Chalker-Scott L. Environmental significance of anthocyanins in plant stress responses. Photochem Photobiol. 1999;70:1–9.
Article
CAS
Google Scholar
Zhang Y, Butelli E, Martin C. Engineering anthocyanin biosynthesis in plants. Curr Opin Plant Biol. 2014;19:81–90.
Article
CAS
Google Scholar
Shang Y, Venail J, Mackay S, Bailey PC, Schwinn KE, Jameson PE, et al. The molecular basis for venation patterning of pigmentation and its effect on pollinator attraction in flowers of Antirrhinum. New Phytol. 2011;189:602–15.
Article
CAS
Google Scholar
Feild TS, Lee DW, Holbrook NM. Why leaves turn red in autumn. The role of anthocyanins in senescing leaves of red-osier dogwood. Plant Physiol. 2001;127:566–74.
Article
CAS
Google Scholar
Li J. Arabidopsis flavonoid mutants are hypersensitive to UV-B irradiation. Plant Cell Online. 1993;5:171–9.
Article
CAS
Google Scholar
Lorenc-Kukuła K, Jafra S, Oszmiański J, Szopa J. Ectopic expression of anthocyanin 5-O-glucosyltransferase in potato tuber causes increased resistance to bacteria. J Agric Food Chem. 2005;53:272–81.
Article
Google Scholar
Nakabayashi R, Yonekura-Sakakibara K, Urano K, Suzuki M, Yamada Y, Nishizawa T, et al. Enhancement of oxidative and drought tolerance in Arabidopsis by overaccumulation of antioxidant flavonoids. Plant J. 2014;77:367–79.
Article
CAS
Google Scholar
Yousuf B, Gul K, Wani AA, Singh P. Health benefits of anthocyanins and their encapsulation for potential use in food systems: a review. Crit Rev Food Sci Nutr. 2016;56:2223–30.
Article
CAS
Google Scholar
Pojer E, Mattivi F, Johnson D, Stockley CS. The case for anthocyanin consumption to promote human health: a review. Compr Rev Food Sci Food Saf. 2013;12:483–508.
Article
CAS
Google Scholar
Wang LS, Stoner GD. Anthocyanins and their role in cancer prevention. Cancer Lett. 2008;269:281–90.
Article
CAS
Google Scholar
Hirner AA, Veit S, Seitz HU. Regulation of anthocyanin biosynthesis in UV-A-irradiated cell cultures of carrot and in organs of intact carrot plants. Plant Sci. 2001;161:315–22.
Article
CAS
Google Scholar
Xu ZS, Huang Y, Wang F, Song X, Wang GL, Xiong AS. Transcript profiling of structural genes involved in cyanidin-based anthocyanin biosynthesis between purple and non-purple carrot (Daucus carota L.) cultivars reveals distinct patterns. BMC Plant Biol. 2014;14:262.
Article
Google Scholar
Jaakola L, Määttä K, Pirttilä AM, Törrönen R, Kärenlampi S, Hohtola A. Expression of genes involved in anthocyanin biosynthesis in relation to anthocyanin, proanthocyanidin, and flavonol levels during bilberry fruit development. Plant Physiol. 2002;130:729–39.
Article
CAS
Google Scholar
Cavagnaro PF, Iorizzo M, Yildiz M, Senalik D, Parsons J, Ellison S, et al. A gene-derived SNP-based high resolution linkage map of carrot including the location of QTL conditioning root and leaf anthocyanin pigmentation. BMC Genomics. 2014;15:1118.
Article
Google Scholar
Baudry A, Heim MA, Dubreucq B, Caboche M, Weisshaar B, Lepiniec L. TT2, TT8, and TTG1 synergistically specify the expression of BANYULS and proanthocyanidin biosynthesis in Arabidopsis thaliana. Plant J. 2004;39:366–80.
Article
CAS
Google Scholar
Koes R, Verweij W, Quattrocchio F. Flavonoids: a colorful model for the regulation and evolution of biochemical pathways. Trends Plant Sci. 2005;10:236–42.
