[1] Jones-Rhoades MW, Bartel DP, Bartel B. 2006. MicroRNAS and their regulatory roles in plants. Annu. Rev. Plant Biol. 57:19−53 doi: 10.1146/annurev.arplant.57.032905.105218
[2] Chen X. 2009. Small RNAs and their roles in plant development. Annu. Rev. Cell Dev. Bi. 25:21−44 doi: 10.1146/annurev.cellbio.042308.113417
[3] Sunkar R. 2010. MicroRNAs with macro-effects on plant stress responses. Semin. Cell Dev. Biol. 21:805−11 doi: 10.1016/j.semcdb.2010.04.001
[4] Taylor RS, Tarver JE, Hiscock SJ, Donoghue PC. 2014. Evolutionary history of plant microRNAs. Trends Plant Sci. 19:175−82 doi: 10.1016/j.tplants.2013.11.008
[5] Cong L, Zhao Y, Pogue AI, Lukiw WJ. 2018. Role of microRNA (miRNA) and viroids in lethal diseases of plants and animals. Potential contribution to human neurodegenerative disorders. Biochemistry (Mosc) 83:1018−29 doi: 10.1134/S0006297918090031
[6] Lim PO, Kim HJ, Nam HG. 2007. Leaf senescence. Annu. Rev. Plant Biol. 58:115−36 doi: 10.1146/annurev.arplant.57.032905.105316
[7] Fouracre JP, Poethig RS. 2016. The role of small RNAs in vegetative shoot development. Curr. Opin. Plant Biol. 29:64−72 doi: 10.1016/j.pbi.2015.11.006
[8] Rodriguez RE, Schommer C, Palatnik JF. 2016. Control of cell proliferation by microRNAs in plants. Curr. Opin. Plant Biol. 34:68−76 doi: 10.1016/j.pbi.2016.10.003
[9] Koyama T, Sato F, Ohme-Takagi M. 2017. Roles of miR319 and TCP transcription factors in leaf development. Plant Physiol. 175:874−85 doi: 10.1104/pp.17.00732
[10] Kozomara A, Birgaoanu M, Griffiths-Jones S. 2019. miRBase: from microRNA sequences to function. Nucleic Acids Res. 47:D155−D162 doi: 10.1093/nar/gky1141
[11] Palatnik JF, Allen E, Wu X, Schommer C, Schwab R, et al. 2003. Control of leaf morphogenesis by microRNAs. Nature 425:257−63 doi: 10.1038/nature01958
[12] Schommer C, Palatnik JF, Aggarwal P, Chételat A, Cubas P, et al. 2008. Control of jasmonate biosynthesis and senescence by miR319 Targets. PLoS Biol. 6:e230 doi: 10.1371/journal.pbio.0060230
[13] Nag A, King S, Jack T. 2009. miR319a targeting of TCP4 is critical for petal growth and development in Arabidopsis. Proc. Natl. Acad. Sci. U. S. A. 106:22534−9 doi: 10.1073/pnas.0908718106
[14] Gleave AP, Ampomah-Dwamena C, Berthold S, Dejnoprat S, Karunairetnam S, et al. 2008. Identification and characterisation of primary microRNAs from apple (Malus domestica cv. Royal Gala) expressed sequence tags. Tree Genet. Genomes 4:343−58 doi: 10.1007/s11295-007-0113-1
[15] Prabu GR, Mandal AKA. 2010. Computational identification of miRNAs and their target genes from expressed sequence tags of tea (Camellia sinensis). Genom. Proteom. Bioinf. 8:113−21 doi: 10.1016/S1672-0229(10)60012-5
[16] Morin RD, Aksay G, Dolgosheina E, Ebhardt HA, Magrini V, et al. 2008. Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa. Genome Res. 18:571−84 doi: 10.1101/gr.6897308
[17] Qiu D, Pan X, Wilson IW, Li F, Liu M, et al. 2009. High throughput sequencing technology reveals that the taxoid elicitor methyl jasmonate regulates microRNA expression in Chinese yew (Taxus chinensis). Gene 436:37−44 doi: 10.1016/j.gene.2009.01.006
