{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T20:56:18Z","timestamp":1792788978229,"version":"4.5.0"},"reference-count":44,"publisher":"MDPI AG","issue":"18","license":[{"start":{"date-parts":[[2026,9,20]],"date-time":"2026-09-20T00:00:00Z","timestamp":1789862400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32260746"],"award-info":[{"award-number":["32260746"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"award":["32260746"],"award-info":[{"award-number":["32260746"]}],"id":[{"id":"https:\/\/ror.org\/01h0zpd94","id-type":"ROR","asserted-by":"publisher"}]},{"DOI":"10.13039\/100012547","name":"Guangxi Natural Science Foundation","doi-asserted-by":"publisher","award":["2023GXNSFAA026345"],"award-info":[{"award-number":["2023GXNSFAA026345"]}],"id":[{"id":"10.13039\/100012547","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100012547","name":"Guangxi Natural Science Foundation","doi-asserted-by":"publisher","award":["2023GXNSFBA026226"],"award-info":[{"award-number":["2023GXNSFBA026226"]}],"id":[{"id":"10.13039\/100012547","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Special Project for Basic Scientific Research Business of Guangxi Academy of Agricultural Sciences","award":["Guinongke2026YP025"],"award-info":[{"award-number":["Guinongke2026YP025"]}],"id":[{"id":"https:\/\/ror.org\/020rkr389","id-type":"ROR","asserted-by":"crossref"}]},{"award":["Guinongke2026YP025"],"award-info":[{"award-number":["Guinongke2026YP025"]}],"id":[{"id":"https:\/\/ror.org\/020rkr389","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Biology"],"abstract":"<jats:p>In peach production, the chilling requirement (CR) of cultivars has emerged as one of the most important limiting factors. DNA methylation plays an important role in regulating plant growth and development, environmental adaptation, and phenotypic establishment. However, the influence of DNA methylation on the CR of peach cultivars remains unclear. This study performed whole-genome methylation sequencing and transcriptome sequencing on two peach cultivars with distinct CRs and conducted an integrated analysis. The results revealed substantial differences between the two cultivars in methylation of the PpDAM5\/6 promoters, which are associated with key genes governing peach CR, and in the expression of key DNA methylation enzyme genes. These results suggest that the expression of key genes associated with CRs in peach may be affected by DNA methylation. These findings provide a new research perspective for the study of CRs in peach.<\/jats:p>","DOI":"10.3390\/biology15181664","type":"journal-article","created":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T09:01:38Z","timestamp":1789981298000},"page":"1664","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["DNA Methylation Analysis of Buds from Two Peach Varieties with Distinct Chilling Requirements During the Dormancy Induction Period"],"prefix":"10.3390","volume":"15","author":[{"given":"Xin","family":"Jiang","sequence":"first","affiliation":[{"name":"Horticulture Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"data-curation","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"}]},{"given":"Shikai","family":"Guan","sequence":"additional","affiliation":[{"name":"Flower Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"software","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"given":"Ruihong","family":"Luo","sequence":"additional","affiliation":[{"name":"Horticulture Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"resources","vocabulary":"credit"}]},{"given":"Yiwei","family":"Li","sequence":"additional","affiliation":[{"name":"Horticulture Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"resources","vocabulary":"credit"}]},{"given":"Libao","family":"Deng","sequence":"additional","affiliation":[{"name":"Horticulture Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"resources","vocabulary":"credit"}]},{"given":"Xi","family":"Wang","sequence":"additional","affiliation":[{"name":"Horticulture Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"resources","vocabulary":"credit"}]},{"given":"Yun","family":"Liu","sequence":"additional","affiliation":[{"name":"Horticulture Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"methodology","vocabulary":"credit"},{"role":"software","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"},{"role":"funding-acquisition","vocabulary":"credit"}]}],"member":"1968","published-online":{"date-parts":[[2026,9,20]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1016\/j.tplants.2007.03.012","article-title":"Plant dormancy in the perennial context","volume":"12","author":"Rohde","year":"2007","journal-title":"Trends Plant Sci."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"48","DOI":"10.1016\/j.envexpbot.2013.02.004","article-title":"Declining chilling and its impact on temperate perennial crops","volume":"91","author":"Atkinson","year":"2013","journal-title":"Environ. Exp. Bot."},{"key":"ref_3","first-page":"890","article-title":"Advance of DAM-like genes in bud dormancy of deciduous fruit trees in Rosaceae family","volume":"42","author":"Zhao","year":"2025","journal-title":"J. Fruit Sci."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"789","DOI":"10.21273\/JASHS.119.4.789","article-title":"\u2018Evergreen\u2019 Peach, Its Inheritance and Dormant Behavior","volume":"119","author":"Rodriguez","year":"1994","journal-title":"J. Am. Soc. Hortic. Sci."