Table 3.
Conserved miRNAs differentially expressed in developing wheat grain and their predicted target gene functions
| Grain 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-miR9674b-5p | 13,242 | 14,580 | 19,780 | 2.10E-05 | 14,337 | 14,831 | 20,374 | 3.32E-06 | SCF ubiquitin ligase complex; calcium-dependent protein kinase 20-like |
| tae-miR160 | 3696 | 6919 | 5125 | 3.34E-07 | 4129 | 6157 | 5376 | 5.90E-05 | serine carboxypeptidase; transcription factor; Auxin reponse factor | |
| ata-miR166a-3p | 9081 | 2818 | 4010 | 1.05E-08 | 8443 | 3171 | 4564 | 9.00E-09 | kinesin-1-like protein PSS1; transport | |
| tae-miR159a | 5372 | 1381 | 2706 | 1.28E-06 | 5191 | 1110 | 5056 | 2.89E-07 | MYB; 40D repeat | |
| Relative abundance at early stage(RAES) | osa-miR171a | 1235 | 113 | 58 | 1.10E-09 | 1299 | 172 | 42 | 2.73E-07 | DELLA proteins RGL2; malate dehydrogenase |
| ata-miR172c-3p | 162 | 104 | 0 | 1.65E-05 | 180 | 63 | 0 | 5.64E-06 | cytokinin response factor1; DnaJ | |
| ata-miR396a-5p | 1869 | 967 | 964 | 4.70E-07 | 1726 | 1085 | 762 | 1.40E-07 | phosphatidylinositol 4-phosphate 5-kinase 1; glutamate dehydrogenase; response to GA | |
| ata-miR396c-5p | 144 | 16 | 7 | 4.11E-06 | 134 | 22 | 3 | 2.34E-04 | GTPase activity; HSP protein; RPM1 | |
| ata-miR396e-5p | 2264 | 772 | 709 | 7.40E-08 | 2366 | 931 | 722 | 2.87E-07 | transcription factor TFIID; ribonuclease P activity | |
| ata-miR393-5p_L-1R + 1 | 325 | 45 | 37 | 6.88E-07 | 331 | 44 | 41 | 1.64E-07 | auxin-activated signaling; protein TRANSPORT INHIBITOR RESPONSE 1; LRR kinase | |
| ata-miR167f-3p_L-1R + 1 | 61 | 26 | 19 | 5.86E-04 | 57 | 48 | 9 | 2.89E-04 | ubiquitin ligase complex; lysosomal alpha-mannosidase | |
| ata-miR169e-5p | 38 | 5 | 2 | 1.23E-06 | 63 | 5 | 1 | 8.42E-05 | serine-type endopeptidase; peptidase | |
| osa-miR168a-5p | 108 | 84 | 72 | 4.97E-03 | 110 | 78 | 73 | 5.45E-03 | WRKY; Cul4-RING E3 ubiquitin ligase; | |
| osa-miR168a-3p_L-3 | 115 | 50 | 23 | 1.79E-04 | 162 | 47 | 39 | 5.70E-05 | ubiquitin domain-containing protein DSK2b | |
| ata-miR169g-3p_L + 1R-1 | 250 | 7 | 0 | 4.17E-07 | 326 | 17 | 0 | 5.98E-06 | ubiquitin protein ligase; RPM protein | |
| osa-miR171e-5p_2ss2GA21AG | 344 | 12 | 0 | 1.51E-06 | 361 | 19 | 5 | 9.00E-10 | protein binding | |
| osa-miR530-5p_L + 1 | 126 | 61 | 0 | 3.00E-04 | 134 | 109 | 30 | 8.85E-05 | SCF ubiquitin ligase complex; fructose-bisphosphate aldolase | |
| ata-miR5168-3p | 5692 | 638 | 454 | 2.00E-10 | 5409 | 559 | 511 | 0.00E+ 00 | kinesin-1-like protein PSS1; Transcription factor; | |
| osa-miR530-5p_R + 1 | 52 | 36 | 0 | 3.00E-04 | 52 | 49 | 16 | 1.45E-03 | fructose-bisphosphate aldolase; HSP70; | |
| osa-miR159a.1_L + 1 | 86 | 15 | 41 | 9.85E-03 | 94 | 9 | 85 | 8.26E-05 | MYB; WS40 repeat protein | |
| tae-miR9776_L-1R + 1_1ss18AG | 190 | 167 | 145 | 3.54E-03 | 215 | 158 | 143 | 6.85E-03 | cell division; O-methyltransferase | |
| osa-miR166g-3p_L + 1_1ss21TC | 118 | 14 | 16 | 1.10E-05 | 97 | 24 | 28 | 9.90E-06 | transcription factor; transport | |