[18] Axtell MJ, Bowman JL. 2008. Evolution of plant microRNAs and their targets. Trends Plant Sci. 13:343−9 doi: 10.1016/j.tplants.2008.03.009
[19] Sun G, Stewart CN, Jr, Xiao P, Zhang B. 2012. MicroRNA expression analysis in the cellulosic biofuel crop switchgrass (Panicum virgatum) under abiotic stress. PLoS One 7:e32017 doi: 10.1371/journal.pone.0032017
[20] Sunkar R, Zhu J-K. 2004. Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell 16:2001−19 doi: 10.1105/tpc.104.022830
[21] Zhou M. 2012. Genetic engineering of turfgrass for enhanced performance under environmental stress, Dissertation, Clemson University. U.S. pp. 44. https://tigerprints.clemson.edu/all_dissertations/920
[22] Palatnik JF, Wollmann H, Schommer C, Schwab R, Boisbouvier J, et al. 2007. Sequence and expression differences underlie functional specialization of Arabidopsis microRNAs miR159 and miR319. Dev. Cell 13:115−25 doi: 10.1016/j.devcel.2007.04.012
[23] Zhou M, Li D, Li Z, Hu Q, Yang C, et al. 2013. Constitutive expression of a miR319 gene alters plant development and enhances salt and drought tolerance in transgenic creeping bentgrass. Plant Physiol. 161:1375−91 doi: 10.1104/pp.112.208702
[24] Ori N, Cohen AR, Etzioni A, Brand A, Yanai O, et al. 2007. Regulation of LANCEOLATE by miR319 is required for compound-leaf development in tomato. Nat. Genet. 39:787−91 doi: 10.1038/ng2036
[25] Liu Y, Li D, Yan J, Wang K, Luo H, et al. 2019. MiR319-mediated ethylene biosynthesis, signaling and salt stress response in switchgrass. Plant Biotechnol. J. 17:2370−83 doi: 10.1111/pbi.13154
[26] Yang C, Li D, Mao D, Liu X, Ji C, et al. 2013. Overexpression of microRNA319 impacts leaf morphogenesis and leads to enhanced cold tolerance in rice (Oryza sativa L.). Plant Cell Environ. 36:2207−18 doi: 10.1111/pce.12130
[27] Xie Q, Liu X, Zhang Y, Tang J, Yin D, et al. 2017. Identification and characterization of microRNA319a and its putative target gene, PvPCF5, in the bioenergy grass switchgrass (Panicum virgatum). Front. Plant Sci. 8:396 doi: 10.3389/fpls.2017.00396
[28] Hu Z, Liu T, Cao J. 2019. Functional similarity and difference among Bra-MIR319 family in plant development. Genes 10:952 doi: 10.3390/genes10120952
[29] Wang ST, Sun XL, Hoshino Y, Yu Y, Jia B, et al. 2014. MicroRNA319 positively regulates cold tolerance by targeting OsPCF6 and OsTCP21 in rice (Oryza sativa L.). PLoS One 9:e91357 doi: 10.1371/journal.pone.0091357
[30] Sun X, Wang C, Xiang N, Li X, Yang S, et al. 2017. Activation of secondary cell wall biosynthesis by miR319-targeted TCP4 transcription factor. Plant Biotechnol. J. 15:1284−94 doi: 10.1111/pbi.12715
[31] Lin YJ, Chen H, Li Q, Li W, Wang JP, et al. 2017. Reciprocal cross-regulation of VND and SND multigene TF families for wood formation in Populus trichocarpa. Proc. Natl. Acad. Sci. U. S. A. 114:E9722−E9729 doi: 10.1073/pnas.1714422114
