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Table 3 Conserved miRNAs differentially expressed in developing wheat grain and their predicted target gene functions

From: Identification of microRNAs in developing wheat grain that are potentially involved in regulating grain characteristics and the response to nitrogen levels

Grain filling stagesmiRNAAbundance (RPM)P- valueAbundance (RPM)P- valueTarget function
LN-7LN-17LN-27HN-7HN-17HN-27
Relative abundance during grain filling stages (RAGS)tae-miR9674b-5p13,24214,58019,7802.10E-0514,33714,83120,3743.32E-06SCF ubiquitin ligase complex; calcium-dependent protein kinase 20-like
tae-miR1603696691951253.34E-074129615753765.90E-05serine carboxypeptidase; transcription factor; Auxin reponse factor
ata-miR166a-3p9081281840101.05E-088443317145649.00E-09kinesin-1-like protein PSS1; transport
tae-miR159a5372138127061.28E-065191111050562.89E-07MYB; 40D repeat
Relative abundance at early stage(RAES)osa-miR171a1235113581.10E-091299172422.73E-07DELLA proteins RGL2; malate dehydrogenase
ata-miR172c-3p16210401.65E-051806305.64E-06cytokinin response factor1; DnaJ
ata-miR396a-5p18699679644.70E-07172610857621.40E-07phosphatidylinositol 4-phosphate 5-kinase 1; glutamate dehydrogenase; response to GA
ata-miR396c-5p1441674.11E-061342232.34E-04GTPase activity; HSP protein; RPM1
ata-miR396e-5p22647727097.40E-0823669317222.87E-07transcription factor TFIID; ribonuclease P activity
ata-miR393-5p_L-1R + 132545376.88E-0733144411.64E-07auxin-activated signaling; protein TRANSPORT INHIBITOR RESPONSE 1; LRR kinase
ata-miR167f-3p_L-1R + 16126195.86E-04574892.89E-04ubiquitin ligase complex; lysosomal alpha-mannosidase
ata-miR169e-5p38521.23E-0663518.42E-05serine-type endopeptidase; peptidase
osa-miR168a-5p10884724.97E-0311078735.45E-03WRKY; Cul4-RING E3 ubiquitin ligase;
osa-miR168a-3p_L-311550231.79E-0416247395.70E-05ubiquitin domain-containing protein DSK2b
ata-miR169g-3p_L + 1R-1250704.17E-073261705.98E-06ubiquitin protein ligase; RPM protein
osa-miR171e-5p_2ss2GA21AG3441201.51E-063611959.00E-10protein binding
osa-miR530-5p_L + 11266103.00E-04134109308.85E-05SCF ubiquitin ligase complex; fructose-bisphosphate aldolase
ata-miR5168-3p56926384542.00E-1054095595110.00E+ 00kinesin-1-like protein PSS1; Transcription factor;
osa-miR530-5p_R + 1523603.00E-045249161.45E-03fructose-bisphosphate aldolase; HSP70;
osa-miR159a.1_L + 18615419.85E-03949858.26E-05MYB; WS40 repeat protein
tae-miR9776_L-1R + 1_1ss18AG1901671453.54E-032151581436.85E-03cell division; O-methyltransferase
osa-miR166g-3p_L + 1_1ss21TC11814161.10E-059724289.90E-06transcription factor; transport
tae-miR171a6961251261.00E-107701561933.80E-06DELLA protein RGL2-like; malate dehydrogenase
ata-miR394-5p28642983.46E-06354471413.40E-09SCF ubiquitin ligase complex; glutathione transferase activity
ata-miR9772a-5p_L-2R + 24721161.17E-044030201.13E-02SCF ubiquitin ligase complex
Relative abundance at middle stage(RAMS)ata-miR528-5p394634.89E-042838231.99E-02lectin-rich repeat receptor kinase
bdi-miR531_L-4R + 1_1ss5CT1733187.10E-031238231.27E-02NAD(P)H dehydrogenase; ABC transporter
ata-miR172b-3p2266341.65E-052636201.35E-02Cytokinin response factor; chaperone binding;
tae-miR1127b-3p_1ss12TC71843.57E-02226132.84E-04UDP-glucuronate decarboxylase; SCF ubiquitin ligase complex
tae-miR9652-5p32803.46E-02018102.63E-02retrograde transport
tae-miR167c-5p6817935954.30E-026387903362.95E-05SCF ubiquitin ligase complex
tae-miR9657a-3p37124916.02E-052387685.70E-05serine-type endopeptidase inhibitor activity; amino acid transport; WRKY
tae-miR9655-3p2110313124.10E-07010993332.78E-07L-fucosidase; SCF ubiquitin ligase complex
tae-miR9658-3p2437201.10E-021953154.54E-04SCF ubiquitin ligase complex; RPM1
Relative abundance at later stage (RALS)bdi-miR156h-3p_L + 1321102075.24E-04231032199.19E-06WRKY transcription factor
zma-miR156d-3p_L + 1_1ss9TC5501145.71E-05928643.78E-06catalytic activity
ata-miR167b-5p1115768891.38E-061246346484.41E-07SCF ubiquitin ligase complex
tae-miR3191792276823.93E-0613019910181.94E-06MYB transcription factor; Dnaj protein
osa-miR8273417410027.10E-09415666822.09E-07SPX-domain-containing genes
tae-miR408_L-1282072136.71E-06251272046.88E-05L-ascorbate oxidase; LPEAT1-like
tae-miR9666a-3p043948120.00E+ 0004929113.68E-07Alternative splicing regulator; regulatory protein NPR5
tae-miR9666b-3p32136744.59E-0702553181.46E-07DNA-directed RNA polymerase II subunit 1
tae-miR9664–3p_L-11529554.78E-030621511.67E-07RPM1 protein; zinc finger CCCH domain-containing; glucosidase
hvu-miR399024662.40E-05054622.18E-05NB-ARC domain; glucosyltransferase
lus-miR159b_R + 1_1ss21CT101421509.28E-0478221792.10E-04MYB
osa-miR319a-3p.2-3p_R + 13872106081.23E-055071935373.02E-05SCF ubiquitin ligase complex; MYB
  1. aAbundance is indicated by normalized reads (reads per million of total miRNA reads (RPM)
  2. bRPM ≥ 20 in these libraries
  3. cThe values are the means of three biological replicates
  4. dP-value < 0.05 (5.00E-02) means a significant difference among different developmental stages