56 | 10 | 106 |
| GO:0006519 | cellular amino acid metabolic process | 18 | 17 | 0** | 72 |
| GO:0009653 | anatomical structure morphogenesis | 17 | 42 | 10 | 78 |
| GO:0007165 | signal transduction | 17 | 55 | 22 | 139 |
| GO:0009056 | catabolic process | 14** | 98 | 21 | 172 |
| GO:0009607 | response to biotic stimulus | 13 | 19 | 6 | 36 |
| GO:0009719 | response to endogenous stimulus | 13 | 24 | 2 | 55 |
| GO:0008219 | cell death | 11 | 19 | 7 | 39 |
| GO:0030154 | cell differentiation | 11 | 35 | 5 | 71 |
| GO:0016265 | death | 11 | 19 | 7 | 41 |
| GO:0019748 | secondary metabolic process | 10 | 7 | 0 | 12 |
| GO:0005975 | carbohydrate metabolic process | 9** | 80 | 14 | 94** |
| GO:0006259 | DNA metabolic process | 9 | 17 | 3 | 49 |
| GO:0006629 | lipid metabolic process | 9 | 24 | 5 | 39 |
| GO:0007154 | cell communication | 8 | 16** | 5 | 47** |
| GO:0019725 | cellular homeostasis | 7 | 6 | 4 | 34 |
| GO:0009605 | response to external stimulus | 6 | 10 | 2 | 31 |
| GO:0007267 | cell-cell signaling | 5 | 4 | 1 | 13 |
| GO:0015979 | photosynthesis | 5 | 10 | 3 | 15 |
| GO:0016049 | cell growth | 3 | 10 | 3 | 14 |
| GO:0009991 | response to extracellular stimulus | 3 | 5 | 2 | 17 |
| GO:0007610 | behavior | 2 | 9 | 2 | 34 |
| GO:0009908 | flower development | 2 | 3 | 0 | 8 |
| GO:0009838 | abscission | 1 | 0 | 0 | 1 |
| GO:0040029 | regulation of gene expression, epigenetic | 1 | 8 | 0 | 11 |
* GO categories showing statistically significant overrepresentation of genes (Fisher exact test, FDR ≤ 0.05)
** GO categories showing statistically significant underrepresentation of genes (Fisher exact test, FDR ≤ 0.05)