Table 1.
Expression of sucrose responsive miRNAs (p-adjusted < 0.05, this study), their putative functions, and the target mRNA expression along with expression profile in response to various nutrient deficiencies (Liang et al., 2015).
| Treatment | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| sRNA family | Family members | Exogenous sucrose (+C, overall) | (-C) | (-N) | (-Pi) | (-S) | Target | Annotation | Log2FC | pvalue | padj | Relationship with the targeting sRNA | Potential roles |
| miR156 | b/c/d/e/f | down | up | up | up | AT2G33810.1 | SPL3, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 3 | -3.106 | 0.000 | 0.000 | concordant | juvenile-to-adult phase transition (Ronemus et al., 2006; Wang et al., 2009; Cui et al., 2014; Xu et al., 2016) | |
| AT1G27370.1 | SPL10, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 10 | -0.833 | 0.000 | 0.002 | concordant | ||||||||
| AT5G43270.2 | SPL2, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 2 | -0.957 | 0.001 | 0.003 | concordant | ||||||||
| miR158 | b | up | down | down | AT1G64100.1 | pentatricopeptide (PPR) repeat-containing protein | 2.151 | 0.001 | 0.006 | concordant | abiotic stress tolerance (Rhoades et al., 2002; Zhang et al., 2011; Liang et al., 2012) | ||
| AT2G03220.1 | FUCOSYLTRANSFERASE 1, ATFT1, ATFUT1, FT1, FUCOSYLTRANSFERASE 1, FUT1, MUR2, MURUS 2 | 0.730 | 0.000 | 0.000 | concordant | ||||||||
| miR159 | a/b | up | down | AT4G26930.1 | ATMYB97, MYB DOMAIN PROTEIN 97, MYB97 | 2.256 | 0.001 | 0.004 | concordant | Ather development and flowering time regulation (Reyes and Chua, 2007; Millar et al., 2019) | |||
| miR163 | down | up | up | AT1G66700.1 | SABATH FAMILY PARAXANTHINE METHYL TRANSFERASE; PXMT1 | 5.693 | 0.000 | 0.000 | anti-concordant | abiotic and biotic stress response (Allen et al., 2004; Ng et al., 2011; Chow and Ng, 2017) | |||
| AT3G44860.1 | FAMT, FARNESOIC ACID CARBOXYL-O-METHYLTRANSFERASE | 3.589 | 0.000 | 0.000 | anti-concordant | ||||||||
| AT5G38100.1 | SABATH family methyltransferase | 2.191 | 0.000 | 0.000 | anti-concordant | ||||||||
| AT3G44870.1 | FAMT-L, FARNESOIC ACID METHYL TRANSFERASE-LIKE | 2.053 | 0.000 | 0.000 | anti-concordant | ||||||||
| miR164 | a/b | up | down | up | up | AT3G12977.1 | NAC1 LIKE TRANSCRIPTION FACTOR, NAC1L | -2.483 | 0.000 | 0.000 | anti-concordant | growth, development, response to biotic and abiotic stresses (Raman et al., 2008; Koyama et al., 2010; Fang et al., 2014) | |
| AT5G39610.1 | ANAC092, ARABIDOPSIS NAC DOMAIN CONTAINING PROTEIN 92 | -1.603 | 0.002 | 0.007 | anti-concordant | ||||||||
| AT5G07680.1 | NAC DOMAIN CONTAINING PROTEIN 80, NAC080 | -0.637 | 0.004 | 0.015 | anti-concordant | ||||||||
| AT5G61430.1 | NAC DOMAIN CONTAINING PROTEIN 100, NAC100 | 1.429 | 0.006 | 0.021 | concordant | ||||||||
| miR167 | c | up | down | up | up | down | AT5G37020.1 | ARF8, ATARF8, AUXIN RESPONSE FACTOR 8 | -0.615 | 0.001 | 0.004 | anti-concordant | auxin signaling, flower development, and root development (Wu et al., 2006; Liu X. et al., 2021) |
| AT1G51760.1 | IAA-ALANINE RESISTANT 3, IAR3 | 2.014 | 0.000 | 0.000 | concordant | (Kinoshita et al., 2012) | |||||||
