The same but different: How small scale hidden variations can have large effects
Expression of cell-wall related genes is highly variable and correlates with sepal morphology
Recommendation: posted 11 September 2023, validated 14 September 2023
Sabot, F. (2023) The same but different: How small scale hidden variations can have large effects. Peer Community in Genomics, 100243. 10.24072/pci.genomics.100243
For ages, we considered only single genes, or just a few, in order to understand the relationship between phenotype and genotype in response to environmental challenges. Recently, the use of meaningful groups of genes, e.g. gene regulatory networks, or modules of co-expression, allowed scientists to have a larger view of gene regulation. However, all these findings were based on contrasted genotypes, e.g. between wild-types and mutants, as the implicit assumption often made is that there is little transcriptomic variability within the same genotype context.
Hartasànchez and collaborators (2023) decided to challenge both views: they used a single genotype instead of two, the famous A. thaliana Col0, and numerous plants, and considered whole gene networks related to sepal morphology and its variations. They used a clever approach, combining high-level phenotyping and gene expression to better understand phenomena and regulations underlying sepal morphologies. Using multiple controls, they showed that basic variations in the expression of genes related to the cell wall regulation, as well as the ones involved in chloroplast metabolism, influenced the global transcriptomic pattern observed in sepal while being in near-identical genetic background and controlling for all other experimental conditions.
The paper of Hartasànchez et al. is thus a tremendous call for humility in biology, as we saw in their work that we just understand the gross machinery. However, the Devil is in the details: understanding those very small variations that may have a large influence on phenotypes, and thus on local adaptation to environmental challenges, is of great importance in these times of climatic changes.
Hartasánchez DA, Kiss A, Battu V, Soraru C, Delgado-Vaquera A, Massinon F, Brasó-Vives M, Mollier C, Martin-Magniette M-L, Boudaoud A, Monéger F. 2023. Expression of cell-wall related genes is highly variable and correlates with sepal morphology. bioRxiv, ver. 4, peer-reviewed and recommended by Peer Community in Genomics. https://doi.org/10.1101/2022.04.26.489498
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article. The authors declared that they comply with the PCI rule of having no financial conflicts of interest in relation to the content of the article.
This work was funded by the French National Research Agency (ANR) through a European ERA-NET Coordinating Action in Plant Sciences (ERA-CAPS) grant (Grant No. ANR-17-CAPS-0002-01 V-Morph) and through a direct grant (Grant No. ANR-17-CE20-0023-02 WALLMIME), by Fond de Recherche ENS Lyon (Projet émergent FLORIVAR), and by BAP INRAE (Projet FLORIVAR)
Evaluation round #1
DOI or URL of the preprint: https://doi.org/10.1101/2022.04.26.489498
Version of the preprint: 2
Author's Reply, 18 Jul 2023
Decision by Francois Sabot, posted 30 May 2023, validated 31 May 2023
Dear Dr Hartasànchez and Dr Monéger
Your manuscript "Expression of cell-wall related genes is highly variable and correlates with sepal morphology" has been reviewed by two independent reviewers, and they found it of high interest and valuable for publication. However, they propose some minor corrections, in order to improve it a slight bit.
If you are able to perform these revisions as requested, I will accept it without anymore revisions.