Table 1.
Expression of switchgrass genes involved in cell wall development
| Gene information | Expression information | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Microarray Probe | PvGene | Clade/Gene | Cluster | 0 h | Induced | Non-induced | Compare | |||||
| 6 h | 1 Day | 3 Days | 7 Days | 1 Day | 7 Days | 1 Day | 7 Days | |||||
| Expansin | ||||||||||||
| AP13ITG71529_at | Pavir.Aa00711 | α-Expansin | 4 | 260 | 1176 | 3260 | 2120 | 1002 | 2025 | 737 | 1 | 0 |
| KanlowCTG26349_s_at | Pavir.Aa00711 | α-Expansin | 4 | 185 | 572 | 1927 | 942 | 603 | 1215 | 397 | 1 | 0 |
| AP13ITG57935_at | Pavir.Aa00840 | β-Expansin | 5 | 3692 | 3666 | 134 | 71 | 40 | 16,793 | 8354 | − 1 | 0 |
| AP13CTG27439_s_at | Pavir.Ia02285 | β-Expansin | 5 | 2721 | 5043 | 2475 | 440 | 346 | 13636 | 6467 | − 1 | 0 |
| CESA | ||||||||||||
| AP13.12059.m00001_s_at | Pavir.Ca01073 | OsCESA1 | 2 | 1771 | 6165 | 4553 | 3517 | 2713 | 3351 | 2759 | 0 | 0 |
| AP13CTG00607_s_at | Pavir.Ba01088 | OsCESA3 | 4 | 1160 | 2574 | 2285 | 3019 | 1894 | 1391 | 1362 | 0 | 0 |
| AP13CTG25870_s_at | Pavir.J35010 | OsCESA8 | 2702 | 4804 | 3832 | 4513 | 3535 | 3877 | 3669 | 0 | 0 | |
| KanlowCTG12907_s_at | Pavir.J30974 | OsCESA4 | 16 | 51 | 30 | 98 | 94 | 114 | 58 | 65 | 1 | 1 |
| KanlowCTG34110_at | Pavir.Ib00804 | OsCESA7 | 0 | 8 | 11 | 9 | 10 | 9 | 9 | 8 | 0 | 0 |
| AP13CTG25049_s_at | Pavir.Bb02205 | OsCESA9 | 0 | 52 | 44 | 56 | 52 | 66 | 56 | 56 | 0 | 0 |
| KanlowCTG15421_s_at | Pavir.Ea00385 | OsCESA1 | 15 | 1795 | 1003 | 1622 | 2469 | 1176 | 1956 | 1810 | 0 | 0 |
| OTHSWCTG06249_s_at | OsCESA5 | 7 | 820 | 904 | 1810 | 803 | 1300 | 939 | 1094 | 1 | 0 | |
| AP13CTG06255_s_at | Pavir.J12858 | OsCESA2 | 16 | 917 | 549 | 827 | 1418 | 774 | 941 | 868 | 0 | 0 |
| COBRA | ||||||||||||
| AP13CTG00322_s_at | Pavir.Ia00526 | COB | 2 | 3061 | 6252 | 5466 | 3902 | 3750 | 4715 | 3158 | 0 | 0 |
| AP13ITG43381_at | Pavir.Ia00525 | COB | 5 | 1771 | 2628 | 697 | 164 | 697 | 3370 | 4215 | 0 | − 1 |
| Cellulose-like synthases | ||||||||||||
| AP13CTG01955_at | Pavir.Ia02025 | CSLA | 16 | 204 | 201 | 246 | 269 | 213 | 411 | 224 | 0 | 0 |
| AlamoCTG01742_s_at | Pavir.Ib01792 | CSLA | 12 | 86 | 145 | 279 | 474 | 394 | 207 | 233 | 0 | 1 |
| AP13CTG06284RC_s_at | Pavir.Ia00426 | CSLC | 13 | 350 | 151 | 187 | 161 | 144 | 228 | 133 | 0 | 0 |
| AP13CTG27051_s_at | Pavir.Fa01312 | CSLC | 5 | 133 | 251 | 39 | 25 | 32 | 147 | 98 | − 1 | 0 |
| KanlowCTG19494_s_at | Pavir.Fb00422 | CSLF | 5 | 335 | 304 | 327 | 150 | 134 | 154 | 125 | 1 | 0 |
| KanlowCTG37527_s_at | Pavir.Ba00688 | CSLF | 0 | 164 | 212 | 199 | 147 | 190 | 202 | 174 | 0 | 0 |
| Callose synthesis | ||||||||||||
