doi:10.48130/OPR-2023-0009

[1]

Liu X, Gu J, Wang J, Lu Y. 2014. Lily breeding by using molecular tools and transformation systems. Molecular Biology Reports 41:6899−908

doi: 10.1007/s11033-014-3576-9

[2]

Jaakola L. 2013. New insights into the regulation of anthocyanin biosynthesis in fruits. Trends in Plant Science 18:477−83

doi: 10.1016/j.tplants.2013.06.003

[3]

Lotkowska ME, Tohge T, Fernie AR, Xue GP, Balazadeh S, et al. 2015. The Arabidopsis transcription factor MYB112 promotes anthocyanin formation during salinity and under high light stress. Plant Physiology 169:1862−80

doi: 10.1104/pp.15.00605

[4]

Liu Y, Tikunov Y, Schouten RE, Marcelis LFM, Visser RGF, et al. 2018. Anthocyanin biosynthesis and degradation mechanisms in solanaceous vegetables: a review. Frontiers in Chemistry 6:52

doi: 10.3389/fchem.2018.00052

[5]

Nishihara M, Nakatsuka T. 2011. Genetic engineering of flavonoid pigments to modify flower color in floricultural plants. Biotechnology Letters 33:433−41

doi: 10.1007/s10529-010-0461-z

[6]

Gonzalez A, Zhao M, Leavitt JM, Lloyd AM. 2008. Regulation of the anthocyanin biosynthetic pathway by the TTG1/bHLH/Myb transcriptional complex in Arabidopsis seedlings. The Plant Journal 53:814−27

doi: 10.1111/j.1365-313X.2007.03373.x

[7]

Quattrocchio F, Wing JF, Leppen HTC, Mol JNM, Koes RE. 1993. Regulatory genes controlling anthocyanin pigmentation are functionally conserved among plant species and have distinct sets of target genes. The Plant Cell 5:1497−512

doi: 10.2307/3869734

[8]

Xu W, Dubos C, Lepiniec L. 2015. Transcriptional control of flavonoid biosynthesis by MYB-bHLH-WDR complexes. Trends in Plant Science 20:176−85

doi: 10.1016/j.tplants.2014.12.001

[9]

El-Sharkawy I, Liang D, Xu K. 2015. Transcriptome analysis of an apple (Malus × domestica) yellow fruit somatic mutation identifies a gene network module highly associated with anthocyanin and epigenetic regulation. Journal of Experimental Botany 66:7359−76

doi: 10.1093/jxb/erv433

[10]

Cho K, Cho KS, Sohn HB, Ha IJ, Hong SY, et al. 2016. Network analysis of the metabolome and transcriptome reveals novel regulation of potato pigmentation. Journal of Experimental Botany 67:1519−33

doi: 10.1093/jxb/erv549

[11]

Xu L, Yang P, Yuan S, Feng Y, Xu H, et al. 2016. Transcriptome analysis identifies key candidate genes mediating purple ovary coloration in Asiatic hybrid lilies. International Journal of Molecular Sciences 17:1881

doi: 10.3390/ijms17111881

[12]

Yamagishi M. 2016. A novel R2R3-MYB transcription factor regulates light-mediated floral and vegetative anthocyanin pigmentation patterns in Lilium regale. Molecular Breeding 36:3

doi: 10.1007/s11032-015-0426-y

[13]

Yamagishi M. 2018. Involvement of a LhMYB18 transcription factor in large anthocyanin spot formation on the flower tepals of the Asiatic hybrid lily (Lilium spp. ) cultivar "Grand Cru". Molecular Breeding 38:60

doi: 10.1007/s11032-018-0806-1

[14]

Li X, Hou Y, Xie X, Li H, Li X, et al. 2020. A blueberry MIR156a-SPL12 module coordinates the accumulation of chlorophylls and anthocyanins during fruit ripening. Journal of Experimental Botany 71:5976−89

doi: 10.1093/jxb/eraa327

[15]

Liu R, Lai B, Hu B, Qin Y, Hu G, et al. 2016. Identification of microRNAs and their target genes related to the accumulation of anthocyanins in Litchi chinensis by high-throughput sequencing and degradome analysis. Frontiers in Plant Science 7:2059

[16]

Jaakola L, Poole M, Jones MO, Kämäräinen-Karppinen T, Koskimäki JJ, et al. 2010. A SQUAMOSA MADS box gene involved in the regulation of anthocyanin accumulation in bilberry fruits. Plant Physiology 153:1619−29

doi: 10.1104/pp.110.158279

[17]

