Table 3 Potential targets of miRNAs with significantly changed expression during rice grain filling

Up-regulated

miR159

LOC_Os01g12700(1)

Myb-like DNA-binding domain

Signal transduction or/TF

LOC_Os05g41166(1)

Transcription factor GAMYB

Signal transduction or/TF

miR164

LOC_Os02g36880(1)

NAC domain protein NAC5

Signal transduction or/TF

LOC_Os06g46270(1)

NAC domain-containing protein 21/22

Signal transduction or/TF

miR1850

LOC_Os04g33510 (2.5)

Expressed protein

Unknown pathway

LOC_Os09g29200 (3.5)

Glutathione S-transferase

Redox homeostasis

miR1862

LOC_Os02g30730(3)

SART-1 family protein

Cell cycle/biogenesis

LOC_Os02g48300(4)

Flavonol synthase/flavanone 3- hydroxylase

secondary metabolism

LOC_Os05g03174(4)

F-box domain containing protein

Protein degradation

LOC_Os01g53700(4.5)

Glycosyltransferase

Carbohydrate metabolism

LOC_Os03g58290(4.5)

Mitochondrial-processing peptidase alpha subunit

Amide acid metabolism

LOC_Os07g22930(4.5)

Granule bound starch synthase GBSS1b,

Carbohydrate metabolism

LOC_Os07g09460(4.5)

Indole-3-glycerol phosphate lyase

Lipid metabolism

miR1874-3p

LOC_Os01g05680(4)

Geranylgeranyl transferase type-1 beta subunit

Protein folding and transport

LOC_Os07g38110(5)

Tic20-like protein

Protein folding and transport

miR1874-5p

LOC_Os03g02590(3.5)

Peroxisomal membrane protein PEX11-

Redox homeostasis

LOC_Os05g18774(3.5)

Protein phosphatase 1

Signal transduction or/TF

LOC_Os01g16870(4.5)

Argonaute-like protein

RNA processing

LOC_Os08g28410(4.5)

Anther-specific proline-rich protein APG

Organ development

LOC_Os06g51084(5)

1,4-alpha-glucan branching enzyme

Carbohydrate metabolism

Down-regulated

miR160

LOC_Os06g47150(1)

Auxin response factor

Signal transduction or/TF

miR166

LOC_Os03g43930(3.5)

Class III HD-Zip protein 4

Signal transduction or/TF

LOC_Os03g01890(3.5)

Rolled leaf1

Organ development

miR167

LOC_Os04g57610(3.5)

Auxin response factor 8

Signal transduction or/TF

miR171

LOC_Os02g44360(0)

SCARECROW gene regulator

Signal transduction or/TF

miR396

LOC_Os02g47280(1)

Growth-regulating factor

Cell cycle/biogenesis

miR444

LOC_Os02g36924(0)

MADS-box transcription factor 27

Signal transduction or/TF

LOC_Os04g38780(0)

MADS-box transcription factor 27

Signal transduction or/TF

LOC_Os02g49840(1)

MADS-box transcription factor 57

Signal transduction or/TF

LOC_Os08g06510(2)

Zinc finger, C3HC4 type family protein

Signal transduction or/TF

miR530

LOC_Os02g14990(2)

Zinc finger, C3HC4 type family protein

Signal transduction or/TF

LOC_Os01g01120(2.5)

E-1 enzyme, putative

Protein degradation

LOC_Os01g43380(3)

Transferase, transferring glycosyl groups

Carbohydrate metabolism