A Computation Method Based on the Combination of Chlorophyll Fluorescence Parameters to Improve the Discrimination of Visually Similar Phenotypes Induced by Bacterial Virulence Factors.
Bhattacharyya distance
biotic stress
chlorophyll fluorescence parameters
hierarchical clustering
imaging analysis
Journal
Frontiers in plant science
ISSN: 1664-462X
Titre abrégé: Front Plant Sci
Pays: Switzerland
ID NLM: 101568200
Informations de publication
Date de publication:
2020
2020
Historique:
received:
21
06
2019
accepted:
11
02
2020
entrez:
17
3
2020
pubmed:
17
3
2020
medline:
17
3
2020
Statut:
epublish
Résumé
Phenotyping biotic stresses in plant-pathogen interactions studies is often hindered by phenotypes that can hardly be discriminated by visual assessment. Particularly, single gene mutants in virulence factors could lack visible phenotypes. Chlorophyll fluorescence (CF) imaging is a valuable tool to monitor plant-pathogen interactions. However, while numerous CF parameters can be measured, studies on plant-pathogen interactions often focus on a restricted number of parameters. It could result in limited abilities to discriminate visually similar phenotypes. In this study, we assess the ability of the combination of multiple CF parameters to improve the discrimination of such phenotypes. Such an approach could be of interest for screening and discriminating the impact of bacterial virulence factors without prior knowledge. A computation method was developed, based on the combination of multiple CF parameters, without any parameter selection. It involves histogram Bhattacharyya distance calculations and hierarchical clustering, with a normalization approach to take into account the inter-leaves and intra-phenotypes heterogeneities. To assess the efficiency of the method, two datasets were analyzed the same way. The first dataset featured single gene mutants of a
Identifiants
pubmed: 32174949
doi: 10.3389/fpls.2020.00213
pmc: PMC7055487
doi:
Types de publication
Journal Article
Langues
eng
Pagination
213Informations de copyright
Copyright © 2020 Méline, Brin, Lebreton, Ledroit, Sochard, Hunault, Boureau and Belin.
Références
Mol Plant Pathol. 2018 Jul;19(7):1779-1794
pubmed: 29277959
Appl Environ Microbiol. 2015 Aug 15;81(16):5395-410
pubmed: 26048944
New Phytol. 2014 Dec;204(4):823-32
pubmed: 25539004
PLoS One. 2009 Aug 14;4(8):e6632
pubmed: 19680562
J Exp Bot. 2013 Oct;64(13):3983-98
pubmed: 23913954
FEMS Microbiol Rev. 2016 Nov 1;40(6):894-937
pubmed: 28201715
Plant Methods. 2014 Nov 06;10(1):38
pubmed: 25400689
Mol Plant Pathol. 2019 Jan;20(1):33-50
pubmed: 30076773
Indian J Ophthalmol. 2008 Jan-Feb;56(1):45-50
pubmed: 18158403
BMC Genomics. 2013 Nov 06;14:761
pubmed: 24195767
BMC Genomics. 2010 Apr 13;11:238
pubmed: 20388224
Multivariate Behav Res. 1987 Apr 1;22(2):235-43
pubmed: 26782067
PLoS One. 2016 Aug 29;11(8):e0161977
pubmed: 27571391
Plant J. 2009 Dec;60(6):1096-108
pubmed: 19709387
Front Plant Sci. 2015 Jan 05;5:734