| miR169 | a/b/c | down | up | down | down | down | AT1G17590.1 | NF-YA8, NUCLEAR FACTOR Y, SUBUNIT A8 | 1.720 | 0.000 | 0.003 | anti-concordant | ABA signaling, nitrogen homeostasis (Ronemus et al., 2006; Zhao et al., 2011; Sorin et al., 2014; Xu et al., 2014; Li J. et al., 2021) |
| AT1G54160.1 | NF-YA5, NUCLEAR FACTOR Y A5 | 1.842 | 0.011 | 0.044 | anti-concordant | ||||||||
| AT3G05690.1 | NF-YA2, NUCLEAR FACTOR Y, SUBUNIT A2 | 1.711 | 0.000 | 0.001 | anti-concordant | ||||||||
| AT1G48500.1 | ATJAZ4, JASMONATE-ZIM-DOMAIN PROTEIN 4 | 1.377 | 0.011 | 0.011 | anti-concordant | (Karlova et al., 2013; Gyula et al., 2018) | |||||||
| AT5G06510.1 | NF-YA10, NUCLEAR FACTOR Y, SUBUNIT A10 | 3.166 | 0.006 | 0.028 | anti-concordant | ||||||||
| miR393 | b | up | down | up | AT3G62980.1 | ATTIR1, TIR1, TRANSPORT INHIBITOR RESPONSE 1 | -1.088 | 0.001 | 0.004 | anti-concordant | auxin signaling (Ronemus et al., 2006; Si-Ammour et al., 2011; Wang et al., 2018) | ||
| miR396 | a/b | up | down | down | AT3G52910.1 | ATGRF4, GRF4, GROWTH-REGULATING FACTOR 4 | 2.063 | 0.002 | 0.008 | anti-concordant | cell proliferation (Rodriguez et al., 2010; Szczygieł-Sommer and Gaj, 2019) | ||
| AT5G53660.1 | ATGRF7, GRF7, GROWTH-REGULATING FACTOR 7 | 1.849 | 0.007 | 0.025 | anti-concordant | ||||||||
| miR397 | a/b | up | down | down | down | down | AT2G29130.1 | ATLAC2, LAC2, LACCASE 2 | -1.676 | 0.011 | 0.035 | concordant | lignin accumulation and stress tolerance (Lu et al., 2013; Li et al., 2019) |
| miR398 | a/b/c | up | down | down | down | down | AT2G28190.1 | ATSOD2, COPPER/ZINC SUPEROXIDE DISMUTASE 2, CSD2 | -1.404 | 0.000 | 0.000 | concordant | copper starvation response; ROS homeostasis (Sunkar et al., 2006; Beauclair et al., 2010) |
| AT5G14550.1 | Core-2/I-branching beta-1,6-N-acetylglucosaminyl transferase family protein | 0.882 | 0.003 | 0.011 | anti-concordant | (Sunkar et al., 2004) | |||||||
| AT3G15640.1 | Rubredoxin-like superfamily protein | 0.717 | 0.004 | 0.014 | anti-concordant | ||||||||
| AT1G12520.1 | ATCCS, COPPER CHAPERONE FOR SOD1 | -1.810 | 0.000 | 0.000 | anti-concordant | ||||||||
| AT5G20230.1 | ATBCB, BLUE COPPER BINDING PROTEIN | -3.537 | 0.000 | 0.000 | anti-concordant | ||||||||
| miR398b* | AT5G61670.1 | AtORANGE; Cysteine-rich zinc finger; DnaJ-like | -1.500 | 0.000 | 0.000 | anti-concordant | this work; novel non-canonical target; chromoplast development (Yazdani et al., 2019) | ||||||
| miR399 | a/b/c/f | up | down | down | up | down | AT3G09922.1 | IPS1; induced by phosphate starvation1 | 9.672 | 0.000 | 0.000 | concordant | nutrient recycling; Pi uptake and translocation (Kim et al., 2011) |
| miR408 | up | down | down | up | down | AT5G21930.1 | P-type ATPase of Arabidopsis 2, PAA2 | -3.329 | 0.000 | 0.000 | anti-concordant | responds to the availability of copper, iron homeostasis, oxidative stress response, regulation of lignin biosynthesis also controls various aspects plant growth and development (Chorostecki et al., 2012; Liang et al., 2012; Ma et al., 2015; Li et al., 2019; Gao et al., 2022). | |
| AT2G44790.1 | UCC2, UCLACYANIN 2 | -1.000 | 0.000 | 0.000 | anti-concordant | ||||||||