Lalusin AG, Nishita K, Kim SH, Ohta M, Fujimura T. 2006. A new MADS-box gene (IbMADS10) from sweet potato (Ipomoea batatas (L.) Lam) is involved in the accumulation of anthocyanin. Molecular Genetics and Genomics 275:44−54

doi: 10.1007/s00438-005-0080-x

[18]

Zhang S, Chen Y, Zhao L, Li C, Yu J, et al. 2020. A novel NAC transcription factor, MdNAC42, regulates anthocyanin accumulation in red-fleshed apple by interacting with MdMYB10. Tree Physiology 40:413−23

doi: 10.1093/treephys/tpaa004

[19]

Sun Q, Jiang S, Zhang T, Xu H, Fang H, et al. 2019. Apple NAC transcription factor MdNAC52 regulates biosynthesis of anthocyanin and proanthocyanidin through MdMYB9 and MdMYB11. Plant Science 289:110286

doi: 10.1016/j.plantsci.2019.110286

[20]

Mahmood K, Xu Z, El-Kereamy A, Casaretto JA, Rothstein SJ. 2016. The Arabidopsis transcription factor ANAC032 represses anthocyanin biosynthesis in response to high sucrose and oxidative and abiotic stresses. Frontiers in Plant Science 7:1548

doi: 10.3389/fpls.2016.01548

[21]

Wang Y, Wang N, Xu H, Jiang S, Fang H, et al. 2018. Auxin regulates anthocyanin biosynthesis through the Aux/IAA-ARF signaling pathway in apple. Horticulture Research 5:59

doi: 10.1038/s41438-018-0068-4

[22]

Rogers K, Chen X. 2013. Biogenesis, turnover, and mode of action of plant microRNAs. The Plant Cell 25:2383−99

doi: 10.1105/tpc.113.113159

[23]

Xia R, Zhu H, An YQ, Beers EP, Liu Z. 2012. Apple miRNAs and tasiRNAs with novel regulatory networks. Genome Biology 13:R47

doi: 10.1186/gb-2012-13-6-r47

[24]

Gou JY, Felippes FF, Liu CJ, Weigel D, Wang JW. 2011. Negative regulation of anthocyanin biosynthesis in Arabidopsis by a miR156-targeted SPL transcription factor. The Plant Cell 23:1512−22

doi: 10.1105/tpc.111.084525

[25]

Bulgakov VP, Avramenko TV. 2015. New opportunities for the regulation of secondary metabolism in plants: focus on microRNAs. Biotechnology Letters 37:1719−27

doi: 10.1007/s10529-015-1863-8

[26]

Gupta OP, Karkute SG, Banerjee S, Meena NL, Dahuja A. 2017. Contemporary understanding of miRNA-based regulation of secondary metabolites biosynthesis in plants. Frontiers in Plant Science 8:374

doi: 10.3389/fpls.2017.00374

[27]

Feyissa BA, Arshad M, Gruber MY, Kohalmi SE, Hannoufa A. 2019. The interplay between miR156/SPL13 and DFR/WD40-1 regulate drought tolerance in alfalfa. BMC Plant Biology 19:434

doi: 10.1186/s12870-019-2059-5

[28]

Gupta OP, Dahuja A, Sachdev A, Kumari S, Jain PK, et al. 2019. Conserved miRNAs modulate the expression of potential transcription factors of isoflavonoid biosynthetic pathway in soybean seeds. Molecular Biology Reports 46:3713−30

doi: 10.1007/s11033-019-04814-7

[29]

Bonar N, Liney M, Zhang R, Austin C, Dessoly J, et al. 2018. Potato miR828 is associated with purple tuber skin and flesh color. Frontiers in Plant Science 9:1742

doi: 10.3389/fpls.2018.01742

[30]

Hsieh LC, Lin SI, Shih ACC, Chen JW, Lin WY, et al. 2009. Uncovering small RNA-mediated responses to phosphate deficiency in Arabidopsis by deep sequencing. Plant Physiology 151:2120−32

doi: 10.1104/pp.109.147280

[31]

Luo QJ, Mittal A, Jia F, Rock CD. 2012. An autoregulatory feedback loop involving PAP1 and TAS4 in response to sugars in Arabidopsis. Plant Molecular Biology 80:117−29

doi: 10.1007/s11103-011-9778-9

[32]

Jia X, Shen J, Liu H, Li F, Ding N, et al. 2015. Small tandem target mimic-mediated blockage of microRNA858 induces anthocyanin accumulation in tomato. Planta 242:283−93

doi: 10.1007/s00425-015-2305-5

[33]

Rock CD. 2013. Trans-acting small interfering RNA4: key to nutraceutical synthesis in grape development? Trends in Plant Science 18:601−10

doi: 10.1016/j.tplants.2013.07.006

[34]

