Alappat B, Alappat J. 2020. Anthocyanin pigments: Beyond aesthetics. Molecules, 25, 5500.

An F, Zhang K, Zhang L K, Li X, Chen S M, Wang H S, Cheng F. 2022. Genome-wide identification, evolutionary selection, and genetic variation of DNA methylation-related genes in Brassica rapa and Brassica oleracea. Journal of Integrative Agriculture, 21, 1620–1632.

An J P, Qu F J, Yao J F, Wang X N, You C X, Wang X F, Hao Y J. 2017. The bZIP transcription factor MdHY5 regulates anthocyanin accumulation and nitrate assimilation in apple. Horticulture Research, 4, 17023.

Ayvaz H, Cabaroglu T, Akyildiz A, Pala C U, Temizkan R, Agcam E, Ayvaz Z, Durazzo A, Lucarini M, Direito R, Diaconeasa Z. 2022. Anthocyanins: Metabolic digestion, bioavailability, therapeutic effects, current pharmaceutical/industrial use, and innovation potential. Antioxidants (Basel), 12, 48.

Azuma A, Kobayashi S. 2022. Demethylation of the 3´ LTR region of retrotransposon in VvMYBA1BEN allele enhances anthocyanin biosynthesis in berry skin and flesh in ‘Brazil’ grape. Plant Science, 322, 111341.

Bai S L, Tao R Y, Tang Y X, Yin L, Ma Y J, Ni J B, Yan X H, Yang Q S, Wu Z Y, Zeng Y L, Teng Y W. 2019a. BBX16, a B-box protein, positively regulates light-induced anthocyanin accumulation by activating MYB10 in red pear. Plant Biotechnology Journal, 17, 1985–1997.

Bai S L, Tao R Y, Yin L, Ni J B, Yang Q S, Yan X H, Yang F, Guo X P, Li H X, Teng Y W. 2019b. Two B-box proteins, PpBBX18 and PpBBX21, antagonistically regulate anthocyanin biosynthesis via competitive association with Pyrus pyrifolia ELONGATED HYPOCOTYL 5 in the peel of pear fruit. The Plant Journal, 100, 1208–1223.

Benetatos L, Vartholomatos G. 2018. Enhancer DNA methylation in acute myeloid leukemia and myelodysplastic syndromes. Cellular and Molecular Life Sciences, 75, 1999–2009.

Bewick A J, Niederhuth C E, Ji L, Rohr N A, Griffin P T, Leebens-Mack J, Schmitz R J. 2017. The evolution of CHROMOMETHYLASES and gene body DNA methylation in plants. Genome Biology, 18, 65.

Bu H D, Sun X H, Yue P T, Qiao J L, Sun J M, Wang A D, Yuan H, Yu W Q. 2022. The MdAux/IAA2 transcription repressor regulates cell and fruit size in apple fruit. International Journal of Molecular Sciences, 23, 9454.

Bursch K, Toledo-Ortiz G, Pireyre M, Lohr M, Braatz C, Johansson H. 2020. Identification of BBX proteins as rate-limiting cofactors of HY5. Nature Plants, 6, 921–928.

Chakraborty M, Gangappa S N, Maurya J P, Sethi V, Srivastava A K, Singh A, Dutta S, Ojha M, Gupta N, Sengupta M, Ram H, Chattopadhyay S. 2019. Functional interrelation of MYC2 and HY5 plays an important role in Arabidopsis seedling development. The Plant Journal, 99, 1080–1097.

Chang C S, Li Y H, Chen L T, Chen W C, Hsieh W P, Shin J, Jane W N, Chou S J, Choi G, Hu J M, Somerville S, Wu S H. 2008. LZF1, a HY5-regulated transcriptional factor, functions in Arabidopsis de-etiolation. The Plant Journal, 54, 205–219.

Chen Q M, Li Q H, Qiao X, Yin H, Zhang S L. 2020. Genome-wide identification of lysin motif containing protein family genes in eight rosaceae species, and expression analysis in response to pathogenic fungus Botryosphaeria dothidea in Chinese white pear. BMC Genomics, 21, 612.

Chen R, Yang C, Gao H, Shi C M, Zhang Z Y, Lu G Y, Shen X Y, Tang Y P, Li F, Lu Y E, Ouyang B. 2022. Induced mutation in ELONGATED HYPOCOTYL5 abolishes anthocyanin accumulation in the hypocotyl of pepper. Theoretical and Applied Genetics, 135, 3455–3468.