Article
CAS
Google Scholar
Xu Z, Feng K, Que F, Wang F, Xiong A. A MYB transcription factor, DcMYB6, is involved in regulating anthocyanin biosynthesis in purple carrot taproots. Sci Rep. 2017;7:45324.
Article
CAS
Google Scholar
Albert NW, Lewis DH, Zhang H, Schwinn KE, Jameson PE, Davies KM. Members of an R2R3-MYB transcription factor family in Petunia are developmentally and environmentally regulated to control complex floral and vegetative pigmentation patterning. Plant J. 2011;65:771–84.
Article
CAS
Google Scholar
Walker AR, Davison PA, Bolognesi-Winfield AC, James CM, Srinivasan N, Blundell TL, et al. The TRANSPARENT TESTA GLABRA1 locus, which regulates trichome differentiation and anthocyanin biosynthesis in Arabidopsis, encodes a WD40 repeat protein. Plant Cell. 1999;11:1337–49.
Article
CAS
Google Scholar
Wang Y, Zhou L, Yu X, Stover E, Luo F, Duan Y. Transcriptome profiling of Huanglongbing (HLB) tolerant and susceptible citrus plants reveals the role of basal resistance in HLB tolerance. Front Plant Sci. 2016;7:933.
PubMed
PubMed Central
Google Scholar
Matus JT, Aquea F, Arce-Johnson P. Analysis of the grape MYB R2R3 subfamily reveals expanded wine quality-related clades and conserved gene structure organization across Vitis and Arabidopsis genomes. BMC Plant Biol. 2008;8:1–15.
Article
Google Scholar
Aharoni A, De Vos CHR, Wein M, Sun Z, Greco R, Kroon A, et al. The strawberry FaMYB1 transcription factor suppresses anthocyanin and flavonol accumulation in transgenic tobacco. Plant J. 2001;28:319–32.
Article
CAS
Google Scholar
Jaakola L. New insights into the regulation of anthocyanin biosynthesis in fruits. Trends Plant Sci. 2013;18:477–83.
Article
CAS
Google Scholar
Espley RV, Hellens RP, Putterill J, Stevenson DE, Kutty-Amma S, Allan AC. Red colouration in apple fruit is due to the activity of the MYB transcription factor, MdMYB10. Plant J. 2007;49:414–27.
Article
CAS
Google Scholar
Li L, Ban ZJ, Li XH, Wu MY, Wang AL, Jiang YQ, et al. Differential expression of anthocyanin biosynthetic genes and transcription factor PcMYB10 in pears (Pyrus communis L.). PLoS One. 2012;7:e46070.
Article
CAS
Google Scholar
Mano H, Ogasawara F, Sato K, Higo H, Minobe Y. Isolation of a regulatory gene of anthocyanin biosynthesis in tuberous roots of purple-fleshed sweet potato. Plant Physiol. 2007;143:1252–68.
Article
CAS
Google Scholar
Yildiz M, Willis DK, Cavagnaro PF, Iorizzo M, Abak K, Simon PW. Expression and mapping of anthocyanin biosynthesis genes in carrot. Theor Appl Genet. 2013;126:1689–702.
Article
CAS
Google Scholar
Kirca A, Özkan M, Cemeroǧlu B. Effects of temperature, solid content and pH on the stability of black carrot anthocyanins. Food Chem. 2006;101:212–8.
Article
Google Scholar
Kaur C, Kapoor HC. Anti-oxidant activity and total phenolic content of some Asian vegetables. Int J Food Sci Technol. 2002;37:153–61.
Article
CAS
Google Scholar
Alasalvar C, Al-Farsi M, Quantick PC, Shahidi F, Wiktorowicz R. Effect of chill storage and modified atmosphere packaging (MAP) on antioxidant activity, anthocyanins, carotenoids, phenolics and sensory quality of ready-to-eat shredded orange and purple carrots. Food Chem. 2005;89:69–76.
