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Table 1 Identified key miRNA-mRNA interaction pairs for tartary buckwheat seed development

From: Integrated microRNA and transcriptome profiling reveal key miRNA-mRNA interaction pairs associated with seed development in Tartary buckwheat (Fagopyrum tataricum)

miRNA Target gene ID Annotation of targets Function of targets Orthologs Pearson P-value
fta-miR156c-5p FtPinG0000496000.01 Squamosa promoter binding-like protein 16 Grain size and quality OsSPL16/Os08g0531600 −0.70892 0.00340
fta-miR156h-5p FtPinG0001940300.01 Nodulin MtN21-like transporter family protein NA AT1G21890.1 −0.86151 0.00021
FtPinG0005289100.01 Ceramide synthase Long chain fatty acid biosynthesis AT1G13580.1 −0.91146 0.00033
FtPinG0005522500.01 JAZ protein 9 Response to jasmonic acid AT1G70700.1 −0.91696 0.00024
FtPinG0005624200.01 CELLULOSE SYNTHASE-INTERACTIVE PROTEIN 1 Cell elongation AT2G22125.1 −0.80006 0.00044
FtPinG0009120200.01 Sulfite exporter TauE/SafE family protein NA AT1G61740.1 −0.93448 0.00228
fta-miR157-5p FtPinG0007350700.01 DNA replication protein Cell proliferation, embryo development, pollen development, AT2G16440.1 −0.87897 0.00077
FtPinG0008009600.01 NPH3-like protein Involved in auxin-mediated organogenesis AT4G37590.1 −0.92728 0.00073
fta-miR164a-5p FtPinG0000240100.01 NAC domain-containing protein 1 Involved in shoot apical meristem formation and auxin-mediated lateral root formation, auxin response, plant growth and abiotic stress resistance AT1G56010.1 −0.89303 0.00275
FtPinG0003134600.01 NAC domain-containing protein 1 Involved in shoot apical meristem formation and auxin-mediated lateral root formation, auxin response, plant growth and abiotic stress resistance AT1G56010.1 −0.818700 0.00281
FtPinG0002339300.01 NAC domain-containing protein 5 NA AT5G61430.1 −0.83097 0.00842
fta-miR164c-5p FtPinG0006614900.01 Putative ligands homologous to the Clavata3 gene Regulates stomatal and vascular development, stomatal closure AT1G26600.1 −0.75278 0.00301
fta-miR166b-3p FtPinG0006632200.01 Mn transporter 8 Mn transport, Mn and Fe enrichment in seed embryos AT3G58060.1 −0.68351 0.00137
FtPinG0006851000.01 Glutathione transferase 8 Auxin, cytokinin, drought, and oxidative stress response AT1G78380.1 −0.84863 0.02431
FtPinG0009174800.01 Uncharacterized protein NA AT5G54980.1 −0.82859 0.00233
fta-miR166c-3p FtPinG0008845600.01 Homeodomain-leucine zipper protein 8 Involved in cell differentiation and proliferation, auxin response AT4G32880.1 −0.77425 0.00131
fta-miR166g-3p FtPinG0008326500.01 NA NA NA −0.64002 0.00146
fta-miR166i-5p FtPinG0004865100.01 Pentatricopeptide repeat protein Cell proliferation during embryogenesis, embryo development AT3G06430.1 −0.95992 0.000002
fta-miR166j-3p FtPinG0009852300.01 Clathrin adaptor complexes medium subunit family protein Vesicle-mediated transport AT1G10730.1 −0.66005 0.00071
fta-miR167c-5p FtPinG0002560000.01 NAC domain-containing protein Grain size NAC024/Os05g0415400 −0.73942 0.00003
FtPinG0005477800.01 RING/U-box superfamily protein NA AT1G24440.1 −0.79803 0.00003
fta-miR390a-5p FtPinG0008213400.01 Polygalacturonase inhibiting protein Involved in defense response AT5G06860.1 −0.82038 0.00261
fta-miR396a-5p FtPinG0000680700.01 Sucrose synthase Starch and cellulose biosynthesis, grain size and grain weight SUS3/Os07g0616800 −0.72690 0.00059
FtPinG0003172000.01 Neutral ceramidase Sphingolipid homeostasis, oxidative stress responses, ceramide catabolic process, long-chain fatty acid biosynthetic AT1G07380.1 −0.78815 0.00060
FtPinG0005517700.01 Phosphoglucomutase 2 Plant growth; seed, root, male and female gametophyte development, and carbohydrate partitioning AT1G70730.1 −0.69606 0.00076
fta-miR396c-3p FtPinG0005040200.01 Sulfur dioxygenase Embryo and endosperm development, abiotic stress resistance, T1G53580.1 −0.778492 0.00799