Clermont P L, Parolia A, Liu H H, Helgason C D. 2016. DNA methylation at enhancer regions: Novel avenues for epigenetic biomarker development. Frontiers in Bioscience-Landmark, 21, 430–446.

Dai X N, Li Q Y, Jiang F D, Song Z Z, Tang X L, Su S Q, Yao R T, Yang H Y, Yang Y Q, Zhang H X, Li J Z. 2022. Transcriptome analysis of branches reveals candidate genes involved in anthocyanin biosynthesis of ‘Red Bartlett’ pear (Pyrus communis L.). Scientia Horticulturae, 305, 111392

Dondini L, Pierantoni L, Ancarani V, D’angelo M, Cho K H, Shin I S, Musacchi S, Kang S J, Sansavini S. 2008. The inheritance of the red colour character in European pear (Pyrus communis) and its map position in the mutated cultivar ‘Max Red Bartlett’. Plant Breeding, 127, 524–526.

Dussi M C, Sugar D, Wrolstad R E. 1995. Characterizing and quantifying anthocyanins in red pears and the effect of light quality on fruit color. Journal of the American Society for Horticultural Science, 120, 785–789.

El-Sharkawy I, Liang D, Xu K N. 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, 7359–7376.

Espley R V, Brendolise C, Chagne D, Kutty-Amma S, Green S, Volz R, Putterill J, Schouten H J, Gardiner S E, Hellens R P, Allan A C. 2009. Multiple repeats of a promoter segment causes transcription factor autoregulation in red apples. The Plant Cell, 21, 168–183.

Gangappa S N, Botto J F. 2016. The multifaceted roles of HY5 in plant growth and development. Molecular Plant, 9, 1353–1365.

Gao Y, Ge F F, Zhang R, Yin D Y, Zhao Y, Tang H, Zhang L, Yang L. 2021. PID: An integrative and comprehensive platform of plant intron. Computational Biology and Chemistry, 93, 107528.

Huang J Q, Zhang G, Li Y H, Lyu M J, Zhang H, Zhang N, Chen R. 2023. Integrative genomic and transcriptomic analyses of a bud sport mutant ‘Jinzao Wuhe’ with the phenotype of large berries in grapevines. PeerJ, 11, e14617.

Jeong S W, Das P K, Jeoung S C, Song J Y, Lee H K, Kim Y K, Kim W J, Park Y I, Yoo S D, Choi S B, Choi G, Park Y I. 2010. Ethylene suppression of sugar-induced anthocyanin pigmentation in Arabidopsis. Plant Physiology, 154, 1514–1531.

Jiang S H, Chen M, He N B, Chen X L, Wang N, Sun Q G, Zhang T L, Xu H F, Fang H C, Wang Y C, Zhang Z Y, Wu S J, Chen X S. 2019. MdGSTF6, activated by MdMYB1, plays an essential role in anthocyanin accumulation in apple. Horticulture Research, 6, 40.

Jiang S H, Wang N, Chen M, Zhang R, Sun Q G, Xu H F, Zhang Z Y, Wang Y C, Sui X Q, Wang S F, Fang H C, Zuo W F, Su M Y, Zhang J, Fei Z J, Chen X S. 2020. Methylation of MdMYB1 locus mediated by RdDM pathway regulates anthocyanin biosynthesis in apple. Plant Biotechnology Journal, 18, 1736–1748.

Job N, Yadukrishnan P, Bursch K, Datta S, Johansson H. 2018. Two B-Box proteins regulate photomorphogenesis by oppositely modulating HY5 through their diverse C-terminal domains. Plant Physiology, 176, 2963–2976.

Kim D, Shivakumar M, Han S, Sinclair M S, Lee Y J, Zheng Y, Olopade O I, Kim D, Lee Y. 2018. Population-dependent intron retention and DNA methylation in breast cancer. Molecular Cancer Research, 16, 461–469.

Kohler C, Springer N. 2017. Plant epigenomics-deciphering the mechanisms of epigenetic inheritance and plasticity in plants. Genome Biology, 18, 132.

Kovinich N, Kayanja G, Chanoca A, Riedl K, Otegui M S, Grotewold E. 2014. Not all anthocyanins are born equal: distinct patterns induced by stress in Arabidopsis. Planta, 240, 931–940.

Kumar S, Kirk C, Deng C H, Wiedow C, Qin M, Espley R, Wu J, Brewer L. 2019. Fine-mapping and validation of the genomic region underpinning pear red skin colour. Horticulture Research, 6, 29.