Wang Y, Wang Y, Song Z, Zhang H. 2016. Repression of MYBL2 by both microRNA858a and HY5 leads to the activation of anthocyanin biosynthetic pathway in Arabidopsis. Molecular Plant 9:1395−405

doi: 10.1016/j.molp.2016.07.003

[35]

Zhang H, Zhao X, Li J, Cai H, Deng XW, Li L. 2014. MicroRNA408 is critical for the HY5-SPL7 gene network that mediates the coordinated response to light and copper. The Plant Cell 26:4933−53

doi: 10.1105/tpc.114.127340

[36]

Yang F, Cai J, Yang Y, Liu Z. 2013. Overexpression of microRNA828 reduces anthocyanin accumulation in Arabidopsis. Plant Cell, Tissue and Organ Culture (PCTOC) 115:159−67

doi: 10.1007/s11240-013-0349-4

[37]

Yin X, Lin X, Liu Y, Irfan M, Chen L, et al. 2020. Integrated metabolic profiling and transcriptome analysis of pigment accumulation in diverse petal tissues in the lily cultivar 'Vivian'. BMC Plant Biology 20:446

doi: 10.1186/s12870-020-02658-z

[38]

Shin J, Park E, Choi G. 2007. PIF3 regulates anthocyanin biosynthesis in an HY5-dependent manner with both factors directly binding anthocyanin biosynthetic gene promoters in Arabidopsis. The Plant Journal 49:981−94

doi: 10.1111/j.1365-313X.2006.03021.x

[39]

Chen C, Chen H, Zhang Y, Thomas HR, Frank MH, et al. 2020. TBtools: an integrative toolkit developed for interactive analyses of big biological data. Molecular Plant 13:1194−202

doi: 10.1016/j.molp.2020.06.009

[40]

Pfaffl MW. 2001. A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Research 29:e45

doi: 10.1093/nar/29.9.e45

[41]

Kumar S, Stecher G, Tamura K. 2016. MEGA7:molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution 33:1870−74

doi: 10.1093/molbev/msw054

[42]

Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, et al. 2003. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Research 13:2498−504

doi: 10.1101/gr.1239303

[43]

Yin X, Zhang Y, Zhang L, Wang B, Zhao Y, et al. 2021. Regulation of MYB transcription factors of anthocyanin synthesis in lily flowers. Frontiers in Plant Science 12:761668

doi: 10.3389/fpls.2021.761668

[44]

Tirumalai V, Swetha C, Nair A, Pandit A, Shivaprasad PV. 2019. miR828 and miR858 regulate VvMYB114 to promote anthocyanin and flavonol accumulation in grapes. Journal of Experimental Botany 70:4775−92

doi: 10.1093/jxb/erz264

[45]

Voinnet O. 2009. Origin, biogenesis, and activity of plant microRNAs. Cell 136:669−87

doi: 10.1016/j.cell.2009.01.046

[46]

Zhao X, Zhang H, Li L. 2013. Identification and analysis of the proximal promoters of microRNA genes in Arabidopsis. Genomics 101:187−94

doi: 10.1016/j.ygeno.2012.12.004

[47]

Meng X, Li Y, Zhou T, Sun W, Shan X, et al. 2019. Functional differentiation of duplicated flavonoid 3-O-glycosyltransferases in the flavonol and anthocyanin biosynthesis of Freesia hybrida. Frontiers in Plant Science 10:1330

doi: 10.3389/fpls.2019.01330

[48]

Bäurle I, Dean C. 2006. The timing of developmental transitions in plants. Cell 125:655−64

doi: 10.1016/j.cell.2006.05.005

[49]

Fornara F, de Montaigu A, Coupland G. 2010. SnapShot: control of flowering in Arabidopsis. Cell 141:550.e1−550.e2

doi: 10.1016/j.cell.2010.04.024

[50]

Yan Y, Shen L, Chen Y, Bao S, Thong Z, et al. 2014. A MYB-domain protein EFM mediates flowering responses to environmental cues in Arabidopsis. Developmental Cell 30:437−48

doi: 10.1016/j.devcel.2014.07.004

[51]

Lepiniec L, Debeaujon I, Routaboul JM, Baudry A, Pourcel L, et al. 2006. Genetics and biochemistry of seed flavonoids. Annual Review of Plant Biology 57:405−30

doi: 10.1146/annurev.arplant.57.032905.105252

[52]

Zhao D, Wei M, Shi M, Hao Z, Tao J. 2017. Identification and comparative profiling of miRNAs in herbaceous peony (Paeonia lactiflora Pall.) with red/yellow bicoloured flowers. Scientific Reports 7:44926

doi: 10.1038/srep44926

[53]