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1007\/s11295-007-0126-9","article-title":"Sequencing and annotation of the evergrowing locus in peach [Prunus persica (L.) Batsch] reveals a cluster of six MADS-box transcription factors as candidate genes for regulation of terminal bud formation","volume":"4","author":"Bielenberg","year":"2008","journal-title":"Tree Genet. Genomes"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1007\/s11103-010-9608-5","article-title":"Gene expression of DAM5 and DAM6 is suppressed by chilling temperatures and inversely correlated with bud break rate","volume":"73","author":"Reighard","year":"2010","journal-title":"Plant Mol. Biol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"1","DOI":"10.17660\/eJHS.2022\/046","article-title":"Study on the correlation between the expression of PpDAM5 and PpDAM6 and chilling requirements in peach","volume":"87","author":"Liu","year":"2022","journal-title":"Eur. J. Hortic. Sci."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"3481","DOI":"10.1093\/jxb\/err028","article-title":"Expressional regulation of PpDAM5 and PpDAM6, peach (Prunus persica) dormancy-associated MADS-box genes, by low temperature and dormancy-breaking reagent treatment","volume":"62","author":"Yamane","year":"2011","journal-title":"J. Exp. Bot."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"448","DOI":"10.1093\/plphys\/kiad291","article-title":"MADS-box protein PpDAM6 regulates chilling requirement-mediated dormancy and bud break in peach","volume":"193","author":"Zhao","year":"2023","journal-title":"Plant Physiol."},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Falavigna, V.d.S., Guitton, B., Costes, E., and Andr\u00e9s, F. (2019). I want to (Bud) break free: The potential role of DAM and SVP-like genes in regulating dormancy cycle in temperate fruit trees. Front. Plant Sci., 9.","DOI":"10.3389\/fpls.2018.01990"},{"key":"ref_11","first-page":"330","article-title":"Research progress on dormancy mechanism of peach buds","volume":"37","author":"Jiang","year":"2024","journal-title":"Agric. Res. Appl."},{"key":"ref_12","first-page":"98","article-title":"Research advances in bud dormancy-regrowth mechanisms of deciduous trees","volume":"55","author":"Li","year":"2025","journal-title":"J. Shandong For. Sci. Technol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1038\/s41438-021-00706-9","article-title":"Regulatory circuits involving bud dormancy factor PpeDAM6","volume":"8","author":"Lloret","year":"2021","journal-title":"Hortic. Res."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"1585","DOI":"10.1093\/jxb\/erz516","article-title":"Transcription factor TCP20 regulates peach bud endodormancy by inhibiting DAM5\/DAM6 and interacting with ABF2","volume":"71","author":"Wang","year":"2020","journal-title":"J. Exp. Bot."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"974","DOI":"10.1111\/nph.18393","article-title":"Evidence of chromatin and transcriptional dynamics for cold development in peach flower bud","volume":"236","author":"Canton","year":"2022","journal-title":"New Phytol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1007\/s11295-015-0869-7","article-title":"Genome-wide changes in histone H3 lysine 27 trimethylation associated with bud dormancy release in peach","volume":"11","author":"Conesa","year":"2015","journal-title":"Tree Genet. Genomes"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"114","DOI":"10.1038\/s41438-020-0336-y","article-title":"Thermal-responsive genetic and epigenetic regulation of DAM cluster controlling dormancy and chilling requirement in peach floral buds","volume":"7","author":"Zhu","year":"2020","journal-title":"Hortic. Res."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"204","DOI":"10.1038\/nrg2719","article-title":"Establishing, maintaining and modifying DNA methylation patterns in plants and animals","volume":"11","author":"Law","year":"2010","journal-title":"Nat. Rev. Genet."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"489","DOI":"10.1038\/s41580-018-0016-z","article-title":"Dynamics and function of DNA methylation in plants","volume":"19","author":"Zhang","year":"2018","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"418","DOI":"10.1038\/nature05917","article-title":"Epigenetic inheritance in plants","volume":"447","author":"Henderson","year":"2008","journal-title":"Nature"},{"key":"ref_21","first-page":"1787","article-title":"Research Progress on Epigenetic and Flowering-time Regulation","volume":"40","author":"Zhu","year":"2013","journal-title":"Acta Hortic. Sin."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1016\/j.plantsci.2010.01.012","article-title":"Induction of flowering by DNA demethylation in Perilla frutescens and Silene armeria: Heritability of 5-azacytidine-induced effects and alteration of the DNA methylation state by photoperiodic conditions","volume":"178","author":"Kondo","year":"2010","journal-title":"Plant Sci."