[32] Lin YC, Li W, Sun YH, Kumari S, Wei H, et al. 2013. SND1 transcription factor−directed quantitative functional hierarchical genetic regulatory network in wood formation in Populus trichocarpa. Plant Cell 25:4324−41 doi: 10.1105/tpc.113.117697
[33] Wei H. 2019. Construction of a hierarchical gene regulatory network centered around a transcription factor. Brief. Bioinform. 20:1021−31 doi: 10.1093/bib/bbx152
[34] Xiao H, Wang Y, Liu D, Wang W, Li X, et al. 2003. Functional analysis of the rice AP3 homologue OsMADS16 by RNA interference. Plant Mol. Biol. 52:957−66 doi: 10.1023/A:1025401611354
[35] Shi R, Chiang VL. 2005. Facile means for quantifying microRNA expression by real-time PCR. Biotechniques 39:519−25 doi: 10.2144/000112010
[36] Dai X, Zhao PX. 2011. psRNATarget: a plant small RNA target analysis server. Nucleic Acids Res. 39:W155−W159 doi: 10.1093/nar/gkr319
[37] Sarvepalli K, Nath U. 2011. Interaction of TCP4-mediated growth module with phytohormones. Plant Signal. Behav. 6:1440−3 doi: 10.4161/psb.6.10.17097
[38] Fang Y, Zheng Y, Lu W, Li J, Duan Y, et al. 2020. Roles of miR319-regulated TCPs in plant development and response to abiotic stress. The Crop Journal https://doi.org/10.1016/j.cj.2020.07.007
[39] Olatunji D, Geelen D, Verstraeten I. 2017. Control of endogenous auxin levels in plant root development. Int. J. Mol. Sci. 18:2587 doi: 10.3390/ijms18122587
[40] Millar AA, Gubler F. 2005. The Arabidopsis GAMYB-like genes, MYB33 and MYB65, are microRNA-regulated genes that redundantly facilitate anther development. Plant Cell 17:705−21 doi: 10.1105/tpc.104.027920
[41] Alonso-Peral MM, Li J, Li Y, Allen RS, Schnippenkoetter W, et al. 2010. The microRNA159-regulated GAMYB-like genes inhibit growth and promote programmed cell death in Arabidopsis. Plant Physiol. 154:757−71 doi: 10.1104/pp.110.160630
[42] Koyama T, Mitsuda N, Seki M, Shinozaki K, Ohme-Takagi M. 2010. TCP transcription factors regulate the activities of ASYMMETRIC LEAVES1 and miR164, as well as the auxin response, during differentiation of leaves in Arabidopsis. Plant Cell 22:3574−88 doi: 10.1105/tpc.110.075598
[43] Li X, Gunasekara C, Guo Y, Zhang H, Lei L, et al. 2014. Pop's Pipes: poplar gene expression data analysis pipelines. Tree Genetics & Genomes 10:1093−101 doi: 10.1007/s11295-014-0745-x
[44] Andriankaja M, Dhondt S, De Bodt S, Vanhaeren H, Coppens F, et al. 2012. Exit from proliferation during leaf development in Arabidopsis thaliana: a not-so-gradual process. Dev. Cell 22:64−78 doi: 10.1016/j.devcel.2011.11.011
[45] Bresso EG, Chorostecki U, Rodriguez RE, Palatnik JF, Schommer C. 2018. Spatial control of gene expression by miR319-regulated TCP transcription factors in leaf development. Plant Physiol. 176:1694−708 doi: 10.1104/pp.17.00823
[46] Schulze JO, Schubert WD, Moser J, Jahn D, Heinz DW. 2006. Evolutionary relationship between initial enzymes of tetrapyrrole biosynthesis. J. Mol. Biol. 358:1212−20 doi: 10.1016/j.jmb.2006.02.064
[47] Tanaka R, Tanaka A. 2007. Tetrapyrrole biosynthesis in higher plants. Annu. Rev. Plant Biol. 58:321−46 doi: 10.1146/annurev.arplant.57.032905.105448
