Integrated omic analysis provides insights into the molecular regulation of stress tolerance by partial root-zone drying in rice.
RNA-Seq
metabolomics
omics analysis
osmotic stress
partial root-zone drying (PRD)
regulation of gene expression
rice
transcription factors
Journal
Frontiers in plant science
ISSN: 1664-462X
Titre abrégé: Front Plant Sci
Pays: Switzerland
ID NLM: 101568200
Informations de publication
Date de publication:
2023
2023
Historique:
received:
01
02
2023
accepted:
26
04
2023
medline:
26
6
2023
pubmed:
26
6
2023
entrez:
26
6
2023
Statut:
epublish
Résumé
Partial root-zone drying (PRD) is an effective water-saving irrigation strategy that improves stress tolerance and facilitates efficient water use in several crops. It has long been considered that abscisic acid (ABA)-dependent drought resistance may be involved during partial root-zone drying. However, the molecular mechanisms underlying PRD-mediated stress tolerance remain unclear. It's hypothesized that other mechanisms might contribute to PRD-mediated drought tolerance. Here, rice seedlings were used as a research model and the complex transcriptomic and metabolic reprogramming processes were revealed during PRD, with several key genes involved in osmotic stress tolerance identified by using a combination of physiological, transcriptome, and metabolome analyses. Our results demonstrated that PRD induces transcriptomic alteration mainly in the roots but not in the leaves and adjusts several amino-acid and phytohormone metabolic pathways to maintain the balance between growth and stress response compared to the polyethylene glycol (PEG)-treated roots. Integrated analysis of the transcriptome and metabolome associated the co-expression modules with PRD-induced metabolic reprogramming. Several genes encoding the key transcription factors (TFs) were identified in these co-expression modules, highlighting several key TFs, including TCP19, WRI1a, ABF1, ABF2, DERF1, and TZF7, involved in nitrogen metabolism, lipid metabolism, ABA signaling, ethylene signaling, and stress regulation. Thus, our work presents the first evidence that molecular mechanisms other than ABA-mediated drought resistance are involved in PRD-mediated stress tolerance. Overall, our results provide new insights into PRD-mediated osmotic stress tolerance, clarify the molecular regulation induced by PRD, and identify genes useful for further improving water-use efficiency and/or stress tolerance in rice.
Identifiants
pubmed: 37360728
doi: 10.3389/fpls.2023.1156514
pmc: PMC10288491
doi:
Types de publication
Journal Article
Langues
eng
Pagination
1156514Informations de copyright
Copyright © 2023 Zhao, Du, Zeng, Gao, Zhu, Wang, Zhang, Zhu, Wang, Chen, Wang, Chang, Yang, He, Li and Chen.
Déclaration de conflit d'intérêts
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
Références
J Integr Plant Biol. 2010 Nov;52(11):981-95
pubmed: 20977656
Plant Physiol. 2022 Sep 28;190(2):1057-1073
pubmed: 35512208
Nature. 2018 Apr;556(7700):235-238
pubmed: 29618812
Rice (N Y). 2013 Feb 06;6(1):4
pubmed: 24280374
PLoS One. 2011;6(7):e21789
pubmed: 21760907
Anal Chem. 2015;87(10):5050-5
pubmed: 25884293
Theor Appl Genet. 2020 May;133(5):1427-1442
pubmed: 31915875
New Phytol. 2014 Jul;203(1):32-43
pubmed: 24720847
Bioinformatics. 2001 Apr;17(4):309-18
pubmed: 11301299
Biotechnol Biofuels. 2019 Nov 20;12:274
pubmed: 31832097
Int J Mol Sci. 2018 Dec 14;19(12):
pubmed: 30558142