Article
CAS
Google Scholar
Iorizzo M, Ellison S, Senalik D, Zeng P, Satapoomin P, Huang J, et al. A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution. Nat Genet. 2016;48:657–66.
Article
CAS
Google Scholar
Qiu J, Gao F, Shen G, Li C, Han X, Zhao Q, et al. Metabolic engineering of the phenylpropanoid pathway enhances the antioxidant capacity of Saussurea involucrata. PLoS One. 2013;8:e70665.
Article
CAS
Google Scholar
Maligeppagol M, Chandra GS, Navale PM, Deepa H, Rajeev PR, Asokan R, et al. Anthocyanin enrichment of tomato (Solanum lycopersicum L.) fruit by metabolic engineering. Curr Sci. 2013;105:72–80.
CAS
Google Scholar
Gamborg OL, Miller RA, Ojima K. Nutrient requirements of suspension cultures of soybean root cells. Exp Cell Res. 1968;50:151–8.
Article
CAS
Google Scholar
Barba-Espín G, Glied S, Crocoll C, Dzhanfezova T, Joernsgaard B, Okkels F, et al. Foliar-applied ethephon enhances the content of anthocyanin of black carrot roots (Daucus carota ssp. sativus var. atrorubens Alef.). BMC Plant biol. BioMed Central. 2017;17:70.
Google Scholar
Andrews S. FastQC: A Quality Control tool for High Throughput Sequence Data. http://www.bioinformatics.babraham.ac.uk/projects/fastqc/. Accessed 1 June 2016.
Schmieder R, Edwards R. Quality control and preprocessing of metagenomic datasets. Bioinformatics. 2011;27:863–4.
Article
CAS
Google Scholar
Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, et al. STAR: Ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29:15–21.
Article
CAS
Google Scholar
Liao Y, Smyth GK, Shi W. FeatureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014;30:923–30.
Article
CAS
Google Scholar
Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:550.
Article
Google Scholar
Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2009;26:139–40.
Article
Google Scholar
Chen Y, Lun ATL, Smyth GK. From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline. F1000Research. 2016;5:1438.
PubMed
PubMed Central
Google Scholar
Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, et al. Limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015;43:e47.
Article
Google Scholar
Oshlack A, Robinson MD, Young MD. From RNA-seq reads to differential expression results. Genome Biol. 2010;11:220.
Article
CAS
Google Scholar
Venables WN, Ripley BD. Modern Applied Statistics With S. 4th ed. New York: Springer; 2002.
Book
Google Scholar
Campos MD, Frederico AM, Nothnagel T, Arnholdt-Schmitt B, Cardoso H. Selection of suitable reference genes for reverse transcription quantitative real-time PCR studies on different experimental systems from carrot (Daucus carota L.). Sci Hortic. 2015;186:115–23.
Article
CAS
Google Scholar
Pfaffl MW. A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res. 2001;29:45e–45.
Article
Google Scholar
An JP, Qu FJ, Yao JF, Wang XN, You CX, Wang XF, et al. The bZIP transcription factor MdHY5 regulates anthocyanin accumulation and nitrate assimilation in apple. Hortic Res. 2017;4:17023.
Article
Google Scholar
Zhou H, Lin-Wang K, Wang H, Gu C, Dare AP, Espley RV, et al. Molecular genetics of blood-fleshed peach reveals activation of anthocyanin biosynthesis by NAC transcription factors. Plant J. 2015;82:105–21.
Article
CAS
Google Scholar
Li J, Ren L, Gao Z, Jiang M, Liu Y, Zhou L, et al. Combined transcriptomic and proteomic analysis constructs a new model for light-induced anthocyanin biosynthesis in eggplant (Solanum melongena L.). Plant Cell Environ. 2017;40:3069–87.
Article
CAS
Google Scholar
Hellens RP, Moreau C, Lin-Wang K, Schwinn KE, Thomson SJ, Fiers MWEJ, et al. Identification of Mendel’s white flower character. PLoS One. 2010;5:1–4.
