Primary root development
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MiR393 and miR390 synergistically regulate lateral root growth in rice under different conditions. BMC Plant Biology. 2018 Oct 29;18(1):261. doi: 10.1186/s12870-018-1488-x.; Shafiq S, Chen C, Yang J, Cheng L, Ma F, Widemann E, Sun Q. DNA Topoisomerase 1 Prevents R-loop Accumulation to Modulate Auxin-Regulated Root Development in Rice. Mol Plant. 2017 Jun 05;10(6):821–33. doi: 10.1016/j.molp.2017.04.001. PMID: 28412545.; Cui P, Liu H, Ruan S, Ali B, Gill RA, Ma H, Zheng Z, Zhou W. A zinc finger protein, interacted with cyclophilin, affects root development via IAA pathway in rice. J Integr Plant Biol. 2017 Jul;59(7):496–505. doi: 10.1111/jipb.12531. PMID: 28267270.; Xia R, Xu J, Meyers BC. The Emergence, Evolution, and Diversification of the miR390- TAS3 - ARF Pathway in Land Plants. Plant Cell. 2017 Apr 24;29(6):1232–47. doi: 10.1105/tpc.17.00185.; Wang Y, Wang D, Gan T, Liu L, Long W, Wang Y, Niu M, Li X, Zheng M, Jiang L, Wan J. CRL6, a member of the CHD protein family, is required for crown root development in rice. Plant Physiol Biochem. 2016 Aug;105():185–94. doi: 10.1016/j.plaphy.2016.04.022. PMID: 27108205.; Qin C, Cheng L, Zhang H, He M, Shen J, Zhang Y, Wu P. OsGatB, the Subunit of tRNA-Dependent Amidotransferase, Is Required for Primary Root Development in Rice. Front Plant Sci. 2016;7():599. PMID: 27200067; PMCID: PMC4852291.; Xiao G, Qin H, Zhou J, Quan R, Lu X, Huang R, Zhang H. OsERF2 controls rice root growth and hormone responses through tuning expression of key genes involved in hormone signaling and sucrose metabolism. Plant Molecular Biology. 2015 Dec 10;90(3):293–302. doi: 10.1007/s11103-015-0416-9.; Ma X, Ma J, Zhai H, Xin P, Chu J, Qiao Y, Han L. CHR729 Is a CHD3 Protein That Controls Seedling Development in Rice. PLoS ONE. 2015 Sep 23;10(9):e0138934. doi: 10.1371/journal.pone.0138934.; Zhao Y, Cheng S, Song Y, Huang Y, Zhou S, Liu X, Zhou DX. The Interaction between Rice ERF3 and WOX11 Promotes Crown Root Development by Regulating Gene Expression Involved in Cytokinin Signaling. Plant Cell. 2015 Sep;27(9):2469–83. PMID: 26307379; PMCID: PMC4815106.; Li J, Zhao Y, Chu H, Wang L, Fu Y, Liu P, Upadhyaya N, Chen C, Mou T, Feng Y, Kumar P, Xu J. SHOEBOX Modulates Root Meristem Size in Rice through Dose-Dependent Effects of Gibberellins on Cell Elongation and Proliferation. PLoS Genet. 2015 Aug 14;11(8):e1005464. doi: 10.1371/journal.pgen.1005464.; Jing H, Yang X, Zhang J, Liu X, Zheng H, Dong G, Nian J, Feng J, Xia B, Qian Q, Li J, Zuo J. Peptidyl-prolyl isomerization targets rice Aux/IAAs for proteasomal degradation during auxin signalling. Nat Commun. 2015 Jun 22;6():7395. doi: 10.1038/ncomms8395. PMID: 26096057.; Gao Y, Zhang Y, Zhang D, Dai X, Estelle M, Zhao Y. Auxin binding protein 1 (ABP1) is not required for either auxin signaling or Arabidopsis development. Proc. Natl. Acad. Sci. U.S.A. 2015 Feb 02;112(7):2275–80. doi: 10.1073/pnas.1500365112.; Coudert Y, Le VAT, Adam H, Bès M, Vignols F, Jouannic S, Guiderdoni E, Gantet P. Identification of CROWN ROOTLESS1-regulated genes in rice reveals specific and conserved elements of postembryonic root formation. New Phytologist. 2014 Dec;206(1):243–54. doi: 10.1111/nph.13196.; Mai CD, Phung NT, To HT, Gonin M, Hoang GT, Nguyen KL, Do VN, Courtois B, Gantet P. Genes controlling root development in rice. Rice (N Y). 