Bioinformatics. 2014 Apr 1;30(7):923-30
pubmed: 24227677
Funct Plant Biol. 2006 Mar;33(2):153-163
pubmed: 32689222
Innovation (Camb). 2021 Jul 01;2(3):100141
pubmed: 34557778
Nat Protoc. 2013 Jan;8(1):17-32
pubmed: 23222455
Plant Physiol. 2010 May;153(1):145-58
pubmed: 20130099
Front Genet. 2020 Oct 26;11:556749
pubmed: 33193635
PLoS Comput Biol. 2011 Jan 20;7(1):e1001057
pubmed: 21283776
Plant Physiol. 2018 Feb;176(2):1452-1468
pubmed: 29196539
Plant Cell Environ. 2009 Sep;32(9):1211-29
pubmed: 19389052
Anal Chim Acta. 2013 Mar 20;768:118-28
pubmed: 23473258
Plant Mol Biol. 2011 Apr;75(6):593-605
pubmed: 21331630
Gigascience. 2018 Jan 1;7(1):1-9
pubmed: 29220485
PLoS One. 2011;6(9):e25216
pubmed: 21966459
Plant Physiol. 2017 May;174(1):312-325
pubmed: 28351912
Plant Physiol. 2012 Apr;158(4):1755-68
pubmed: 22301130
J Exp Bot. 2014 Mar;65(4):965-79
pubmed: 24420570
PLoS One. 2016 Jun 17;11(6):e0157089
pubmed: 27315081
Nat Protoc. 2012 Apr 12;7(5):872-81
pubmed: 22498707
J Exp Bot. 2017 Jul 20;68(16):4695-4707
pubmed: 28981779
Plant Cell Environ. 2022 May;45(5):1520-1536
pubmed: 35150141
Plant Biotechnol J. 2019 Feb;17(2):472-487
pubmed: 30051585
Plant J. 2007 Aug;51(3):366-77
pubmed: 17559517
J Integr Plant Biol. 2020 Jan;62(1):25-54
pubmed: 31850654
Plant Sci. 2015 Dec;241:199-210
pubmed: 26706071
Plant Physiol. 2012 Dec;160(4):2052-63
pubmed: 23093362
Nature. 2021 Feb;590(7847):600-605
pubmed: 33408412
Nat Commun. 2022 Apr 19;13(1):2037
pubmed: 35440638
Plant Physiol. 2022 Jun 27;189(3):1608-1624
pubmed: 35512346
Plants (Basel). 2020 Aug 25;9(9):
pubmed: 32854449
Plant Biotechnol J. 2021 Aug;19(8):1588-1601
pubmed: 33638922
Int J Mol Sci. 2020 Sep 08;21(18):
pubmed: 32911801
Front Plant Sci. 2016 May 04;7:571
pubmed: 27200044
Int J Mol Sci. 2021 Feb 22;22(4):
pubmed: 33671842
Plant Direct. 2020 Dec 21;4(12):e00292
pubmed: 33364544
BMC Bioinformatics. 2011 Aug 04;12:323
pubmed: 21816040
New Phytol. 2021 Feb;229(4):1832-1839
pubmed: 32985689
J Exp Bot. 2014 May;65(8):2119-35
pubmed: 24604734
Bioinformatics. 2010 Jan 1;26(1):139-40
pubmed: 19910308
Science. 2020 Apr 17;368(6488):266-269
pubmed: 32299946
Nat Genet. 2015 Jul;47(7):834-8
pubmed: 26053497
Rice (N Y). 2022 Apr 19;15(1):23
pubmed: 35438356
Front Plant Sci. 2021 Nov 23;12:778717
pubmed: 34887895
Nat Methods. 2008 Jul;5(7):621-8
pubmed: 18516045
Front Plant Sci. 2022 Feb 21;13:802337
pubmed: 35265093
Front Plant Sci. 2022 Jan 27;12:764625
pubmed: 35154173
BMC Bioinformatics. 2008 Dec 29;9:559
pubmed: 19114008
PLoS Genet. 2018 Oct 10;14(10):e1007662
pubmed: 30303953
J Exp Bot. 2020 Oct 7;71(19):6032-6042
pubmed: 32585013
Annu Rev Plant Biol. 2016 Apr 29;67:153-78
pubmed: 26735064
Sci Rep. 2021 Mar 25;11(1):6942
pubmed: 33767323
Mol Plant. 2015 Nov 2;8(11):1563-79
pubmed: 26384576
Front Plant Sci. 2016 Sep 29;7:1466
pubmed: 27746797
Nat Rev Genet. 2022 Feb;23(2):104-119
pubmed: 34561623
Science. 2016 Nov 4;354(6312):
pubmed: 27811239
Plant J. 2018 Sep;95(6):1004-1022
pubmed: 29932274
Plant J. 2015 Dec;84(6):1100-13
pubmed: 26506081
Nucleic Acids Res. 2014 Jan;42(Database issue):D1182-7
pubmed: 24174544
Ann N Y Acad Sci. 2014 Sep;1324:7-14
pubmed: 25224455
Plant Biotechnol J. 2021 May;19(5):878-896
pubmed: 33811433
Front Plant Sci. 2019 Jan 14;9:2003
pubmed: 30693013
BMC Plant Biol. 2014 May 17;14:133
pubmed: 24884869
Nucleic Acids Res. 2017 Jan 4;45(D1):D1040-D1045
pubmed: 27924042
Nat Protoc. 2011 Jul 28;6(8):1241-9
pubmed: 21799492