Lescot M, Dehais P, Thijs G, Marchal K, Moreau Y, Van De Peer Y, Rouze P, Rombauts S. 2002. PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Research, 30, 325–327.

Liu H N, Su J, Zhu Y F, Yao G F, Allan A C, Ampomah-Dwamena C, Shu Q, Lin-Wang K, Zhang S L, Wu J. 2019. The involvement of PybZIPa in light-induced anthocyanin accumulation via the activation of PyUFGT through binding to tandem G-boxes in its promoter. Horticulture Research, 6, 134.

Livak K J, Schmittgen T D. 2001. Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method. Methods, 25, 402–408.

Meng F L, Zhao H N, Zhu B, Zhang T, Yang M Y, Li Y, Han Y P, Jiang J M. 2021. Genomic editing of intronic enhancers unveils their role in fine-tuning tissue-specific gene expression in Arabidopsis thaliana. The Plant Cell, 33, 1997–2014.

Niederhuth C E, Schmitz R J. 2017. Putting DNA methylation in context: From genomes to gene expression in plants. Biochimica et Biophysica Acta (Gene Regulatory Mechanisms), 1860, 149–156.

Ong-Abdullah M, Ordway J M, Jiang N, Ooi S E, Kok S Y, Sarpan N, Azimi N, Hashim A T, Ishak Z, Rosli S K, Malike F A, Bakar N A, Marjuni M, Abdullah N, Yaakub Z, Amiruddin M D, Nookiah R, Singh R, Low E T, Chan K L, et al. 2015. Loss of Karma transposon methylation underlies the mantled somaclonal variant of oil palm. Nature, 525, 533–537.

Ordonez R, Martinez-Calle N, Agirre X, Prosper F. 2019. DNA methylation of enhancer elements in myeloid neoplasms: think outside the promoters? Cancers (Basel), 11, 1424.

Ou C Q, Zhang X L, Wang F, Zhang L Y, Zhang Y J, Fang M, Wang J H, Wang J X, Jiang S L, Zhang Z H. 2020. A 14 nucleotide deletion mutation in the coding region of the PpBBX24 gene is associated with the red skin of “Zaosu Red” pear (Pyrus pyrifolia White Pear Group): a deletion in the PpBBX24 gene is associated with the red skin of pear. Horticulture Research, 7, 39.

Qiu Z K, Wang H J, Li D J, Yu B W, Hui Q L, Yan S S, Huang Z J, Cui X, Cao B H. 2019. Identification of candidate HY5-dependent and -independent regulators of anthocyanin biosynthesis in tomato. Plant and Cell Physiology, 60, 643–656.

Reimer F C. 1951. A genetic bud mutation in the pear. Journal of Heredity, 42, 93–94.

Royo C, Torres-Perez R, Mauri N, Diestro N, Cabezas J A, Marchal C, Lacombe T, Ibanez J, Tornel M, Carreno J, Martinez-Zapater J M, Carbonell-Bejerano P. 2018. The major origin of seedless grapes is associated with a missense mutation in the MADS-Box gene VviAGL11. Plant Physiology, 177, 1234–1253.

Shin D H, Choi M, Kim K, Bang G, Cho M, Choi S B, Choi G, Park Y I. 2013. HY5 regulates anthocyanin biosynthesis by inducing the transcriptional activation of the MYB75/PAP1 transcription factor in Arabidopsis. FEBS Letters, 587, 1543–1547.

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, 981–994.

Shlyueva D, Stampfel G, Stark A. 2014. Transcriptional enhancers: From properties to genome-wide predictions. Nature Reviews Genetics, 15, 272–286.

Smemo S, Tena J J, Kim K H, Gamazon E R, Sakabe N J, Gomez-Marin C, Aneas I, Credidio F L, Sobreira D R, Wasserman N F, Lee J H, Puviindran V, Tam D, Shen M, Son J E, Vakili N A, Sung H K, Naranjo S, Acemel R D, Manzanares M, et al. 2014. Obesity-associated variants within FTO form long-range functional connections with IRX3. Nature, 507, 371–375.

Song Y H, Yoo C M, Hong A P, Kim S H, Jeong H J, Shin S Y, Kim H J, Yun D J, Lim C O, Bahk J D, Lee S Y, Nagao R T, Key J L, Hong J C. 2008. DNA-binding study identifies C-box and hybrid C/G-box or C/A-box motifs as high-affinity binding sites for STF1 and LONG HYPOCOTYL5 proteins. Plant Physiology, 146, 1862–1877.