Honma T, Goto K. 2001. Complexes of MADS-box proteins are sufficient to convert leaves into floral organs. Nature 409:525−29

doi: 10.1038/35054083

[54]

Searle I, He Y, Turck F, Vincent C, Fornara F, et al. 2006. The transcription factor FLC confers a flowering response to vernalization by repressing meristem competence and systemic signaling in Arabidopsis. Genes & Development 20:898−912

doi: 10.1101/gad.373506

[55]

Lalusin AG, Ocampo E, Fujimura T. 2011. Arabidopsis thaliana plants over-expressing the IbMADS10 gene from sweetpotato accumulates high level of anthocyanin. Philippine Journal of Crop Science 36:30−36

[56]

Aceto S, Sica M, De Paolo S, D'Argenio V, Cantiello P, et al. 2014. The analysis of the inflorescence miRNome of the orchid Orchis italica reveals a DEF-like MADS-box gene as a new miRNA target. PLoS One 9:e97839

doi: 10.1371/journal.pone.0097839

[57]

Yue P, Lu Q, Liu Z, Lv T, Li X, et al. 2020. Auxin-activated MdARF5 induces the expression of ethylene biosynthetic genes to initiate apple fruit ripening. New phytologist 226:1781−95

doi: 10.1111/nph.16500

[58]

Liu Z, Shi MZ, Xie DY. 2014. Regulation of anthocyanin biosynthesis in Arabidopsis thaliana red pap1-D cells metabolically programmed by auxins. Planta 239:765−81

doi: 10.1007/s00425-013-2011-0

[59]

Lee S, Seo PJ, Lee HJ, Park CM. 2012. A NAC transcription factor NTL4 promotes reactive oxygen species production during drought-induced leaf senescence in Arabidopsis. The Plant Journal 70:831−44

doi: 10.1111/j.1365-313X.2012.04932.x

[60]

Ohashi-Ito K, Oda Y, Fukuda H. 2010. Arabidopsis VASCULAR-RELATED NAC-DOMAIN6 directly regulates the genes that govern programmed cell death and secondary wall formation during xylem differentiation. The Plant Cell 22:3461−73

doi: 10.1105/tpc.110.075036

[61]

Zhong R, Lee C, Zhou J, McCarthy RL, Ye ZH. 2008. A battery of transcription factors involved in the regulation of secondary cell wall biosynthesis in Arabidopsis. The Plant Cell 20:2763−82

doi: 10.1105/tpc.108.061325

[62]

Morishita T, Kojima Y, Maruta T, Nishizawa-Yokoi A, Yabuta Y, et al. 2009. Arabidopsis NAC transcription factor, ANAC078, regulates flavonoid biosynthesis under high-light. Plant and Cell Physiology 50:2210−22

doi: 10.1093/pcp/pcp159

[63]

Zhou H, Wang KL, Wang H, Gu C, Dare AP, et al. 2015. Molecular genetics of blood-fleshed peach reveals activation of anthocyanin biosynthesis by NAC transcription factors. The Plant Journal 82:105−21

doi: 10.1111/tpj.12792

[64]

Wei Z, Hu K, Zhao D, Tang J, Huang Z, et al. 2020. MYB44 competitively inhibits the formation of the MYB340-bHLH2-NAC56 complex to regulate anthocyanin biosynthesis in purple-fleshed sweet potato. BMC Plant Biology 20:258

doi: 10.1186/s12870-020-02451-y

[65]

Wang W, Wang J, Wu Y, Li D, Allan A, et al. 2020. Genome-wide analysis of coding and non-coding RNA reveals a conserved miR164-NAC regulatory pathway for fruit ripening. New Phytologist 225:1618−34

doi: 10.1111/nph.16233

[66]

Vale M, Rodrigues J, Badim H, Geros H, Conde A. 2021. Exogenous application of non-mature miRNA-encoded miPEP164c inhibits proanthocyanidin synthesis and stimulates anthocyanin accumulation in grape berry cells. Frontiers in Plant Science 12:706679

doi: 10.3389/fpls.2021.706679

[67]

Li Y, Cui W, Qi X, Lin M, Qiao C, et al. 2020. MicroRNA858 negatively regulates anthocyanin biosynthesis by repressing AaMYBC1 expression in kiwifruit (Actinidia arguta). Plant Science 296:110476

doi: 10.1016/j.plantsci.2020.110476

[68]

Wu Y, Huang X, Zhang S, Zhang C, Yang H, et al. 2022. Small RNA and degradome sequencing reveal the role of blackberry miRNAs in flavonoid and anthocyanin synthesis during fruit ripening. International Journal of Biological Macromolecules 213:892−901

doi: 10.1016/j.ijbiomac.2022.06.035