title: Probing the reproducibility of leaf growth and molecular phenotypes: a comparison of three Arabidopsis accessions cultivated in ten laboratories.
abstract: 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.
authors.affiliation: INRA, SUPAGRO-UMR LEPSE, 34060 Montpellier cedex, France.
authors.forename: Catherine
authors.initials: C
authors.lastname: Massonnet
authors.forename: Denis
authors.initials: D
authors.lastname: Vile
authors.forename: Juliette
authors.initials: J
authors.lastname: Fabre
authors.forename: Matthew A
authors.initials: MA
authors.lastname: Hannah
authors.forename: Camila
authors.initials: C
authors.lastname: Caldana
authors.forename: Jan
authors.initials: J
authors.lastname: Lisec
authors.forename: Gerrit T S
authors.initials: GT
authors.lastname: Beemster
authors.forename: Rhonda C
authors.initials: RC
authors.lastname: Meyer
authors.forename: Gaëlle
authors.initials: G
authors.lastname: Messerli
authors.forename: Jesper T
authors.initials: JT
authors.lastname: Gronlund
authors.forename: Josip
authors.initials: J
authors.lastname: Perkovic
authors.forename: Emma
authors.initials: E
authors.lastname: Wigmore
authors.forename: Sean
authors.initials: S
authors.lastname: May
authors.forename: Michael W
authors.initials: MW
authors.lastname: Bevan
authors.forename: Christian
authors.initials: C
authors.lastname: Meyer
authors.forename: Silvia
authors.initials: S
authors.lastname: Rubio-Díaz
authors.forename: Detlef
authors.initials: D
authors.lastname: Weigel
authors.forename: José Luis
authors.initials: JL
authors.lastname: Micol
authors.forename: Vicky
authors.initials: V
authors.lastname: Buchanan-Wollaston
authors.forename: Fabio
authors.initials: F
authors.lastname: Fiorani
authors.forename: Sean
authors.initials: S
authors.lastname: Walsh
authors.forename: Bernd
authors.initials: B
authors.lastname: Rinn
authors.forename: Wilhelm
authors.initials: W
authors.lastname: Gruissem
authors.forename: Pierre
authors.initials: P
authors.lastname: Hilson
authors.forename: Lars
authors.initials: L
authors.lastname: Hennig
authors.forename: Lothar
authors.initials: L
authors.lastname: Willmitzer
authors.forename: Christine
authors.initials: C
authors.lastname: Granier
mesh_terms: 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
chemical_list: D012333:RNA, Messenger