[48] Hu WJ, Harding SA, Lung J, Popko JL, Ralph J, et al. 1999. Repression of lignin biosynthesis promotes cellulose accumulation and growth in transgenic trees. Nat. Biotechnol. 17:808−12 doi: 10.1038/11758
[49] Liu Y, Wei M, Hou C, Lu T, Liu L, et al. 2017. Functional characterization of Populus PsnSHN2 in coordinated regulation of secondary wall components in tobacco. Sci. Rep. 7:42 doi: 10.1038/s41598-017-00093-z
[50] Bilsborough GD, Runions A, Barkoulas M, Jenkins HW, Hasson A, et al. 2011. Model for the regulation of Arabidopsis thaliana leaf margin development. Proc. Natl. Acad. Sci. U. S. A. 108:3424−9 doi: 10.1073/pnas.1015162108
[51] Cheng Y, Qin G, Dai X, Zhao Y. 2007. NPY1, a BTB-NPH3-like protein, plays a critical role in auxin-regulated organogenesis in Arabidopsis. Proc. Natl. Acad. Sci. U. S. A. 104:18825−9 doi: 10.1073/pnas.0708506104
[52] Ursache R, Miyashima S, Chen Q, Vatén A, Nakajima K, et al. 2014. Tryptophan-dependent auxin biosynthesis is required for HD-ZIP III-mediated xylem patterning. Development 141:1250−9 doi: 10.1242/dev.103473
[53] Petricka JJ, Clay NK, Nelson TM. 2008. Vein patterning screens and the defectively organized tributaries mutants in Arabidopsis thaliana. Plant J. 56:251−63 doi: 10.1111/j.1365-313X.2008.03595.x
[54] Qin S, Fan C, Li X, Li Y, Hu J, et al. 2020. LACCASE14 is required for the deposition of guaiacyl lignin and affects cell wall digestibility in poplar. Biotechnol. Biofuels 13:197 doi: 10.1186/s13068-020-01843-4
[55] Rieu I, Eriksson S, Powers SJ, Gong F, Griffiths J, et al. 2008. Genetic analysis reveals that C19-GA 2-oxidation is a major gibberellin inactivation pathway in Arabidopsis. Plant Cell 20:2420−36 doi: 10.1105/tpc.108.058818
[56] Nath U, Crawford BC, Carpenter R, Coen E. 2003. Genetic control of surface curvature. Science 299:1404−7 doi: 10.1126/science.1079354
[57] Koyama T, Furutani M, Tasaka M, Ohme-Takagi M. 2007. TCP transcription factors control the morphology of shoot lateral organs via negative regulation of the expression of boundary-specific genes in Arabidopsis. Plant Cell 19:473−84 doi: 10.1105/tpc.106.044792
[58] Efroni I, Blum E, Goldshmidt A, Eshed Y. 2008. A protracted and dynamic maturation schedule underlies Arabidopsis leaf development. Plant Cell 20:2293−306 doi: 10.1105/tpc.107.057521
[59] Du F, Guan C, Jiao Y. 2018. Molecular mechanisms of leaf morphogenesis. Mol. Plant 11:1117−34 doi: 10.1016/j.molp.2018.06.006
[60] Yang W, Choi MH, Noh B, Noh YS. 2020. De Novo shoot regeneration controlled by HEN1 and TCP3/4 in Arabidopsis. Plant Cell Physiol. 61:1600−13 doi: 10.1093/pcp/pcaa083
[61] Schommer C, Debernardi JM, Bresso EG, Rodriguez RE, Palatnik JF. 2014. Repression of cell proliferation by miR319-regulated TCP4. Mol. Plant 7:1533−44 doi: 10.1093/mp/ssu084
[62] Zhou Y, Zhang D, An J, Yin H, Fang S, et al. 2018. TCP transcription factors regulate shade avoidance via directly mediating the expression of both PHYTOCHROME INTERACTING FACTORs and auxin biosynthetic genes. Plant Physiol. 176:1850−61 doi: 10.1104/pp.17.01566
