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 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. Growth results from a complex network of processes occurring at multiple interconnected organizational levels (molecules, molecular complexes, cells, organs, and the whole plant) and is characterized by

Jasmonate Controls Leaf Growth by Repressing Cell Proliferation and the Onset of Endoreduplication while Maintaining a Potential Stand-By Mode

“…S5). This is also in agreement with Massonnet et al (2010) suggesting that endoreduplication in leaf cells could be controlled by leaf growth itself. MeJA seems to contribute to the regulation of both by affecting mitosis, delaying endoreduplication and the start of replication, but at the same time establishing a replication-competent environment to guarantee a prompt recovery.…”

“…However, the role of cell cycle regulation and cell division in plant growth and organ development is controversial. Some experimental data are most easily interpreted from the "cellular perspective," where cell division drives growth, whereas other observations are more consistent with the "organismal perspective," according to which cell division is merely a consequence of organ growth and to a large extent facultative (Massonnet et al, 2010). In the plant Arabidopsis, two types of cell cycle have been identified: the mitotic cell cycle and the endocycle (or endoreduplication cycle).…”

“…Cell division, endoreduplication, and expansion are alternative strategies contributing to plant organ growth and size (Massonnet et al, 2010). JAs have been long associated with the inhibition of plant growth (Creelman and Mullet, 1997) and more recently have been described as negatively affecting cell cycle progression in cell cultures ( Swiątek et al, 2002( Swiątek et al, , 2004Pauwels et al, 2008) and generally mitosis in plants (Zhang and Turner, 2008).…”

“…This could also explain the lack of a compensation effect where increased cell size would make up for reduced cell numbers. Interestingly, Massonnet et al (2010) postulate that leaf growth functions as a hub driving cellular processes where leaf growth is necessary to drive endoreduplication and a direct compensation mechanism between cell division and endoreduplication does not necessarily occur. Our data show that MeJA treatment reduced the expression of pCYCB1;1:Dbox-GUS as well as the relative size of the cell proliferation zone in both leaf and root after 48 h. In addition, in leaves, MeJA delays the onset of endoreduplication as well as blocking G1 prior to S transition.…”

“…The process of endoreduplication, which is an increase of ploidy levels via rereplication of DNA in the absence of mitosis (M phase), has been associated with cell expansion, where an increased cell volume is driven by internal turgor pressure (SugimotoShirasu and Roberts, 2003). However, increased ploidy level by endoreduplication appears not to be the unique determinant of plant cell size (Massonnet et al, 2010). For example, some Arabidopsis dwarf mutants defective in hormone signaling or cell wall biosynthesis retain similar ploidy levels to the wild type but exhibit reduced cell size (Caño-Delgado et al, 2000;Ishida et al, 2009).…”