Short-term transcriptomic analysis at organ scale reveals candidate genes involved in low N responses in NUE-contrasting tomato genotypes.
RNAseq
Solanum lycopersicum L.
abiotic stress
nitrogen use efficiency
weighted gene co-expression network analysis (WGCNA)
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:
16
12
2022
accepted:
13
02
2023
entrez:
20
3
2023
pubmed:
21
3
2023
medline:
21
3
2023
Statut:
epublish
Résumé
Understanding the complex regulatory network underlying plant nitrogen (N) responses associated with high Nitrogen Use Efficiency (NUE) is one of the main challenges for sustainable cropping systems. Nitrate (NO Here, we compared, for the first time, the spatio-temporal transcriptome changes in both root and shoot of two NUE contrasting tomato genotypes, Regina Ostuni (high-NUE) and UC82 (low-NUE), in response to short-term (within 24 h) low (LN) and high (HN) NO Using time-series transcriptome data (0, 8, and 24 h), we identified 395 and 482 N-responsive genes differentially expressed (DEGs) between RO and UC82 in shoot and root, respectively. Protein kinase signaling plant hormone signal transduction, and phenylpropanoid biosynthesis were the main enriched metabolic pathways in shoot and root, respectively, and were upregulated in RO compared to UC82. Interestingly, several N transporters belonging to NRT and NPF families, such as Our results revealed potential candidate genes that independently and/or concurrently may regulate short-term low-N response, suggesting a key role played by cytokinin and ROS balancing in early LN regulation mechanisms adopted by the N-use efficient genotype RO.
Sections du résumé
Background
UNASSIGNED
Understanding the complex regulatory network underlying plant nitrogen (N) responses associated with high Nitrogen Use Efficiency (NUE) is one of the main challenges for sustainable cropping systems. Nitrate (NO
Methods
UNASSIGNED
Here, we compared, for the first time, the spatio-temporal transcriptome changes in both root and shoot of two NUE contrasting tomato genotypes, Regina Ostuni (high-NUE) and UC82 (low-NUE), in response to short-term (within 24 h) low (LN) and high (HN) NO
Results
UNASSIGNED
Using time-series transcriptome data (0, 8, and 24 h), we identified 395 and 482 N-responsive genes differentially expressed (DEGs) between RO and UC82 in shoot and root, respectively. Protein kinase signaling plant hormone signal transduction, and phenylpropanoid biosynthesis were the main enriched metabolic pathways in shoot and root, respectively, and were upregulated in RO compared to UC82. Interestingly, several N transporters belonging to NRT and NPF families, such as
Discussion
UNASSIGNED
Our results revealed potential candidate genes that independently and/or concurrently may regulate short-term low-N response, suggesting a key role played by cytokinin and ROS balancing in early LN regulation mechanisms adopted by the N-use efficient genotype RO.
Identifiants
pubmed: 36938018
doi: 10.3389/fpls.2023.1125378
pmc: PMC10020590
doi:
Types de publication
Journal Article
Langues
eng
Pagination
1125378Informations de copyright
Copyright © 2023 Sunseri, Aci, Mauceri, Caldiero, Puccio, Mercati and Abenavoli.
