Table 4.
Differentially expressed novel miRNAs associated with grain development and their target gene functions
| Grian filling stages | miRNA | Abundance (RPM) | P- value | Abundance (RPM) | P- value | Target function | ||||
|---|---|---|---|---|---|---|---|---|---|---|
| LN-7 | LN-17 | LN-27 | HN-7 | HN-17 | HN-27 | |||||
| Relative abundance during grain filling stages (RAGS) | tae-miR2916-p5_2ss2AG17TG | 1070 | 3667 | 9557 | 2.49E-06 | 1610 | 2067 | 2868 | 1.52E-05 | protein serine/threonine kinase; glutathione S-transferase (GSTF)1; DELLA |
| tae-miR2916-p3_2ss2TC17CA | 2518 | 7110 | 27,736 | 5.92E-08 | 3507 | 4610 | 7049 | 1.66E-06 | Peroxidase; fructose-bisphosphate aldolase; GTPase | |
| tae-miR9655-p5 | 2936 | 24,657 | 11,329 | 2.48E-05 | 668 | 20,120 | 11,554 | 1.30E-09 | transcription factor; oxidation-reduction | |
| Relative abundance at early stages(RAES) | tae-miR166d-p3 | 107 | 46 | 70 | 5.58E-03 | 83 | 56 | 80 | 1.97E-02 | cell differentiation; kinesin-1-like protein PSS1 |
| PC-5p-30718_164 | 39 | 7 | 0 | 6.33E-05 | 49 | 2 | 15 | 4.94E-05 | BRASSINOSTEROID INSENSITIVE 1; 1,3-beta-D-glucan synthase | |
| tae-miR815c-p5_2ss6CT21CT | 107 | 92 | 21 | 3.62E-04 | 121 | 61 | 51 | 4.76E-04 | UDP-arabinose 4-epimerase 1-like; transcription factor TGA2-like; Dnaj | |
| tae-miR9662b-p5 | 128 | 34 | 15 | 5.04E-07 | 153 | 31 | 18 | 4.56E-05 | beta-fructofuranosidase | |
| tae-miR9662a-p5 | 95 | 62 | 46 | 5.53E-04 | 112 | 77 | 67 | 3.96E-02 | beta-fructofuranosidase; | |
| tae-miR9672b-p5 | 125 | 33 | 0 | 1.57E-04 | 94 | 30 | 10 | 1.65E-03 | LRR receptor-like serine/threonine-protein kinase FLS2-like | |
| tae-miR9779-p3 | 244 | 40 | 11 | 1.15E-03 | 361 | 43 | 93 | 9.91E-04 | hexose transmembrane transport | |
| Relative abundance at middle stages (RAMS) | tae-miR5384-p5 | 577 | 627 | 132 | 7.30E-06 | 579 | 686 | 489 | 1.07E-03 | UDP-glycosyltransferase 83A1-like; ethylene-responsive transcription factor 1B |
| PC-5p-3645_2157 | 33 | 175 | 148 | 1.88E-05 | 41 | 154 | 105 | 1.81E-05 | Metalloendopeptidase; SCF ubiquitin ligase | |
| PC-3p-4780_1750 | 4 | 231 | 101 | 3.90E-05 | 0 | 135 | 104 | 1.09E-06 | aspartic endopeptidase; transcription factor | |
| PC-5p-24289_247 | 2 | 23 | 3 | 1.20E-03 | 0 | 26 | 16 | 6.58E-04 | NEDD8-specific protease; protein ECERIFERUM 1-like | |
| PC-5p-18073_397 | 0 | 66 | 26 | 3.34E-03 | 0 | 69 | 26 | 3.51E-06 | beta-glucosidase; BRASSINOSTEROID INSENSITIVE 1-like | |
| PC-3p-21502_303 | 23 | 34 | 0 | 1.30E-03 | 38 | 30 | 25 | 1.03E-02 | Metalloendopeptidase; aspartic-type endopeptidase;MYB | |
| tae-miR164-p3 | 68 | 159 | 143 | 1.24E-03 | 57 | 165 | 131 | 3.76E-03 | auxin response factor 3-like; transcription factor IIB | |
| tae-miR164b-p3 | 16 | 62 | 18 | 1.71E-03 | 16 | 40 | 21 | 3.79E-03 | auxin response factor 2-like; high-affinity nitrate transporter 2.1-like | |
| tae-miR1137a-p5_2ss9GA20GC | 0 | 28 | 2 | 3.31E-02 | 0 | 13 | 2 | 1.77E-03 | DNA mismatch repair protein MSH6 | |
| tae-miR2275-p5 | 0 | 26 | 13 | 1.82E-04 | 0 | 28 | 2 | 1.66E-04 | LRR receptor-like serine/threonine-protein kinase FLS2; BRASSINOSTEROID INSENSITIVE 1 | |
| PC-5p-21100_312 | 0 | 35 | 17 | 2.14E-03 | 0 | 27 | 9 | 2.75E-03 | glycerol-3-phosphate dehydrogenase; protein gar2 | |
| PC-3p-15070_514 | 0 | 61 | 25 | 7.94E-04 | 0 | 44 | 41 | 2.64E-06 | transcription factor | |
| tae-miR9653b-p3 | 6 | 36 | 5 | 8.36E-03 | 20 | 21 | 0 | 5.81E-04 | protein binding | |
| PC-3p-11233_746 | 38 | 65 | 9 | 6.74E-05 | 22 | 58 | 33 | 1.38E-02 | Metalloendopeptidase | |
| PC-3p-16735_445 | 10 | 43 | 13 | 3.99E-06 | 0 | 38 | 23 | 1.72E-05 | O-acyltransferase WSD1-like | |
| PC-5p-12716_642 | 0 | 101 | 75 | 1.14E-04 | 0 | 111 | 79 | 6.00E-04 | MAPK cascade; BRASSINOSTEROID INSENSITIVE 1 | |
| tae-miR6300-p5 | 23 | 312 | 268 | 4.86E-05 | 25 | 258 | 253 | 1.42E-05 | protein RPM1; response to nitrate | |
| Relative abundance at later stages (RALS) | tae-miR2592bj-p3_2ss12TC19AT | 82 | 193 | 380 | 6.17E-04 | 114 | 217 | 135 | 4.57E-04 | protein serine/threonine phosphatase; transporter; protein RPM1-like |
| PC-5p-31845_154 | 0 | 8 | 21 | 4.35E-03 | 0 | 8 | 11 | 5.36E-03 | receptor-like serine/threonine-protein kinase SD1–6 | |
| PC-5p-1231_4743 | 52 | 260 | 372 | 1.48E-06 | 40 | 339 | 453 | 1.35E-07 | serine-type endopeptidase | |
| PC-5p-13909_573 | 0 | 47 | 66 | 6.93E-05 | 0 | 42 | 56 | 7.87E-05 | GTPase | |
| PC-3p-13925_573 | 17 | 11 | 55 | 1.16E-06 | 5 | 9 | 87 | 6.72E-06 | serine-type carboxypeptidase; valine-tRNA ligase | |
| tae-miR408-p5_1ss20GA | – | 16 | 17 | 5.81E-04 | – | 16 | 22 | 9.12E-03 | BRASSINOSTEROID INSENSITIVE 1 | |
aAbundance is represented by normalized reads (reads per million of total miRNA reads (RPM))
bRPM ≥20 in these libraries
cThe values are the means of three biological replicates
dP-value < 0.05 (5.00E-02) means a significant difference among different developmental stages