Song Z, Yan T, Liu J, Bian Y, Heng Y, Lin F, Jiang Y, Deng X W, Xu D. 2020. BBX28/BBX29, HY5 and BBX30/31 form a feedback loop to fine-tune photomorphogenic development. The Plant Journal, 104, 377–390.

Vandenbussche F, Habricot Y, Condiff A S, Maldiney R, Van Der Straeten D, Ahmad M. 2007. HY5 is a point of convergence between cryptochrome and cytokinin signalling pathways in Arabidopsis thaliana. The Plant Journal, 49, 428–441.

Wang N Y, Li X T, Xu C Y, Lian R, Pan T F, Guo Z X, Yu Y, She W Q. 2022. Gene expression in the sugar metabolism between ‘Guanxi’ pummelo and its early-ripening mutant ‘Liuyuezao’. Scientia Horticulturae, 305, 111435.

Wang Y Y, Zhang X D, Zhao Y R, Yang J, He Y Y, Li G C, Ma W R, Huang X L, Su J. 2020. Transcription factor PyHY5 binds to the promoters of PyWD40 and PyMYB10 and regulates its expression in red pear ‘Yunhongli No. 1’. Plant Physiology and Biochemistry, 154, 665–674.

Wang Z G, Meng D, Wang A D, Li T L, Jiang S L, Cong P H, Li T Z. 2013. The methylation of the PcMYB10 promoter is associated with green-skinned sport in Max Red Bartlett pear. Plant Physiology, 162, 885–896.

Weber B, Zicola J, Oka R, Stam M. 2016. Plant enhancers: A call for discovery. Trends in Plant Science, 21, 974–987.

Wu J, Wang Z W, Shi Z B, Zhang S, Ming R, Zhu S L, Khan M A, Tao S T, Korban S S, Wang H, Chen N J, Nishio T, Xu X, Cong L, Qi K J, Huang X S, Wang Y T, Zhao X, Wu J Y, Deng C,.et al. 2013. The genome of the pear (Pyrus bretschneideri Rehd.). Genome Research, 23, 396–408.

Xu W J, Dubos C, Lepiniec L. 2015. Transcriptional control of flavonoid biosynthesis by MYB-bHLH-WDR complexes. Trends in Plant Science, 20, 176–185.

Yang J F, Li B B, Shi W J, Gong Z Z, Chen L, Hou Z X. 2018. Transcriptional activation of anthocyanin biosynthesis in developing fruit of blueberries (Vaccinium corymbosum L.) by preharvest and postharvest UV irradiation. Journal of Agricultural and Food Chemistry, 66, 10931–10942.

Yang M, Koo S I, Song W O, Chun O K. 2011. Food matrix affecting anthocyanin bioavailability: review. Current Medicinal Chemistry, 18, 291–300.

Yao G F, Ming M L, Allan A C, Gu C, Li L T, Wu X, Wang R Z, Chang Y J, Qi K J, Zhang S L, Wu J. 2017. Map-based cloning of the pear gene MYB114 identifies an interaction with other transcription factors to coordinately regulate fruit anthocyanin biosynthesis. Plant Journal, 92, 437–451.

Zhang Z Y, Shi Y N, Ma Y C, Yang X F, Yin X R, Zhang Y Y, Xiao Y W, Liu W L, Li Y D, Li S J, Liu X F, Grierson D, Allan A C, Jiang G H, Chen K S. 2020. The strawberry transcription factor FaRAV1 positively regulates anthocyanin accumulation by activation of FaMYB10 and anthocyanin pathway genes. Plant Biotechnology Journal, 18, 2267–2279.

Zhao Y, Dong W Q, Zhu Y C, Allan A C, Lin-Wang K, Xu C J. 2020. PpGST1, an anthocyanin-related glutathione S-transferase gene, is essential for fruit coloration in peach. Plant Biotechnology Journal, 18, 1284–1295.

Zheng X D, Li Y C, Ma C Q, Chen B Y, Sun Z J, Tian Y K, Wang C H. 2022. A mutation in the promoter of the arabinogalactan protein 7-like gene PcAGP7-1 affects cell morphogenesis and brassinolide content in pear (Pyrus communis L.) stems. The Plant Journal, 109, 47–63.

Zicola J, Liu L Y, Tanzler P, Turck F. 2019. Targeted DNA methylation represses two enhancers of FLOWERING LOCUS T in Arabidopsis thaliana. Nature Plants, 5, 300–307.