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 Exp Bot. 2014 Oct;65(19):5567-76
pubmed: 24942915
New Phytol. 2018 Jan;217(1):35-53
pubmed: 29120059
Nat Commun. 2013;4:1713
pubmed: 23591880
PLoS One. 2020 Oct 29;15(10):e0240662
pubmed: 33119630
Int J Mol Sci. 2021 May 06;22(9):
pubmed: 34066572
Plant Physiol. 2008 Oct;148(2):856-69
pubmed: 18753286
Nat Commun. 2019 Apr 5;10(1):1569
pubmed: 30952851
Proc Natl Acad Sci U S A. 2011 Nov 8;108(45):18524-9
pubmed: 22025711
Plant Physiol. 2003 Jun;132(2):926-35
pubmed: 12805621
Phytochem Rev. 2011 Sep;10(3):397-412
pubmed: 21909286
J Exp Bot. 2021 May 28;72(12):4435-4456
pubmed: 33829261
Curr Opin Biotechnol. 2022 Feb;73:263-269
pubmed: 34560475
Curr Opin Plant Biol. 2015 Oct;27:125-32
pubmed: 26247122
New Phytol. 2014 Jun;202(4):1197-1211
pubmed: 24533947
BMC Plant Biol. 2020 Oct 9;20(1):464
pubmed: 33036562
Front Plant Sci. 2019 Feb 28;10:228
pubmed: 30873200
Plant Cell. 2018 Mar;30(3):638-651
pubmed: 29475937
Plant Physiol Biochem. 2011 Jun;49(6):579-83
pubmed: 21316979
Dev Cell. 2010 Jun 15;18(6):927-37
pubmed: 20627075
Plant Cell. 2012 Jan;24(1):245-58
pubmed: 22227893
Annu Rev Cell Dev Biol. 2012;28:463-87
pubmed: 22856461
Plant Physiol. 2004 Sep;136(1):2483-99
pubmed: 15375205
Transgenic Res. 2022 Feb;31(1):23-42
pubmed: 34524604
J Exp Bot. 2021 May 28;72(12):4237-4253
pubmed: 33711100
Plant Physiol. 2012 Aug;159(4):1582-90
pubmed: 22685171
J Plant Physiol. 2017 Sep;216:17-25
pubmed: 28551475
BMC Bioinformatics. 2007 Jan 24;8:22
pubmed: 17250769
Int J Mol Sci. 2020 Apr 20;21(8):
pubmed: 32326090
Plant Cell. 2017 Oct;29(10):2393-2412
pubmed: 28893852
Genome Biol. 2014;15(12):550
pubmed: 25516281
Plant J. 2001 Jan;25(2):213-21
pubmed: 11169197
Plant Cell Physiol. 2006 Jan;47(1):74-83
pubmed: 16284408
Int J Mol Sci. 2013 Feb 07;14(2):3540-55
pubmed: 23434657
Biology (Basel). 2021 Nov 03;10(11):
pubmed: 34827119
Proc Natl Acad Sci U S A. 2016 Jul 5;113(27):7661-6
pubmed: 27325772
BMC Plant Biol. 2016 Jan 27;16:30
pubmed: 26817455
Arabidopsis Book. 2002;1:e0011
pubmed: 22303192
Anal Biochem. 2009 Apr 15;387(2):238-42
pubmed: 19454243
Int J Mol Sci. 2020 Aug 11;21(16):
pubmed: 32796695
Plant Physiol. 2012 Dec;160(4):2052-63
pubmed: 23093362
J Exp Bot. 2020 Jul 25;71(15):4428-4441
pubmed: 31985788
Plant Physiol. 2016 Mar;170(3):1684-98
pubmed: 26757990
Curr Genomics. 2017 Dec;18(6):483-497
pubmed: 29204078
Trends Plant Sci. 2015 Apr;20(4):219-29
pubmed: 25731753
J Exp Bot. 2014 Oct;65(19):5509-17
pubmed: 25165146
Plant Cell Physiol. 2013 Aug;54(8):1365-77
pubmed: 23749810
Physiol Plant. 2022 Jan;174(1):e13640
pubmed: 35099809
Sci Rep. 2018 May 10;8(1):7451
pubmed: 29748645
J Plant Physiol. 2014 Feb 15;171(3-4):349-58
pubmed: 24120534
BMC Genomics. 2011 Oct 26;12:525
pubmed: 22029603
Front Plant Sci. 2014 Feb 07;5:22
pubmed: 24570678
Plant Cell. 2009 Feb;21(2):668-80
pubmed: 19244136
Plant Physiol. 2006 Mar;140(3):909-21
