Probing the reproducibility of leaf growth and molecular phenotypes: A comparison of three Arabidopsis accessions cultivated in ten laboratories

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Probing the reproducibility of leaf growth and molecular phenotypes: A comparison of three Arabidopsis

accessions cultivated in ten laboratories

Catherine Massonnet, Denis Vile, Juliette Fabre, Matthew A. Hannah, C.

Caldana, J. Lisec, G.T.S. Beemster, R.C. Meyer, G. Messerli, J.T. Gronlund, et al.

To cite this version:

Catherine Massonnet, Denis Vile, Juliette Fabre, Matthew A. Hannah, C. Caldana, et al.. Probing the reproducibility of leaf growth and molecular phenotypes: A comparison of three Arabidopsis accessions cultivated in ten laboratories. Plant Physiology, American Society of Plant Biologists, 2010, 152 (4), pp.2142-2157. �10.1104/pp.109.148338�. �hal-01203861�

Supplemental Figure S1.

Rosette fresh weight data for three genotypes and nine laboratories and its correlation with Rosette leaf area.

(A) boxplot representation of fresh weight (FW) variation for three genotypes (Col-4, Ler and Ws) and for nine laboratories (L1 to L9).

Laboratories with significantly different FW are noted with stars for each genotype (ANOVAS and Tukey’s post hoc tests results). Mean and standard deviation of homogeneous groups are represented on each plot by dashed and dotted lines, respectively.

(B) Mean FW values ranking per genotype across laboratories. The core laboratories (L2, L3, L8 and L9) are represented by closed symbols and straight lines, the others with open symbols and dashed lines. Two ANOVAs were performed: either on the data including all nine laboratories (in italics) or the core (in bold) to evaluate laboratory (L), genotype (G) and interaction (LxG) effects; P values: ***, * and ns indicate significant differences (P < 0.001, P < 0.05) and the absence of significant difference, respectively. (C) Relationship between rosette fresh weight (FW) and rosette leaf area (RA) including data of the three genotypes for the nine laboratories. The core laboratories (L2, L3, L8 and L9) are represented by closed symbols, the others with open symbols.

L1 L2 L3 L4 L5 L6 L7 L8 L9

FW 0.00.20.4

L1 L2 L3 L4 L5 L6 L7 L8 L9

Col

FW 0.00.20.40.60.8

Ler

FW

Ws

FW

Col Ler Ws

L1 L2 L3 L4 L5 L6 L7 L8 L9 L1 L2 L3 L4 L5 L6 L7 L8 L9

*

*

*

* *

* A

B

C

Fresh weight (g)Fresh weight (g)

L: *** G: *** LxG: ***

L: ns G: *** LxG: ns 0.8

0.6 0.4 0.2 0.0

0.4

0.2

0.0

Fresh weight (g)

Rosette leaf area (cm²)

Supplemental Figure S2.

Aggregated core laboratory phenotypes per genotype. (A) Rosette leaf area. (B) Rosette leaf number. (C) Sixth leaf area. (D) epidermal cell density in leaf 6. (E) epidermal cell number in leaf 6. (F) mean epidermal cell area in leaf 6. Col, black; Ler, white; Ws, grey. Values were calculated by pooling data from the four core laboratories (L2, L3, L8, L9). Each variable was compared between genotypes with one-way ANOVA. P values: (***, **, *) indicate significant differences (P < 0.001, P < 0.01, P < 0.05); ns, no difference. Small case letters indicate significant differences according to the Tukey post hoc tests.

Genotypes

Col Ler Ws

Leaf 6 area (mmﾲ)

0 50 100 150 200

Rosette leaf area (mmﾲ)

0 500 1000 1500 2000 2500

Rosette leaf number

0 2 4 6 8 10 12 14

Cell number in the leaf 6

0 20000 40000 60000 80000 100000 Cell density in the leaf 6 (Nbr. mm-2)

0 100 200 300 400 500 600 700

Genotypes

Col Ler Ws

Cell area in the leaf 6 (ﾲm2) 0 1000 2000 3000 4000

***

***

ns

***

***

***

a b

a

a b

a

b

a a

a

b

a

a c

b A

B

C

D

E

F

Supplemental Figure S3. Boxplots of gene-wise cv (coefficient of variation) values for gene expression values in replicate samples. (A) intra-laboratory cv values, (B) inter-laboratory cv values.

A B

Supplemental Figure S4.

Divisive hierarchical clustering of gene expression values for the top-500 most variable genes.

(A) Based on Col samples only. (B) Based on Col, Ler and Ws samples. (C) Based on Col, Ler and Ws samples averaged per laboratory. Letters indicate the genotype: Col, C; Ler, L; Ws, W.

Numbers identify laboratories (L).