| KanlowCTG45113_s_at | Pavir.Aa00017 | Callose synthase | 16 | 215 | 100 | 551 | 879 | 379 | 241 | 233 | 1 | 0 |
| AP13ITG74190RC_at | Pavir.Ib02063 | Callose-binding | 11 | 64 | 83 | 178 | 116 | 66 | 57 | 48 | 1 | 0 |
| Cell wall precursor | ||||||||||||
| KanlowCTG00021_s_at | Pavir.Ia00394 | UGD | 1 | 2487 | 8192 | 2541 | 1710 | 2633 | 4416 | 2852 | 0 | 0 |
| AP13CTG07489_at | Pavir.Ea03089 | UXS | 2 | 416 | 1017 | 583 | 537 | 605 | 637 | 637 | 0 | 0 |
| KanlowCTG22514_s_at | Pavir.Ea03089 | UXS | 0 | 530 | 1003 | 872 | 820 | 780 | 614 | 813 | 1 | 0 |
| AP13CTG10419_s_at | Pavir.Gb00500 | UXE | 1 | 792 | 1820 | 696 | 695 | 809 | 927 | 934 | 0 | 0 |
| AP13CTG28681_s_at | Pavir.Ba03802 | UXE | 3 | 186 | 396 | 335 | 329 | 488 | 374 | 300 | 0 | 1 |
| AP13CTG00023_s_at | Pavir.Gb00638 | UXT | 4 | 63 | 249 | 409 | 338 | 1273 | 72 | 156 | 1 | 1 |
| KanlowCTG06720_s_at | Pavir.Ia00627 | UXT | 2 | 695 | 1531 | 855 | 1053 | 1227 | 588 | 666 | 1 | 1 |
| AP13CTG08328RC_s_at | Pavir.Ab02692 | UER | 5 | 1017 | 969 | 566 | 639 | 474 | 2925 | 1380 | − 1 | 0 |
| Arabinoxylan (AX) and glucuronoarabinoxylan (GAX) synthesis (backbone) | ||||||||||||
| AP13CTG08590_s_at | Pavir.J27018 | IRX9 | 3 | 280 | 635 | 729 | 481 | 563 | 627 | 441 | 0 | 0 |
| AP13ITG73683_s_at | Pavir.Ib01337 | IRX9 | 5 | 461 | 385 | 195 | 116 | 124 | 469 | 345 | − 1 | − 1 |
| AlamoCTG02760_s_at | Pavir.Ea01094 | IRX9L | 12 | 136 | 139 | 207 | 370 | 362 | 87 | 174 | 1 | 1 |
| AP13ITG60236_at | Pavir.Ea01094 | IRX9L | 16 | 194 | 153 | 292 | 666 | 548 | 148 | 227 | 1 | 1 |
| AP13ITG74502_x_at | Pavir.J37721 | IRX14L | 1 | 221 | 2740 | 402 | 234 | 121 | 513 | 208 | 0 | 0 |
| KanlowCTG18373_s_at | Pavir.J06597 | IRX14L | 1 | 4068 | 5793 | 3770 | 2684 | 3800 | 3711 | 4190 | 0 | 0 |
| AP13CTG44601_s_at | Pavir.Ea03872 | IRX10 | 2 | 388 | 3191 | 1018 | 714 | 930 | 609 | 896 | 0 | 0 |
| AP13CTG03198_s_at | Pavir.J03056 | IRX10 | 2 | 443 | 3104 | 851 | 809 | 882 | 1413 | 1262 | − 1 | − 1 |
| Arabinoxylan (AX) and glucuronoarabinoxylan (GAX) synthesis (side chain) | ||||||||||||
| AP13ITG71461_at | Pavir.Aa01690 | GUX | 3 | 74 | 274 | 261 | 122 | 419 | 184 | 226 | 0 | 0 |
| KanlowCTG10196_x_at | Pavir.J03459 | GUX | 1 | 135 | 419 | 170 | 165 | 135 | 353 | 303 | 0 | 0 |
| AP13CTG04376_s_at | Pavir.Aa01745 | XAX1 | 5 | 146 | 236 | 85 | 73 | 64 | 330 | 217 | − 1 | 0 |
| AP13ITG43704_at | Pavir.Ea01415 | XAT1 | 13 | 136 | 29 | 19 | 15 | 20 | 73 | 53 | − 1 | 0 |
| AP13.12340.m00010_s_at | Pavir.Da01068 | XAT1 | 0 | 179 | 147 | 173 | 190 | 146 | 212 | 227 | 0 | − 1 |
| PF02458 (candidates for forming the ester linkages in GAX) | ||||||||||||