pubmed: 16415211
Plant Physiol Biochem. 2016 Oct;107:21-32
pubmed: 27235648
Genome Biol. 2010;11(3):R25
pubmed: 20196867
Curr Opin Plant Biol. 2019 Feb;47:112-118
pubmed: 30496968
Science. 2002 Aug 30;297(5586):1551-5
pubmed: 12202830
Genome Res. 2003 Nov;13(11):2498-504
pubmed: 14597658
J Exp Bot. 2014 Oct;65(19):5611-8
pubmed: 25129132
Plant Physiol. 2001 Sep;127(1):345-59
pubmed: 11553762
J Exp Bot. 2008;59(11):2933-44
pubmed: 18552353
PLoS One. 2020 May 6;15(5):e0232011
pubmed: 32374731
Plant Cell Physiol. 2016 Apr;57(4):733-42
pubmed: 26823528
Plant Physiol Biochem. 2021 Oct;167:970-979
pubmed: 34571390
Plant Cell. 2014 Feb;26(2):585-601
pubmed: 24510723
Sci Rep. 2020 Jan 24;10(1):1152
pubmed: 31980689
Plant Mol Biol. 2016 Feb;90(3):293-302
pubmed: 26659593
Plant Cell Environ. 2013 Feb;36(2):328-42
pubmed: 22789031
Plant Cell. 2009 Oct;21(10):3152-69
pubmed: 19837870
Plant Cell. 2008 Sep;20(9):2514-28
pubmed: 18780802
Planta. 2005 Mar;220(5):678-88
pubmed: 15452707
Bioinformatics. 2013 Jan 1;29(1):15-21
pubmed: 23104886
Plant Biotechnol J. 2018 Nov;16(11):1858-1867
pubmed: 29577547
Annu Rev Plant Biol. 2006;57:431-49
pubmed: 16669769
Plant Cell Physiol. 2007 Jul;48(7):1022-35
pubmed: 17566055
Plant J. 2018 Oct;96(1):223-232
pubmed: 29979480
Plant Cell. 2009 Nov;21(11):3567-84
pubmed: 19933203
Plant Cell. 2005 Feb;17(2):616-27
pubmed: 15659623
Cells. 2022 Mar 24;11(7):
pubmed: 35406664
Curr Opin Plant Biol. 2008 Oct;11(5):521-9
pubmed: 18775665
Front Genet. 2020 Sep 30;11:583785
pubmed: 33193713
J Plant Res. 2003 Jun;116(3):253-7
pubmed: 12836045
Plant Physiol. 2013 Oct;163(2):844-56
pubmed: 24006285
Plant J. 2009 Jan;57(2):264-78
pubmed: 18798873
Commun Biol. 2020 Apr 1;3(1):151
pubmed: 32238902
Methods. 2001 Dec;25(4):402-8
pubmed: 11846609
BMC Bioinformatics. 2008 Dec 29;9:559
pubmed: 19114008
New Phytol. 2019 Oct;224(2):585-604
pubmed: 31369160
Nature. 2017 May 18;545(7654):311-316
pubmed: 28489820
BMC Bioinformatics. 2006 Apr 05;7:191
pubmed: 16597342
Curr Opin Plant Biol. 2012 Apr;15(2):185-91
pubmed: 22480431
Planta. 2016 Dec;244(6):1315-1328
pubmed: 27541496
Plant Physiol Biochem. 2021 Sep;166:634-644
pubmed: 34198052
J Agric Food Chem. 2020 Feb 26;68(8):2445-2456
pubmed: 31899627
Nat Plants. 2019 Apr;5(4):339-340
pubmed: 30911124
Plant Cell Physiol. 2020 Feb 1;61(2):342-352
pubmed: 31730198
Plant J. 2008 Jun;54(5):820-8
pubmed: 18266918
Plant J. 2021 Jan;105(2):421-430
pubmed: 33015901
J Plant Physiol. 2020 Mar - Apr;246-247:153137
pubmed: 32112956
Plant Sci. 2017 Jul;260:101-108
pubmed: 28554467
Nature. 2018 Nov;563(7730):259-264
pubmed: 30356219
J Plant Physiol. 2022 May;272:153684
pubmed: 35349936
J Exp Bot. 2019 Mar 27;70(6):1859-1873
pubmed: 30759246
Plant Physiol. 2007 Oct;145(2):478-90
pubmed: 17720762
Science. 2010 Feb 19;327(5968):1008-10
pubmed: 20150447
Proc Natl Acad Sci U S A. 2018 Jun 19;115(25):6494-6499
pubmed: 29769331