fta-miR396d-3p FtPinG0007060600.01 Kinase interacting (KIP1-like) family protein NA AT2G22560.1 −0.65160 0.01957
fta-miR396g-5p FtPinG0005901900.01 Chloroplast-localized protein with a zinc finger motif and four GTP-binding domains Brassinosteroid responses, positive regulation of carotenoid and chlorophyll biosynthetic process AT3G57180.1 −0.59428 0.00063
FtPinG0009355400.01 Chloroplast RNA editing factor NA AT1G08070.1 −0.54344 0.00062
fta-miR399b-3p FtPinG0002932000.01 Alkaline/neutral invertase Modulating hormone balance, sucrose catabolic AT3G06500.1 −0.57593 0.00190
FtPinG0003424700.01 Phosphate transporter Phosphate transport and homeostasis AT3G54700.1 −0.81570 0.00232
fta-miR530c-5p FtPinG0002594600.01 GRF1-interacting factor 3 Regulates the sizes of stems, leaves, and grains OsGIF1/Os03g0733600 −0.59617 0.01955
fta-miR858a-5p FtPinG0000919400.01 MYB transcription factor 13 Regulation of flower development, responses to cold stress AT1G06180.1 −0.91268 0.00001
FtPinG0001149900.01 RNA recognition motif (RRM)-containing protein Involved in phytochrome B signal transduction AT5G25060.1 −0.53630 0.00001
FtPinG0002607600.01 Parallel spindle 1 Pollen development AT1G34355.1 −0.71400 0.00001
FtPinG0003084400.01 DNA-binding bromodomain-containing protein NA AT5G55040.1 −0.54089 0.00001
FtPinG0003543800.01 MYB transcription factor 7 Inhibition of seed germination AT2G16720.1 −0.76017 0.00001
FtPinG0005011800.01 MYB transcription factor 5 Regulation trichome and endosperm development AT3G13540.1 −0.79056 0.00001
FtPinG0007213700.01 MYB transcription factor 123 Regulation the proanthocyanidin accumulation of developing seed AT5G35550.1 −0.89174 0.00001
FtPinG0007214000.01 MYB transcription factor 23 Regulate trichome formation AT5G40330.1 −0.797669 0.00001
FtPinG0008420900.01 MYB transcription factor 103 Regulate cellulose and lignin biosynthesis AT1G63910.1 −0.934255 0.00001
FtPinG0009153900.01 MYB transcription factor 12 Regulate flavonol biosynthesis AT2G47460.1 −0.935509 0.00001
fta_novel_miR17 FtPinG0000491900.01 receptor-like kinase Regulation of secondary growth, protein phosphorylation AT5G67280.1 −0.98523 0.00002
FtPinG0000612500.01 Calcium binding protein Involved in photomorphogensis AT4G08810.1 −0.75677 0.00002
FtPinG0001194500.01 Calcium binding protein Involved in photomorphogensis AT4G08810.1 −0.98204 0.00002
FtPinG0005891600.01 SUMO protease Regulation flowering, shoot and inflorescence development. AT4G15880.1 −0.96316 0.00002
FtPinG0007576600.01 Argonaute protein Regulate the development of embryo and shoot meristem development, embryo development, seed size AGO17/AK240838 −0.54760 0.00002
fta_novel_miR37 FtPinG0004072300.01 CBL-interacting protein kinase Response to salt and osmotic stress, protein phosphorylation AT5G57630.1 −0.56995 0.00126
FtPinG0004651400.01 Intrinsic thylakoid membrane protein NA AT2G17750.1 −0.87363 0.00773
fta_novel_miR41 FtPinG0002471300.01 Carboxyesterase 13 NA AT3G48700.1 −0.55115 0.00159
FtPinG0007248800.01 Receptor-like protein kinase Defense response to bacterium, protein phosphorylation AT4G23180.1 −0.79183 0.00150
fta_novel_miR55 FtPinG0005410000.01 MYB transcription factor 73 Auxin and abiotic stress responses a MYB73/AT4G37260.1 −0.63527 0.01789
fta_novel_miR118 FtPinG0003617400.01 GRAS transcription factor 15 Cell differentiation, repressing the seed maturation programme, AT4G36710.1 −0.88771 0.01772
fta_novel_miR123 FtPinG0000299300.01 C2H2 zinc finger protein Transfer cell differentiation AT4G27240.1 −0.65706 0.00569
FtPinG0003531700.01 CONSTANS-like 5 Flower development, and flowering AT5G57660.1 −0.65534 0.00585
FtPinG0006913600.01 Galactosyltransferase family protein Embryo development GALT31A/AT1G32930.1 −0.64824 0.00570