| AP13CTG59034RC_at | Pavir.Gb00939 | 12 | 22 | 34 | 103 | 280 | 171 | 27 | 30 | 0 | 1 | |
| AP13ITG73138_at | Pavir.Fa02187 | 5 | 190 | 143 | 60 | 27 | 106 | 68 | 135 | 0 | 0 | |
| KanlowCTG26994RC_at | Pavir.Aa01433 | 12 | 73 | 138 | 256 | 626 | 354 | 98 | 105 | 1 | 1 | |
| AP13ITG72773_s_at | Pavir.Eb00373 | 13 | 1226 | 269 | 126 | 89 | 117 | 509 | 311 | − 1 | 0 | |
| Pectin biosynthesis | ||||||||||||
| AP13CTG05511_s_at | Pavir.Ba00640 | ARAD1 | 1 | 79 | 95 | 65 | 80 | 75 | 131 | 80 | − 1 | 0 |
| AP13CTG06439_at | Pavir.Aa00624 | GALS1 | 4 | 114 | 422 | 512 | 481 | 490 | 212 | 186 | 1 | 1 |
| AP13CTG14035_at | Pavir.J20866 | RGXT4 | 4 | 129 | 211 | 228 | 254 | 217 | 291 | 219 | − 1 | 0 |
| AP13ITG63440_at | Pavir.J14339 | RGXT4 | 4 | 120 | 209 | 247 | 280 | 235 | 304 | 239 | 0 | 0 |
| AP13CTG02428_s_at | Pavir.Ba01601 | GAUT1 | 0 | 1418 | 1296 | 1565 | 1607 | 1332 | 1562 | 1462 | 0 | 0 |
| AP13CTG18174_at | Pavir.Ba00237 | GAUT7 | 2 | 118 | 331 | 247 | 232 | 125 | 447 | 315 | − 1 | − 1 |
| KanlowCTG43804_at | Pavir.Fb01281 | GAUT4 | 16 | 90 | 77 | 138 | 150 | 95 | 206 | 162 | − 1 | − 1 |
| AP13CTG09682_s_at | Pavir.Ab01751 | GAUT8 | 5 | 609 | 755 | 369 | 449 | 225 | 573 | 371 | − 1 | − 1 |
| Pectin esterases | ||||||||||||
| AP13ITG41170_at | Pavir.Ea01491 | PME | 5 | 699 | 484 | 73 | 80 | 72 | 104 | 97 | 0 | 0 |
| AP13CTG29622_at | Pavir.Ia02028 | PME | 13 | 55 | 13 | 7 | 9 | 26 | 12 | 12 | 0 | 0 |
| AP13ITG67053RC_at | Pavir.Eb02306 | PAE | 5 | 83 | 92 | 27 | 15 | 10 | 602 | 200 | − 1 | 0 |
| AP13CTG10801RC_at | Pavir.Ba00334 | PAE | 9 | 838 | 495 | 289 | 407 | 78 | 852 | 353 | − 1 | 0 |
| KanlowCTG09579_s_at | Pavir.Eb04062 | PAE | 1 | 174 | 290 | 170 | 167 | 145 | 280 | 180 | − 1 | 0 |
| Wall structural protein | ||||||||||||
| AP13CTG23898_at | Pavir.J33924 | AGP13 | 5 | 923 | 976 | 127 | 126 | 121 | 774 | 399 | − 1 | 0 |
| AP13ITG74104_at | Pavir.J33924 | AGP13 | 5 | 120 | 158 | 13 | 13 | 16 | 174 | 67 | − 1 | − 1 |
| AP13ITG53973_s_at | Pavir.Eb02706 | FLA | 1 | 315 | 1924 | 529 | 352 | 111 | 188 | 146 | 1 | 0 |
Expression values at each data point represent the mean of three biological replicates. Cluster represents the expression groups of filtered genes in induced samples defined by self-organizing map (SOM) method (Fig. 6a). Differential expression genes between induced and non-induced samples on 1 and 7 days were identified by the linear model in LIMMA [84]; − 1 (represented by bold italic), significant lower expression in induced samples than in non-induced samples, 1 (represented by italic), significant higher expression in induced samples than in non-induced samples, 0, no change between induced and non-induced samples