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"1189","DOI":"10.1093\/plcell\/koab319","article-title":"Somatic DNA demethylation generates tissue-specific methylation states and impacts flowering time","volume":"34","author":"Williams","year":"2022","journal-title":"Plant Cell"},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Kang, D., Khan, M.A., Song, P., Liu, Y., Wu, Y., Ai, P., Li, Z., and Wang, Z. (2023). Comparative analysis of the chrysanthemum transcriptome with DNA methylation inhibitors treatment and silencing MET1 lines. BMC Plant Biol., 23.","DOI":"10.1186\/s12870-023-04036-x"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"2077","DOI":"10.1126\/science.1059745","article-title":"Requirement of CHROMOMETHYLASE3 for Maintenance of CpXpG Methylation","volume":"292","author":"Lindroth","year":"2001","journal-title":"Science"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"1461","DOI":"10.1038\/s41477-021-01008-7","article-title":"An siRNA-guided ARGONAUTE protein directs RNA polymerase V to initiate DNA methylation","volume":"7","author":"Sigman","year":"2021","journal-title":"Nat. Plants"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"2041","DOI":"10.1104\/pp.16.00393","article-title":"Analysis of chromatin regulators reveals specific features of rice DNA methylation pathways","volume":"171","author":"Tan","year":"2016","journal-title":"Plant Physiol."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"1617","DOI":"10.1105\/tpc.18.00053","article-title":"Loss of RNA-directed DNA methylation in maize chromomethylase and DDM1-type nucleosome remodeler mutants","volume":"30","author":"Fu","year":"2018","journal-title":"Plant Cell"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/S0092-8674(02)00807-3","article-title":"DEMETER, a DNA Glycosylase Domain Protein, Is Required for Endosperm Gene Imprinting and Seed Viability in Arabidopsis","volume":"110","author":"Choi","year":"2002","journal-title":"Cell"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1038\/s41477-022-01322-8","article-title":"Molecular basis of the plant ROS1-mediated active DNA demethylation","volume":"9","author":"Du","year":"2023","journal-title":"Nat. Plants"},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Xi, Y., and Li, W. (2009). BSMAP: Whole genome bisulfite sequence MAPping program. BMC Bioinform., 10.","DOI":"10.1186\/1471-2105-10-232"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1038\/nature08514","article-title":"Human DNA methylomes at base resolution show widespread epigenomic differences","volume":"462","author":"Lister","year":"2009","journal-title":"Nature"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"R87","DOI":"10.1186\/gb-2012-13-10-r87","article-title":"methylKit: A comprehensive R package for the analysis of genome-wide DNA methylation profiles","volume":"13","author":"Akalin","year":"2012","journal-title":"Genome Biol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: A flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"fastp: An ultra-fast all-in-one FASTQ preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.3317","article-title":"HISAT: A fast spliced aligner with low memory requirements","volume":"12","author":"Kim","year":"2015","journal-title":"Nat. Methods"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"402","DOI":"10.1006\/meth.2001.1262","article-title":"Analysis of relative gene expression data using real-time quantitative PCR and the 2\u2212\u0394\u0394CT method","volume":"25","author":"Livak","year":"2001","journal-title":"Methods"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"4213","DOI":"10.1016\/j.cell.2025.04.036","article-title":"Inheritance of acquired adaptive cold tolerance in rice through DNA methylation","volume":"188","author":"Song","year":"2025","journal-title":"Cell"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"481","DOI":"10.1126\/science.286.5439.481","article-title":"Epigenetics: Regulation Through Repression","volume":"286","author":"Wolffe","year":"1999","journal-title":"Science"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"1103","DOI":"10.1126\/science.293.5532.1103","article-title":"Genes, Genetics, and Epigenetics: A Correspondence","volume":"293","author":"Morris","year":"2001","journal-title":"Science"},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Liu, G., Xia, Y., Liu, T., Dai, S., and Hou, X. (2018). The DNA methylome and association of differentially methylated regions with differential gene expression during heat stress in Brassica rapa. Int. J. Mol. Sci., 19.","DOI":"10.3390\/ijms19051414"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"102552","DOI":"10.1016\/j.pbi.2024.102552","article-title":"Targeted gene regulation through epigenome editing in plants","volume":"80","author":"Cheng","year":"2024","journal-title":"Curr. Opin. Plant Biol."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"784","DOI":"10.1038\/s41477-018-0249-z","article-title":"Genome encode analyses reveal the basis of convergent evolution of fleshy fruit ripening","volume":"4","author":"Yu","year":"2018","journal-title":"Nat. Plants"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"2117","DOI":"10.1111\/nph.20347","article-title":"Enhancing nature\u2019s palette through the epigenetic breeding of flower color in chrysanthemum","volume":"245","author":"Li","year":"2025","journal-title":"New Phytol."}],"container-title":["Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2079-7737\/15\/18\/1664\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T10:06:47Z","timestamp":1789985207000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2079-7737\/15\/18\/1664"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,20]]},"references-count":44,"journal-issue":{"issue":"18","published-online":{"date-parts":[[2026,9]]}},"alternative-id":["biology15181664"],"URL":"https:\/\/doi.org\/10.3390\/biology15181664","relation":{},"ISSN":["2079-7737"],"issn-type":[{"value":"2079-7737","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,20]]}}}