2014 Dec;7(1):30. PMID: 26224559; PMCID: PMC4884052.; Wu S, Lee CM, Hayashi T, Price S, Divol F, Henry S, Pauluzzi G, Perin C, Gallagher KL. A plausible mechanism, based upon Short-Root movement, for regulating the number of cortex cell layers in roots. Proc Natl Acad Sci U S A. 2014 Nov 11;111(45):16184–9. PMID: 25352666; PMCID: PMC4234584.; Chen J, Yang Z. Novel ABP1-TMK auxin sensing system controls ROP GTPase-mediated interdigitated cell expansion in Arabidopsis. Small GTPases. 2014 Jun 30;():e29711. doi: 10.4161/sgtp.29711.; Wang S, Xu Y, Li Z, Zhang S, Lim J, Lee KO, Li C, Qian Q, Jiang DA, Qi Y. OsMOGS is required for N-glycan formation and auxin-mediated root development in rice (Oryza sativa L.). The Plant Journal. 2014 Apr 15;78(4):632–45. doi: 10.1111/tpj.12497.; Xia J, Yamaji N, Che J, Shen RF, Ma JF. Normal root elongation requires arginine produced by argininosuccinate lyase in rice. Plant J. 2014 Apr;78(2):215–26. doi: 10.1111/tpj.12476. PMID: 24528386.; Korasick DA, Westfall CS, Lee SG, Nanao MH, Dumas R, Hagen G, Guilfoyle TJ, Jez JM, Strader LC. Molecular basis for AUXIN RESPONSE FACTOR protein interaction and the control of auxin response repression. Proc Natl Acad Sci U S A. 2014 Apr 08;111(14):5427–32. PMID: 24706860; PMCID: PMC3986151.; Xu T, Dai N, Chen J, Nagawa S, Cao M, Li H, Zhou Z, Chen X, De Rycke R, Rakusová H, Wang W, Jones AM, Friml J, Patterson SE, Bleecker AB, Yang Z. Cell surface ABP1-TMK auxin-sensing complex activates ROP GTPase signaling. Science. 2014 Feb 27;343(6174):1025–8. PMID: 24578577; PMCID: PMC4166562.; Chen X, Friml J. Rho-GTPase-regulated vesicle trafficking in plant cell polarity. Biochem Soc Trans. 2014 Feb;42(1):212–8. doi: 10.1042/bst20130269. PMID: 24450654.; Peer WA. From perception to attenuation: auxin signalling and responses. Curr Opin Plant Biol. 2013 Oct;16(5):561–8. doi: 10.1016/j.pbi.2013.08.003. PMID: 24004572.; Chu H, Liang W, Li J, Hong F, Wu Y, Wang L, Wang J, Wu P, Liu C, Zhang Q, Xu J, Zhang D. A CLE-WOX signalling module regulates root meristem maintenance and vascular tissue development in rice. J Exp Bot. 2013 Dec;64(17):5359–69. doi: 10.1093/jxb/ert301. PMID: 24043854.; Zheng H, Li S, Ren B, Zhang J, Ichii M, Taketa S, Tao Y, Zuo J, Wang H. LATERAL ROOTLESS2, a cyclophilin protein, regulates lateral root initiation and auxin signaling pathway in rice. Mol Plant. 2013 Sep;6(5):1719–21. doi: 10.1093/mp/sst052. PMID: 23501875.; Orman-Ligeza B, Parizot B, Gantet PP, Beeckman T, Bennett MJ, Draye X. Post-embryonic root organogenesis in cereals: branching out from model plants. Trends Plant Sci. 2013 Aug;18(8):459–67. doi: 10.1016/j.tplants.2013.04.010. PMID: 23727199.; Cho S, Yoo S, Zhang H, Pandeya D, Koh H, Hwang J, Kim G, Paek N. The rice narrow leaf2 and narrow leaf3 loci encode WUSCHEL-related homeobox 3A (OsWOX3A) and function in leaf, spikelet, tiller and lateral root development. New Phytologist. 2013 Apr 02;198(4):1071–84. doi: 10.1111/nph.12231.; Chen X, Shi J, Hao X, Liu H, Shi J, Wu Y, Wu Z, Chen M, Wu P, Mao C. OsORC3 is required for lateral root development in rice. The Plant Journal. 2013 Mar 16;74(2):339–50. doi: 10.1111/tpj.12126.; Ishiwata A, Ozawa M, Nagasaki H, Kato M, Noda Y, Yamaguchi T, Nosaka M, Shimizu-Sato S, Nagasaki A, Maekawa M, Hirano HY, Sato Y. Two WUSCHEL-related homeobox genes, narrow leaf2 and narrow leaf3, control leaf width in rice. Plant Cell Physiol. 2013 May;54(5):779–92. doi: 10.1093/pcp/pct032. PMID: 23420902.; Qin C, Li Y, Gan J, Wang W, Zhang H, Liu Y, Wu P. OsDGL1, a homolog of an oligosaccharyltransferase complex subunit, is involved in N-glycosylation and root development in rice. Plant Cell Physiol. 