In recent years, we have experienced an increasing availability of -omic methods, more and more robust, for determining global changes in gene expression at the level of either gene transcription (transcriptomics), or protein mapping in quantity and quality (proteomics), or even detection of epigenetic changes (epigenomics), among others. This has made possible a substantial number of studies dealing with these kinds of changes undergone by plants when they grow in a microgravity environment, either real (spaceflight) or simulated. Transcriptomic studies, using microarray or, more recently, microsequencing (RNAseq) techniques are, by far, the most frequently performed.
Transcriptomic studies have produced a great deal of information on the plant responses to microgravity and spaceflight environment. The processing and interpretation of this information is, however, an arduous task, for different reasons. Spaceflight experiments are much less frequent and are subjected to much more constraints than experiments performed in ground laboratories, and this affects the reproducibility of the experiments and the statistical treatment of data. Furthermore, genotypes, growth conditions, hardware used and developmental periods of experimental samples show a great dispersion among different experiments, seriously compromising the harmonization of data. An important effort of data sharing and harmonizing has been undertaken in the project called GeneLab, under the leadership of NASA and the participation of laboratories from different countries. The project is organized into different analysis working groups (AWGs), one of them specifically devoted to plants (Barker et al. 2020; Ray et al. 2018).
Different genotypes, mostly from the model species Arabidopsis thaliana, and even different ecotypes of this species have been analyzed in their response to spaceflight. No phenotypical differences were appreciated between them after growing in the space environment, but the transcriptomic results showed highly significant differences in the number and the identity of genes showing altered regulation in comparison to the respective ground controls. This would mean that each genotype, either mutant or ecotype, used a different strategy – a different set of genes – to physiologically adapt to the environmental change (Manzano et al. 2020). It is very difficult to discriminate which of the found changes are actually adaptive and which are circumstantial, unnecessary for adaptation and therefore dispensable. The definition of an affected “core set of functions”, constituted, according to available data, by the system of heat shock response genes, the oxidative stress pathways, involving the production of Reactive Oxygen Species (ROS), and the cell wall remodeling complex, though still incomplete, may help in this discrimination, but the specificities of each genotype, organ (root or aerial part) and even each cell type, in the adaptive response, should be taken into account, thus complicating the task. A subtle general stress response linked to mitochondrial function is the common response observed across both plant and animal kingdoms so far, usually observed in synergy with the adaptation to suboptimal environments as those observed in spaceflight and microgravity simulation experiments (Silveira et al. 2020; Herranz et al. 2010).
Different –omics research experiments will play an increasingly chief role in approaching these objectives, but establishing cross-comparisons between the transcriptomic data from different plant spaceflight experiments is now mandatory (Barker et al. 2020-npjMicrogravity). New consortia are appearing at the European and International levels (Madrigal et al. 2020; Rutter et al. 2020) to support GeneLab database curation of the data, providing more insight and common criteria for the exploitation and comparison of the datasets. There is also a need for the spaceflight community to be aware of the constraints of the spaceflight research, including a particular care in the preparation and analysis of ground-based reference experiments and controls (Manzano et al. 2020). Recent reviews (at The Biology of Spaceflight compendium at Cell) present to the scientific community the current opportunities for space -omics research and discuss how to give to space biology research the opportunity to meet good practice standards similar to those of other plant biology studies, in the attempt to avoid the criticisms that are used from researchers outside of the research field (Overbey et al. 2020; Afshinnekoo et al. 2020).