| AT3G51240.1 | F3’H; flavanone 3-hydroxylase | 4.357 | 0.000 | 0.000 | concordant | this work; novel non-canonical target; anthocyanin biosynthesis (Plotnikova et al., 2019; Liu J. et al., 2021) | |||||||
| AT5G05390.1 | Laccase 12 | 2.417 | 0.000 | 0.001 | concordant | ||||||||
| AT5G07130.1 | Laccase 13 | 2.090 | 0.001 | 0.003 | concordant | ||||||||
| AT2G02850.1 | ARPN, PLANTACYANIN | 0.968 | 0.007 | 0.024 | concordant | ||||||||
| AT2G47020.1 | Peptide chain release factor 1 | 1.032 | 0.000 | 0.000 | concordant | (Sunkar et al., 2004) | |||||||
| miR773 | a | up | down | up | AT4G14140.2 | DNA methyltransferase 2 | -2.896 | 0.000 | 0.000 | anti-concordant | biotic stress response (Li et al., 2010; Zhang et al., 2011) | ||
| miR827 | up | down | down | up | down | AT1G02860.1 | BAH1, BENZOIC ACID HYPERSENSITIVE 1, NITROGEN LIMITATION ADAPTATION, NLA, SYG1 | -1.664 | 0.000 | 0.000 | anti-concordant | nutrient recycling; Pi uptake and translocation, plant-pathogen interaction (Hsieh et al., 2009; Lin et al., 2010; Liang et al., 2012) | |
| AT1G63010.5 | PHT5;1, VACUOLAR PHOSPHATE TRANSPORTER 1, VPT1 | 0.880 | 0.001 | 0.006 | concordant | ||||||||
| miR828 | up | up | AT3G25795.1 | TAS4, TRANS ACTING SIRNA 4 | 5.339 | 0.000 | 0.000 | concordant | anthocyanin biosynthesis (Rajagopalan et al., 2006; Guan et al., 2014; Tirumalai et al., 2019; Zhang et al., 2020) | ||||
| AT5G52600.1 | ATMYB82, MYB DOMAIN PROTEIN 82, MYB82 | 1.990 | 0.000 | 0.000 | concordant | This work | |||||||
| AT1G56650.1 | ATMYB75, PAP1 | 3.125 | 0.001 | 0.003 | concordant | ||||||||
| AT1G66390.1 | ATMYB90, PAP2 | 4.210 | 0.000 | 0.000 | concordant | ||||||||
| AT1G66370.1 | ATMYB113, MYB DOMAIN PROTEIN 113, MYB113 | 3.519 | 0.010 | 0.034 | concordant | ||||||||
| miR842 | up | AT5G38550.1 | Jacalin lectin family protein gene | 2.904 | 0.000 | 0.000 | concordant | (De Felippes et al., 2008; Jia and Rock, 2013) | |||||
| miR856 | down | AT5G41610.1 | CATION/H+ EXCHANGER 18, ATCHX18 | 2.131 | 0.000 | 0.000 | anti-concordant | Na+/H+ antiporter family (Fahlgren et al., 2007) | |||||
| miR858 | a/b | up | AT2G47460.1 | ATMYB12, MYB DOMAIN PROTEIN 12 | 3.625 | 0.000 | 0.000 | concordant | involved in phenylpropanoid pathway and plant development (Fahlgren et al., 2007; Guan et al., 2014; Tirumalai et al., 2019) | ||||
| AT5G49330.1 | ARABIDOPSIS MYB DOMAIN PROTEIN 111, ATMYB111 | 5.469 | 0.000 | 0.000 | concordant | ||||||||
| AT1G06180.1 | ATMYB13, ATMYBLFGN, MYB DOMAIN PROTEIN 13, MYB13 | 1.419 | 0.000 | 0.000 | concordant | ||||||||
| AT3G62610.1 | ATMYB11, MYB DOMAIN PROTEIN 11 | 4.078 | 0.000 | 0.000 | concordant | ||||||||
| AT1G71030.1 | MYB-LIKE 2, ATMYBL2 | -4.619 | 0.000 | 0.000 | anti-concordant | this work | |||||||
| TAS4-3’D4(-) | up | up | AT1G56650.1 | MYB75, PAP1-D, PRODUCTION OF ANTHOCYANIN PIGMENT 1 | 3.125 | 0.001 | 0.003 | concordant | anthocyanin biosynthesis (Rajagopalan et al., 2006; Hsieh et al., 2009; Luo et al., 2012) | ||||
| AT1G66390.1 | ATMYB90, MYB DOMAIN PROTEIN 90, PAP2, PRODUCTION OF ANTHOCYANIN PIGMENT 2 | 4.210 | 0.000 | 0.000 | concordant | ||||||||
| AT1G66370.1 | ATMYB113, MYB DOMAIN PROTEIN 113, MYB113 | 3.519 | 0.010 | 0.034 | concordant |