. (2010) Probing the reproducibility of leaf growth and molecular phenotypes: a comparison of three arabidopsis accessions cultivated in ten laboratories. Plant Physiology, Vol.152 (No.4). pp. 2142-2157. ISSN 0032-0889

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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 3 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.

Item Type:	Journal Article
Subjects:	S Agriculture > SB Plant culture
Divisions:	Faculty of Science > Life Sciences (2010- ) > Warwick HRI (2004-2010)
Journal or Publication Title:	Plant Physiology
Publisher:	American Society of Plant Biologists
ISSN:	0032-0889
Date:	April 2010
Volume:	Vol.152
Number:	No.4
Number of Pages:	16
Page Range:	pp. 2142-2157
Identification Number:	10.1104/pp.109.148338
Status:	Peer Reviewed
Publication Status:	Published
Access rights to Published version:	Restricted or Subscription Access
Funder:	European Commission
Grant number:	LSHG-CT-2006-037704
URI:	http://wrap.warwick.ac.uk/id/eprint/6136

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