pubmed: 25601871
mBio. 2013 Jun 04;4(3):e00538-12
pubmed: 23736288
Sensors (Basel). 2014 Oct 24;14(11):20078-111
pubmed: 25347588
PLoS One. 2013 Aug 09;8(8):e73469
pubmed: 23951354
Sensors (Basel). 2012;12(1):1052-71
pubmed: 22368511
Photosynth Res. 2017 Apr;132(1):13-66
pubmed: 27815801
PLoS One. 2015 Jan 26;10(1):e0116902
pubmed: 25621489
Photosynth Res. 1990 Sep;25(3):249-57
pubmed: 24420355
Plant Methods. 2013 Jun 13;9(1):17
pubmed: 23758798
J Plant Physiol. 2011 Nov 15;168(17):2035-40
pubmed: 21820756
Physiol Plant. 2016 Aug;157(4):442-52
pubmed: 26926417
Mol Ecol. 2017 Nov;26(21):5939-5952
pubmed: 28869687
Curr Opin Plant Biol. 2011 Jun;14(3):310-7
pubmed: 21530367
PLoS One. 2014 May 13;9(5):e97047
pubmed: 24823485
Plant Methods. 2015 Apr 03;11:24
pubmed: 25866549
Sensors (Basel). 2013 Feb 06;13(2):2117-30
pubmed: 23389343
Plant J. 2009 Aug;59(4):634-44
pubmed: 19392708
Mol Plant Pathol. 2003 Sep 1;4(5):307-14
pubmed: 20569391
Annu Rev Phytopathol. 2016 Aug 4;54:163-87
pubmed: 27296145
Physiol Plant. 2015 Jan;153(1):161-74
pubmed: 24871330
Plant J. 2018 Mar;93(5):856-870
pubmed: 29285819
J Exp Bot. 2007;58(4):797-806
pubmed: 17138624
Front Plant Sci. 2017 May 18;8:833
pubmed: 28572814
Front Plant Sci. 2017 Aug 29;8:1509
pubmed: 28900440
Mol Plant Microbe Interact. 2005 Nov;18(11):1161-74
pubmed: 16353551
Front Plant Sci. 2016 Jan 08;6:1209
pubmed: 26779238
Plant Dis. 2008 Apr;92(4):530-541
pubmed: 30769647
Front Plant Sci. 2018 Feb 14;9:164
pubmed: 29491881
EMBO J. 2002 Apr 15;21(8):1909-15
pubmed: 11953310
PLoS Pathog. 2015 May 20;11(5):e1004878
pubmed: 25993128
BMC Plant Biol. 2012 May 03;12:63
pubmed: 22553969
Annu Rev Plant Biol. 2008;59:89-113
pubmed: 18444897
Trends Plant Sci. 2002 May;7(5):193-5
pubmed: 11992820
Planta. 2006 Dec;225(1):1-12
pubmed: 16807755
Photosynth Res. 2008 Apr;96(1):27-35
pubmed: 18000760
Biochim Biophys Acta. 1998 Oct 5;1367(1-3):88-106
pubmed: 9784616
Planta. 1987 Apr;170(4):489-504
pubmed: 24233012
Z Naturforsch C J Biosci. 2016 Sep 1;71(9-10):355-368
pubmed: 27626766
Photosynth Res. 2014 Nov;122(2):121-58
pubmed: 25119687
Environ Microbiol Rep. 2016 Oct;8(5):572-581
pubmed: 27059897
Front Plant Sci. 2015 Dec 22;6:1126
pubmed: 26734033
Plant Cell Physiol. 2018 Jan 1;59(1):30-43
pubmed: 29370434
Biochim Biophys Acta. 2010 Aug;1797(8):1428-38
pubmed: 20144585
Trends Plant Sci. 2010 Aug;15(8):419-22
pubmed: 20542721
Plant Cell Physiol. 2004 Jul;45(7):887-96
pubmed: 15295072
Appl Environ Microbiol. 2012 Jan;78(2):371-84
pubmed: 22101042
Plant Methods. 2012 Jan 24;8(1):3
pubmed: 22273513
J Bacteriol. 2011 Oct;193(19):5450-64
pubmed: 21784931
J Opt Soc Am A Opt Image Sci Vis. 2004 Jul;21(7):1231-40
pubmed: 15260255
Plant Dis. 2016 Feb;100(2):241-251
pubmed: 30694129
Nat Plants. 2015 Jun 01;1:15074
pubmed: 27250009
Plant Methods. 2015 Mar 26;11:23
pubmed: 25870650
Nature. 2012 Apr 15;485(7396):114-8
pubmed: 22504181
Mol Plant Microbe Interact. 1991 Nov-Dec;4(6):593-601
pubmed: 1666525