HAL Id: hal-02800816
https://hal.inrae.fr/hal-02800816
Submitted on 5 Jun 2020
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Transcriptome and ecophysiological data of Populus nigra genotypes during drought stress
Marie Garavillon-Tournayre, Boris Fumanal, Aurelie Gousset, Jean-Stéphane Venisse, Romain de Oliveira, Pierrick Benoit, Benjamin Alary, Philippe Label
To cite this version:
Marie Garavillon-Tournayre, Boris Fumanal, Aurelie Gousset, Jean-Stéphane Venisse, Romain de Oliveira, et al.. Transcriptome and ecophysiological data of Populus nigra genotypes during drought stress. JOBIM 2015, Jul 2015, Clermont-Ferrand, France. pp.1, 2015. �hal-02800816�
α = 0.90 AL L-29 SPM -28 SPM -40 STR -10 SPM -12 ER S-05 α = 0.95 1,5 MM sequences 30 M sequences/sample 47 samples
σ
CV =
µ
Levene’s test
Transcriptome and ecophysiological data of Populus nigra genotypes
during drought stress
Garavillon-Tournayre M., Fumanal B., Gousset-Dupont A., Venisse J. S., De Oliveira R., Benoit P., Alary B. and Label P.
Marie.GARAVILLON@univ-bpclermont.fr
stress
Ecole Doctorale
Sciences de la Vie, Santé, Agronomie et Environnement
Experimental design
Statistical analysis
Do poplars responses to drought stress depend
on plasticity?
Is the leaf transcriptome modified
by drought treatment?
Questions
Explained variables Normalisation HomoscedasticityCV
matrix
Placticity response to drought
Ascendant Hierarchical Clustering
Distance: euclidian
Contrast: Ward
Clustering Statistic choiceGenotype effect
ANOVA 2
Boxcox’s
transformation
Shapiro-Wilk’s test
Phenotypic data Reference transcriptome Populus trichocarpa 73013 Populus nigra leaf 47739 > library("DESeq2")Wald’s statistic
False Discovery Rate 0.1‰
Principal Component Analysis
NAAAA < 60 pb
> 30% redundancy contaminants
Leaf transcriptome in drought
Transcriptional data Cleaning RNAseq paired-end Mapping Filtered reads 7%
Treatment impact on transcription
Multivariate analysis 9689 up 8836 down 29214 non-differential 0,9 1,1 -1,0 -0,5 0,0 0,5 1,0 Log RLD (RN As eq)
Log Relative Quantity (RT-qPCR)
Pearson’s correlation
Validation of aquaporins expression
A T C G G C
A G C
T C G
Issue
Global warming
Increase of drought in progress…
Treatment Genotype Biological
repetition WD SPM-28 R1 WD SPM-28 R2 WD SPM-28 R3 WD SPM-28 R4 WD SPM-40 R1 WD SPM-40 R2 WD SPM-40 R3 WD SPM-40 R4 WD STR-10 R1 WD STR-10 R2 WD STR-10 R3 WD STR-10 R4 WD ERS-05 R1 WD ERS-05 R2 WD ERS-05 R3 WD ERS-05 R4 WD SPM-12 R1 WD SPM-12 R2 WD SPM-12 R3 WD SPM-12 R4 WD ALL-29 R1 WD ALL-29 R2 WD ALL-29 R3 WD ALL-29 R4 WW SPM-28 R1 WW SPM-28 R2 WW SPM-28 R3 WW SPM-28 R4 WW SPM-40 R1 WW SPM-40 R2 WW SPM-40 R3 WW SPM-40 R4 WW STR-10 R1 WW STR-10 R2 WW STR-10 R3 WW STR-10 R4 WW ERS-05 R1 WW ERS-05 R2 WW ERS-05 R3 WW ERS-05 R4 WW SPM-12 R1 WW SPM-12 R2 WW SPM-12 R3 WW SPM-12 R4 WW ALL-29 R1 WW ALL-29 R2 WW ALL-29 R3 WW ALL-29 R4
6 levels
2 levels
Explanatory variables4 levels
n = 48
Phenotypes Transcriptome V1 … V133 V1 … V73013 SPM-28 SPM-40 STR-10 ERS-05 SPM-12 ALL-29 V1 … Vx Selection of variables Dim 1 (29.96%) Dim 2 (14.69%) Density Curves Data D e n si ty 0 5 10 15 0 .0 0 0 .0 2 0 .0 4 0 .0 6 0 .0 8 0 .1 0 0 .1 2 Density Density Curves Data D e n si ty 0 100 200 300 400 0 .0 0 0 0 .0 0 5 0 .0 1 0 0 .0 1 5 Density WD WWWell-Watered
Water Deficit
Water movement
in well-watered Populus nigra
Leaf
Vascular tissues
2 m
1 cm
1 µm