Article
Google Scholar
Spelt C, Quattrocchio F, Mol JNM, Koes R. anthocyanin1 of petunia encodes a basic helix-loop-helix protein that directly activates transcription of structural anthocyanin genes. Plant Cell. 2000;12:1619.
Article
CAS
Google Scholar
Lim S-H, Kim D-H, Kim JK, Lee J-Y, Ha S-H. A radish basic helix-loop-helix transcription factor, RsTT8 acts a positive regulator for anthocyanin biosynthesis. Front Plant Sci. 2017;8:1–14.
Article
Google Scholar
Jin S-W, Rahim MA, Kim H-T, Park J-I, Kang J-G, Nou I-S. Molecular analysis of anthocyanin-related genes in ornamental cabbage. Genome. 2018;61:111–20.
Article
CAS
Google Scholar
Sharma S, Holme IB, Dionisio G, Dzhanfezova T, Joernsgaard B, Kodama M, et al. Ectopic expression of AmRosea1 and AmDelila leads to synthesis and accumulation of cyanidin based anthocyanins in orange carrots (Daucus carota subsp. sativus). In prep.
Butelli E, Titta L, Giorgio M, Mock HP, Matros A, Peterek S, et al. Enrichment of tomato fruit with health-promoting anthocyanins by expression of select transcription factors. Nat Biotechnol. 2008;26:1301–8.
Article
CAS
Google Scholar
Wang F, Zhu H, Kong W, Peng R, Liu Q, Yao Q. The Antirrhinum AmDEL gene enhances flavonoids accumulation and salt and drought tolerance in transgenic Arabidopsis. Planta. 2016;244:59–73.
Article
CAS
Google Scholar
Hichri I, Heppel SC, Pillet J, Léon C, Czemmel S, Delrot S, et al. The basic helix-loop-helix transcription factor MYC1 is involved in the regulation of the flavonoid biosynthesis pathway in grapevine. Mol Plant. 2010;3:509–23.
Article
CAS
Google Scholar
Stracke R, Werber M, Weisshaar B. The R2R3 - MYB gene family in Arabidopsis thaliana. Curr Opin Plant Biol. 2001;4:447–56.
Article
CAS
Google Scholar
Muller D, Schmitz G, Theres K. Blind homologous R2R3 Myb genes control the pattern of lateral meristem initiation in Arabidopsis. Plant Cell Online. 2006;18:586–97.
Article
Google Scholar
Ehrenreich IM, Stafford PA, Purugganan MD. The genetic architecture of shoot branching in Arabidopsis thaliana: a comparative assessment of candidate gene associations vs. quantitative trait locus mapping. Genetics. 2007;176:1223–36.
Article
CAS
Google Scholar
Zentella R, Zhang Z-L, Park M, Thomas SG, Endo A, Murase K, et al. Global analysis of DELLA direct targets in early gibberellin signaling in Arabidopsis. Plant Cell. 2007;19:3037–57.
Article
CAS
Google Scholar
Nicolas P, Lecourieux D, Gomès E, Delrot S, Lecourieux F. The grape berry-specific basic helix-loop-helix transcription factor VvCEB1 affects cell size. J Exp Bot. 2013;64:991–1003.
Article
CAS
Google Scholar
Muñoz-Espinoza C, Di Genova A, Correa J, Silva R, Maass A, González-Agüero M, et al. Transcriptome profiling of grapevine seedless segregants during berry development reveals candidate genes associated with berry weight. BMC Plant biol. BMC Plant Biol. 2016;16:1–17.
Article
Google Scholar
Zhou M, Sun Z, Wang C, Zhang X, Tang Y, Zhu X, et al. Changing a conserved amino acid in R2R3-MYB transcription repressors results in cytoplasmic accumulation and abolishes their repressive activity in Arabidopsis. Plant J. 2015;84:395–403.
Article
CAS
Google Scholar