| tae-miR171a | 696 | 125 | 126 | 1.00E-10 | 770 | 156 | 193 | 3.80E-06 | DELLA protein RGL2-like; malate dehydrogenase | |
| ata-miR394-5p | 286 | 42 | 98 | 3.46E-06 | 354 | 47 | 141 | 3.40E-09 | SCF ubiquitin ligase complex; glutathione transferase activity | |
| ata-miR9772a-5p_L-2R + 2 | 47 | 21 | 16 | 1.17E-04 | 40 | 30 | 20 | 1.13E-02 | SCF ubiquitin ligase complex | |
| Relative abundance at middle stage(RAMS) | ata-miR528-5p | 39 | 46 | 3 | 4.89E-04 | 28 | 38 | 23 | 1.99E-02 | lectin-rich repeat receptor kinase |
| bdi-miR531_L-4R + 1_1ss5CT | 17 | 33 | 18 | 7.10E-03 | 12 | 38 | 23 | 1.27E-02 | NAD(P)H dehydrogenase; ABC transporter | |
| ata-miR172b-3p | 22 | 66 | 34 | 1.65E-05 | 26 | 36 | 20 | 1.35E-02 | Cytokinin response factor; chaperone binding; | |
| tae-miR1127b-3p_1ss12TC | 7 | 18 | 4 | 3.57E-02 | 2 | 26 | 13 | 2.84E-04 | UDP-glucuronate decarboxylase; SCF ubiquitin ligase complex | |
| tae-miR9652-5p | 3 | 28 | 0 | 3.46E-02 | 0 | 18 | 10 | 2.63E-02 | retrograde transport | |
| tae-miR167c-5p | 681 | 793 | 595 | 4.30E-02 | 638 | 790 | 336 | 2.95E-05 | SCF ubiquitin ligase complex | |
| tae-miR9657a-3p | 37 | 124 | 91 | 6.02E-05 | 23 | 87 | 68 | 5.70E-05 | serine-type endopeptidase inhibitor activity; amino acid transport; WRKY | |
| tae-miR9655-3p | 21 | 1031 | 312 | 4.10E-07 | 0 | 1099 | 333 | 2.78E-07 | L-fucosidase; SCF ubiquitin ligase complex | |
| tae-miR9658-3p | 24 | 37 | 20 | 1.10E-02 | 19 | 53 | 15 | 4.54E-04 | SCF ubiquitin ligase complex; RPM1 | |
| Relative abundance at later stage (RALS) | bdi-miR156h-3p_L + 1 | 32 | 110 | 207 | 5.24E-04 | 23 | 103 | 219 | 9.19E-06 | WRKY transcription factor |
| zma-miR156d-3p_L + 1_1ss9TC | 5 | 50 | 114 | 5.71E-05 | 9 | 28 | 64 | 3.78E-06 | catalytic activity | |
| ata-miR167b-5p | 111 | 576 | 889 | 1.38E-06 | 124 | 634 | 648 | 4.41E-07 | SCF ubiquitin ligase complex | |
| tae-miR319 | 179 | 227 | 682 | 3.93E-06 | 130 | 199 | 1018 | 1.94E-06 | MYB transcription factor; Dnaj protein | |
| osa-miR827 | 34 | 174 | 1002 | 7.10E-09 | 41 | 566 | 682 | 2.09E-07 | SPX-domain-containing genes | |
| tae-miR408_L-1 | 28 | 207 | 213 | 6.71E-06 | 25 | 127 | 204 | 6.88E-05 | L-ascorbate oxidase; LPEAT1-like | |
| tae-miR9666a-3p | 0 | 439 | 4812 | 0.00E+ 00 | 0 | 492 | 911 | 3.68E-07 | Alternative splicing regulator; regulatory protein NPR5 | |
| tae-miR9666b-3p | 3 | 213 | 674 | 4.59E-07 | 0 | 255 | 318 | 1.46E-07 | DNA-directed RNA polymerase II subunit 1 | |
| tae-miR9664–3p_L-1 | 15 | 29 | 55 | 4.78E-03 | 0 | 62 | 151 | 1.67E-07 | RPM1 protein; zinc finger CCCH domain-containing; glucosidase | |
| hvu-miR399 | 0 | 24 | 66 | 2.40E-05 | 0 | 54 | 62 | 2.18E-05 | NB-ARC domain; glucosyltransferase | |
| lus-miR159b_R + 1_1ss21CT | 101 | 42 | 150 | 9.28E-04 | 78 | 22 | 179 | 2.10E-04 | MYB | |
| osa-miR319a-3p.2-3p_R + 1 | 387 | 210 | 608 | 1.23E-05 | 507 | 193 | 537 | 3.02E-05 | SCF ubiquitin ligase complex; MYB | |
aAbundance is indicated 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