[63] Nicolas M, Cubas P. 2016. TCP factors: new kids on the signaling block. Curr. Opin. Plant Biol. 33:33−41 doi: 10.1016/j.pbi.2016.05.006
[64] Sun J, Xu Y, Ye S, Jiang H, Chen Q, et al. 2009. Arabidopsis ASA1 is important for jasmonate-mediated regulation of auxin biosynthesis and transport during lateral root formation. Plant Cell 21:1495−511 doi: 10.1105/tpc.108.064303
[65] Lu S, Li Q, Wei H, Chang MJ, Tunlaya-Anukit S, et al. 2013. Ptr-miR397a is a negative regulator of laccase genes affecting lignin content in Populus trichocarpa. Proc. Natl. Acad. Sci. U. S. A. 110:10848−53 doi: 10.1073/pnas.1308936110
[66] Yamaguchi M, Kubo M, Fukuda H, Demura T. 2008. VASCULAR-RELATED NAC-DOMAIN7 is involved in the differentiation of all types of xylem vessels in Arabidopsis roots and shoots. Plant J. 55:652−64 doi: 10.1111/j.1365-313X.2008.03533.x
[67] Li Q, Min D, Wang JP, Peszlen I, Horvath L, et al. 2011. Down-regulation of glycosyltransferase 8D genes in Populus trichocarpa caused reduced mechanical strength and xylan content in wood. Tree Physiol. 31:226−36 doi: 10.1093/treephys/tpr008
[68] Zhao Y, Song X, Zhou H, Wei K, Jiang C, et al. 2020. KNAT2/6b, a class I KNOX gene, impedes xylem differentiation by regulating NAC domain transcription factors in poplar. New Phytol. 225:1531−44 doi: 10.1111/nph.16036
[69] Wagner H, Morgenstern B, Dress A. 2008. Stability of multiple alignments and phylogenetic trees: an analysis of ABC-transporter proteins family. Algorithms Mol. Biol. 3:15 doi: 10.1186/1748-7188-3-15
[70] Speer EO. 1987. A method of retaining phloroglucinol proof of lignin. Stain Technol. 62:279−80 doi: 10.3109/10520298709108008
[71] Pomar F, Merino F, Barceló AR. 2002. O-4-Linked coniferyl and sinapyl aldehydes in lignifying cell walls are the main targets of the Wiesner (phloroglucinol-HCl) reaction. Protoplasma 220:17−28 doi: 10.1007/s00709-002-0030-y
[72] Chang S, Puryear J, Cairney J. 1993. A simple and efficient method for isolating RNA from pine trees. Plant Mol. Biol. Rep. 11:113−6 doi: 10.1007/BF02670468
[73] Shi R, Sun YH, Zhang XH, Chiang VL. 2012. Poly(T) adaptor RT-PCR. Methods Mol. Biol. 822:53−66 doi: 10.1007/978-1-61779-427-8_4
[74] Wang J, Abbas M, Wen Y, Niu D, Wang L, et al. 2018. Selection and validation of reference genes for quantitative gene expression analyses in black locust (Robinia pseudoacacia L.) using real-time quantitative PCR. PLoS One 13:e0193076 doi: 10.1371/journal.pone.0193076
[75] Trapnell C, Roberts A, Goff L, Pertea G, Kim D, et al. 2012. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat. Protoc. 7:562−78 doi: 10.1038/nprot.2012.016
[76] Li D, Zhou M, Li Z, Luo H. 2014. MicroRNAs and their potential applications in switchgrass improvements. Edited by Luo H and Wu Y. Compendium of Bioenergy Plants: Switchgrass. Florida: CRC Press. pp. 228–52
[77] Robinson MD, McCarthy DJ, Smyth GK. 2010. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26:139−40 doi: 10.1093/bioinformatics/btp616