2013 Jan;54(1):129–37. doi: 10.1093/pcp/pcs159. PMID: 23220823.; Kitomi Y, Inahashi H, Takehisa H, Sato Y, Inukai Y. OsIAA13-mediated auxin signaling is involved in lateral root initiation in rice. Plant Sci. 2012 Jul;190():116–22. doi: 10.1016/j.plantsci.2012.04.005. PMID: 22608525.; Xia K, Wang R, Ou X, Fang Z, Tian C, Duan J, Wang Y, Zhang M. OsTIR1 and OsAFB2 Downregulation via OsmiR393 Overexpression Leads to More Tillers, Early Flowering and Less Tolerance to Salt and Drought in Rice. PLoS ONE. 2012 Jan 10;7(1):e30039. doi: 10.1371/journal.pone.0030039.; Zhang JW, Xu L, Wu YR, Chen XA, Liu Y, Zhu SH, Ding WN, Wu P, Yi KK. OsGLU3, a putative membrane-bound endo-1,4-beta-glucanase, is required for root cell elongation and division in rice (Oryza sativa L.). Mol Plant. 2012 Jan;5(1):176–86. doi: 10.1093/mp/ssr084. PMID: 21976713.; Zhu ZX, Liu Y, Liu SJ, Mao CZ, Wu YR, Wu P. A gain-of-function mutation in OsIAA11 affects lateral root development in rice. Mol Plant. 2012 Jan;5(1):154–61. doi: 10.1093/mp/ssr074. PMID: 21914651.; Huang CF, Yamaji N, Ono K, Ma JF. A leucine-rich repeat receptor-like kinase gene is involved in the specification of outer cell layers in rice roots. Plant J. 2012 Feb;69(4):565–76. doi: 10.1111/j.1365-313x.2011.04824.x. PMID: 22014207.; Jun N, Gaohang W, Zhenxing Z, Huanhuan Z, Yunrong W, Ping W. OsIAA23-mediated auxin signaling defines postembryonic maintenance of QC in rice. Plant J. 2011 Nov;68(3):433–42. doi: 10.1111/j.1365-313x.2011.04698.x. PMID: 21736653.; Kitomi Y, Ito H, Hobo T, Aya K, Kitano H, Inukai Y. The auxin responsive AP2/ERF transcription factor CROWN ROOTLESS5 is involved in crown root initiation in rice through the induction of OsRR1, a type-A response regulator of cytokinin signaling. The Plant Journal. 2011 May 31;67(3):472–84. doi: 10.1111/j.1365-313x.2011.04610.x.; Wang XF, He FF, Ma XX, Mao CZ, Hodgman C, Lu CG, Wu P. OsCAND1 is required for crown root emergence in rice. Mol Plant. 2011 Mar;4(2):289–99. doi: 10.1093/mp/ssq068. PMID: 20978084.; Jia L, Wu Z, Hao X, Carrie C, Zheng L, Whelan J, Wu Y, Wang S, Wu P, Mao C. Identification of a novel mitochondrial protein, short postembryonic roots 1 (SPR1), involved in root development and iron homeostasis in Oryza sativa. New Phytol. 2011 Feb;189(3):843–55. doi: 10.1111/j.1469-8137.2010.03513.x. PMID: 21039568.; Li YF, Zheng Y, Addo-Quaye C, Zhang L, Saini A, Jagadeeswaran G, Axtell MJ, Zhang W, Sunkar R. Transcriptome-wide identification of microRNA targets in rice. Plant J. 2010 Jun 01;62(5):742–59. doi: 10.1111/j.1365-313x.2010.04187.x. PMID: 20202174.; Krecek P, Skupa P, Libus J, Naramoto S, Tejos R, Friml J, Zažímalová E. The PIN-FORMED (PIN) protein family of auxin transporters. Genome Biology. 2009 Dec 29;10(12):249. doi: 10.1186/gb-2009-10-12-249.; Wang JR, Hu H, Wang GH, Li J, Chen JY, Wu P. Expression of PIN genes in rice (Oryza sativa L.): tissue specificity and regulation by hormones. Mol Plant. 2009 Jul;2(4):823–31. doi: 10.1093/mp/ssp023. PMID: 19825657.; Liu S, Wang J, Wang L, Wang X, Xue Y, Wu P, Shou H. Adventitious root formation in rice requires OsGNOM1 and is mediated by the OsPINs family. Cell Res. 2009 Sep;19(9):1110–9. doi: 10.1038/cr.2009.70. PMID: 19546891.; Zhao Y, Hu Y, Dai M, Huang L, Zhou DX. The WUSCHEL-related homeobox gene WOX11 is required to activate shoot-borne crown root development in rice. Plant Cell. 2009 Mar;21(3):736–48. PMID: 19258439; PMCID: PMC2671696.; Suzaki T, Yoshida A, Hirano HY. Functional diversification