Probing the reproducibility of leaf growth and molecular phenotypes: a comparison of three Arabidopsis accessions cultivated in ten laboratories.
A major goal of the life sciences is to understand how molecular processes control phenotypes. Because understanding biological systems relies on the work of multiple laboratories, biologists implicitly assume that organisms with the same genotype will display similar phenotypes when grown in comparable conditions. We investigated to what extent this holds true for leaf growth variables and metabolite and transcriptome profiles of three Arabidopsis (Arabidopsis thaliana) genotypes grown in 10 laboratories using a standardized and detailed protocol. A core group of four laboratories generated similar leaf growth phenotypes, demonstrating that standardization is possible. But some laboratories presented significant differences in some leaf growth variables, sometimes changing the genotype ranking. Metabolite profiles derived from the same leaf displayed a strong genotype x environment (laboratory) component. Genotypes could be separated on the basis of their metabolic signature, but only when the analysis was limited to samples derived from one laboratory. Transcriptome data revealed considerable plant-to-plant variation, but the standardization ensured that interlaboratory variation was not considerably larger than intralaboratory variation. The different impacts of the standardization on phenotypes and molecular profiles could result from differences of temporal scale between processes involved at these organizational levels. Our findings underscore the challenge of describing, monitoring, and precisely controlling environmental conditions but also demonstrate that dedicated efforts can result in reproducible data across multiple laboratories. Finally, our comparative analysis revealed that small variations in growing conditions (light quality principally) and handling of plants can account for significant differences in phenotypes and molecular profiles obtained in independent laboratories.
Massonnet
Catherine
C
INRA, SUPAGRO-UMR LEPSE, 34060 Montpellier cedex, France.
Vile
Denis
D
Fabre
Juliette
J
Hannah
Matthew A
MA
Caldana
Camila
C
Lisec
Jan
J
Beemster
Gerrit T S
GT
Meyer
Rhonda C
RC
Messerli
Gaëlle
G
Gronlund
Jesper T
JT
Perkovic
Josip
J
Wigmore
Emma
E
May
Sean
S
Bevan
Michael W
MW
Meyer
Christian
C
Rubio-Díaz
Silvia
S
Weigel
Detlef
D
Micol
José Luis
JL
Buchanan-Wollaston
Vicky
V
Fiorani
Fabio
F
Walsh
Sean
S
Rinn
Bernd
B
Gruissem
Wilhelm
W
Hilson
Pierre
P
Hennig
Lars
L
Willmitzer
Lothar
L
Granier
Christine
C
D017360:Arabidopsis / Q000235:genetics*; D020869:Gene Expression Profiling; D005838:Genotype; D010641:Phenotype; D018515:Plant Leaves / Q000254:growth & development*; D012333:RNA, Messenger / Q000235:genetics; D015203:Reproducibility of Results; D013045:Species Specificity
D012333:RNA, Messenger