Combined Profiling of Transcriptome and DNA Methylome Reveal Genes Involved in Accumulation of Soluble Sugars and Organic Acid in Apple Fruits.
DNA methylation
Malus domestica
fruit acidity
soluble sugar content
transcript profiling
transcriptomics
Journal
Foods (Basel, Switzerland)
ISSN: 2304-8158
Titre abrégé: Foods
Pays: Switzerland
ID NLM: 101670569
Informations de publication
Date de publication:
16 Sep 2021
16 Sep 2021
Historique:
received:
11
08
2021
revised:
08
09
2021
accepted:
14
09
2021
entrez:
28
9
2021
pubmed:
29
9
2021
medline:
29
9
2021
Statut:
epublish
Résumé
Organic acids and soluble sugars are the major determinants of fruit organoleptic quality. Additionally, DNA methylation has crucial regulatory effects on various processes. However, the epigenetic modifications in the regulation of organic acid and soluble sugar accumulation in apple fruits remain uncharacterized. In this study, DNA methylation and the transcriptome were compared between 'Honeycrisp' and 'Qinguan' mature fruits, which differ significantly regarding soluble sugar and organic acid contents. In both 'Honeycrisp' and 'Qinguan' mature fruits, the CG context had the highest level of DNA methylation, and then CHG and CHH contexts. The number and distribution of differentially methylated regions (DMRs) varied among genic regions and transposable elements. The DNA methylation levels in all three contexts in the DMRs were significantly higher in 'Honeycrisp' mature fruits than in 'Qinguan' mature fruits. A combined methylation and transcriptome analysis revealed a negative correlation between methylation levels and gene expression in DMRs in promoters and gene bodies in the CG and CHG contexts and in gene bodies in the CHH context. Two candidate genes (
Identifiants
pubmed: 34574306
pii: foods10092198
doi: 10.3390/foods10092198
pmc: PMC8467953
pii:
doi:
Types de publication
Journal Article
Langues
eng
Subventions
Organisme : National Natural Science Foundation of China
ID : 32072527 and 31701875
Organisme : The Key S&T Special Projects of Shaanxi Province, China
ID : 2020zdzx03-01-02
Références
BMC Genomics. 2019 Feb 7;20(1):117
pubmed: 30732560
Plant Physiol. 2018 Feb;176(2):1384-1407
pubmed: 29295940
Metabolites. 2018 Oct 31;8(4):
pubmed: 30384454
Nat Struct Mol Biol. 2014 Jan;21(1):64-72
pubmed: 24336224
Cell. 2013 Jan 17;152(1-2):352-64
pubmed: 23313553
Plant Physiol. 2011 Dec;157(4):1664-76
pubmed: 21984725
Nature. 2015 Dec 24;528(7583):575-9
pubmed: 26675734
Proc Natl Acad Sci U S A. 2013 Jan 29;110(5):1797-802
pubmed: 23319627
Nat Rev Genet. 2005 May;6(5):351-60
pubmed: 15861207
Plant J. 2018 Aug;95(3):427-443
pubmed: 29750477
Plant Physiol. 2020 Feb;182(2):992-1006
pubmed: 31772076
Proc Natl Acad Sci U S A. 2021 Jan 5;118(1):
pubmed: 33443220
Plants (Basel). 2020 Oct 22;9(11):
pubmed: 33105724
Plant Biotechnol J. 2019 Apr;17(4):826-835
pubmed: 30256509
Nat Rev Genet. 2010 Mar;11(3):204-20
pubmed: 20142834
Nat Rev Genet. 2004 Jul;5(7):532-44
pubmed: 15211355
Nat Rev Mol Cell Biol. 2018 Aug;19(8):489-506
pubmed: 29784956
Planta. 2019 Dec;250(6):1833-1847
pubmed: 31471637
Plant Biotechnol J. 2020 Feb;18(2):540-552
pubmed: 31350935
Nat Rev Genet. 2014 Jun;15(6):394-408
pubmed: 24805120
Int J Mol Sci. 2020 Feb 07;21(3):
pubmed: 32046163
Science. 2013 Aug 9;341(6146):1237905
pubmed: 23828890
Plant J. 2017 Aug;91(3):443-454
pubmed: 28423209
Proc Natl Acad Sci U S A. 2010 May 11;107(19):8689-94
pubmed: 20395551
Plant Mol Biol. 2021 Feb;105(3):321-332
pubmed: 33128723
Cell. 2006 Sep 22;126(6):1025-8
pubmed: 16990127
J Exp Bot. 2013 Apr;64(6):1451-69
pubmed: 23408829
J Sci Food Agric. 2011 Apr;91(6):992-1000
pubmed: 21416474
Food Chem. 2015 Apr 1;172:86-91
pubmed: 25442527
Plant Genome. 2015 Nov;8(3):eplantgenome2015.03.0016
pubmed: 33228269
J Agric Food Chem. 2020 Apr 29;68(17):4812-4829
pubmed: 32227940
Plant Physiol. 2020 May;183(1):236-249
pubmed: 32139477
BMC Plant Biol. 2020 May 6;20(1):191
pubmed: 32375636
Plant Biotechnol J. 2019 Feb;17(2):435-450
pubmed: 29999579
J Exp Bot. 2001 May;52(358):881-9
pubmed: 11432905
Cell. 2006 Sep 22;126(6):1189-201
pubmed: 16949657
Hortic Res. 2018 Dec 1;5:60
pubmed: 30510767
Plant Sci. 2012 Jul;190:52-61
pubmed: 22608519
Phytochemistry. 2009 Jul-Aug;70(11-12):1329-44
pubmed: 19762054
J Agric Food Chem. 2019 May 8;67(18):5250-5264
pubmed: 31008599
J Exp Bot. 2009;60(6):1823-37
pubmed: 19264753
Plant Biotechnol J. 2019 Mar;17(3):674-686
pubmed: 30183123
Plant Biotechnol J. 2018 Feb;16(2):672-687
pubmed: 28796917
Nat Genet. 2017 Jul;49(7):1099-1106
pubmed: 28581499
Plant Physiol. 2016 Mar;170(3):1315-30
pubmed: 26637549
Curr Biol. 2013 Apr 22;23(8):697-702
pubmed: 23583552