of CLAVATA3-related CLE proteins in meristem maintenance in rice. Plant Cell. 2008 Aug;20(8):2049–58. PMID: 18676878; PMCID: PMC2553609.; Abe M, Kuroshita H, Umeda M, Itoh J, Nagato Y. The rice flattened shoot meristem, encoding CAF-1 p150 subunit, is required for meristem maintenance by regulating the cell-cycle period. Dev Biol. 2008 Jul 15;319(2):384–93. doi: 10.1016/j.ydbio.2008.04.040. PMID: 18538315.; Qi J, Qian Q, Bu Q, Li S, Chen Q, Sun J, Liang W, Zhou Y, Chu C, Li X, Ren F, Palme K, Zhao B, Chen J, Chen M, Li C. Mutation of the Rice Narrow leaf1 Gene, Which Encodes a Novel Protein, Affects Vein Patterning and Polar Auxin Transport. Plant Physiol. 2008 Jun 18;147(4):1947–59. doi: 10.1104/pp.108.118778.; Jia L, Zhang B, Mao C, Li J, Wu Y, Wu P, Wu Z. OsCYT-INV1 for alkaline/neutral invertase is involved in root cell development and reproductivity in rice (Oryza sativa L.). Planta. 2008 Jun;228(1):51–9. doi: 10.1007/s00425-008-0718-0. PMID: 18317796.; Koiwai H, Tagiri A, Katoh S, Katoh E, Ichikawa H, Minami E, Nishizawa Y. RING-H2 type ubiquitin ligase EL5 is involved in root development through the maintenance of cell viability in rice. Plant J. 2007 Jul;51(1):92–104. doi: 10.1111/j.1365-313x.2007.03120.x. PMID: 17559513.; Wang D, Pei K, Fu Y, Sun Z, Li S, Liu H, Tang K, Han B, Tao Y. Genome-wide analysis of the auxin response factors (ARF) gene family in rice (Oryza sativa). Gene. 2007 Jun 01;394(1-2):13–24. doi: 10.1016/j.gene.2007.01.006. PMID: 17408882.; Ito Y, Kurata N. Identification and characterization of cytokinin-signalling gene families in rice. Gene. 2006 Nov 01;382():57–65. doi: 10.1016/j.gene.2006.06.020. PMID: 16919402.; Jain M, Kaur N, Garg R, Thakur JK, Tyagi AK, Khurana JP. Structure and expression analysis of early auxin-responsive Aux/IAA gene family in rice (Oryza sativa). Funct Integr Genomics. 2006 Jan;6(1):47–59. doi: 10.1007/s10142-005-0005-0. PMID: 16200395.; Thakur JK, Jain M, Tyagi AK, Khurana JP. Exogenous auxin enhances the degradation of a light down-regulated and nuclear-localized OsiIAA1, an Aux/IAA protein from rice, via proteasome. Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression. 2005 Sep;1730(3):196–205. doi: 10.1016/j.bbaexp.2005.08.002.; Mori Y, Yamamoto T, Sakaguchi N, Ishibashi T, Furukawa T, Kadota Y, Kuchitsu K, Hashimoto J, Kimura S, Sakaguchi K. Characterization of the origin recognition complex (ORC) from a higher plant, rice (Oryza sativa L.). Gene. 2005 Jun 20;353(1):23–30. doi: 10.1016/j.gene.2005.03.047. PMID: 15939553.; Liu H, Wang S, Yu X, Yu J, He X, Zhang S, Shou H, Wu P. ARL1, a LOB-domain protein required for adventitious root formation in rice. Plant J. 2005 Jul;43(1):47–56. doi: 10.1111/j.1365-313x.2005.02434.x. PMID: 15960615.; Jiang H, Wang S, Dang L, Wang S, Chen H, Wu Y, Jiang X, Wu P. A novel short-root gene encodes a glucosamine-6-phosphate acetyltransferase required for maintaining normal root cell shape in rice. Plant Physiol. 2005 May;138(1):232–42. PMID: 15849305; PMCID: PMC1104178.; Kamiya N, Itoh J, Morikami A, Nagato Y, Matsuoka M. The SCARECROW gene's role in asymmetric cell divisions in rice plants. The Plant Journal. 2003 Aug 28;36(1):45–54. doi: 10.1046/j.1365-313x.2003.01856.x.; Kamiya N, Nagasaki H, Morikami A, Sato Y, Matsuoka M. Isolation and characterization of a rice WUSCHEL-type homeobox gene that is specifically expressed in the central cells of a quiescent center in the root apical meristem. The Plant Journal. 2003 Jul 17;35(4):429–41. doi: 10.1046/j.1365-313x.2003.01816.x.