The Genetic Response Of An Earth Plant – Off World – In Microgravity

The Genetic Response Of An Earth Plant – Off World – In Microgravity
The specific assay and tissue types for each dataset are indicated with network clustering based on hardware. See Supplementary Data 1 and 2 for the Matrix driving this visualization. Note the hardware used to analyze plant response to spaceflight often defines the types of tissue that are available and so these two variables are often linked. Purple color circles represent RNAseq analysis of wild-type Col-0 plants, shades of blue represent other WT ecotypes, the pink circle represents RNA-seq analysis performed on mutants. The size of circles is a qualitative representation of the amount of differentially expressed loci relative to other genetic varieties used during that study. Ecotypes: Col Columbia, Cvi Cape Verde Island, Ws Wassilewskija, Ler Landsberg, Col-0 + Ws mixed sample 80% Ws and 20% Col ecotypes. Genotypes: WT wild-type, arg1 altered response to gravity 1, hsfa2 heat shock transcription factor A2, atm1 ataxia-telangiectasia mutated 1, phyD phytochrome D, Hardware: BRIC Biological Research in Canister, EMCS European Modular Cultivation System, VEGGIE Vegetable production system, SIMBOX SIMBOX incubator system, ABRS Advanced Biological Research System. An interactive version of this visualization is available at: gilroy-qlik.botany.wisc.edu/a/sense/app/20aa802b-6915-4b1a-87bd-c029a1812e2b/sheet/6241e71a-a3c5-4c63-9210-e05c743699d7/state/analysis. — Nature

Nature

Spaceflight presents a multifaceted environment for plants, combining the effects on growth of many stressors and factors including altered gravity, the influence of experiment hardware, and increased radiation exposure.

To help understand the plant response to this complex suite of factors this study compared transcriptomic analysis of 15 Arabidopsis thaliana spaceflight experiments deposited in the National Aeronautics and Space Administration’s GeneLab data repository. These data were reanalyzed for genes showing significant differential expression in spaceflight versus ground controls using a single common computational pipeline for either the microarray or the RNA-seq datasets.

Such a standardized approach to analysis should greatly increase the robustness of comparisons made between datasets. This analysis was coupled with extensive cross-referencing to a curated matrix of metadata associated with these experiments.

Our study reveals that factors such as analysis type (i.e., microarray versus RNA-seq) or environmental and hardware conditions have important confounding effects on comparisons seeking to define plant reactions to spaceflight. The metadata matrix allows selection of studies with high similarity scores, i.e., that share multiple elements of experimental design, such as plant age or flight hardware.

Comparisons between these studies then helps reduce the complexity in drawing conclusions arising from comparisons made between experiments with very different designs.

Meta-analysis of the space flight and microgravity response of the Arabidopsis plant transcriptome, Nature (open access)

Meta-analysis of the space flight and microgravity response of the Arabidopsis plant transcriptome, NPJ MIcrogravity via PubMed (open access)

Richard Barker, Colin P. S. Kruse, Christina Johnson, Amanda Saravia-Butler, Homer Fogle, Hyun-Seok Chang, Ralph Møller Trane, Noah Kinscherf, Alicia Villacampa, Aránzazu Manzano, Raúl Herranz, Laurence B. Davin, Norman G. Lewis, Imara Perera, Chris Wolverton, Parul Gupta, Pankaj Jaiswal, Sigrid S. Reinsch, Sarah Wyatt & Simon Gilroy
npj Microgravity volume 9, Article number: 21 (2023)

Astrobiology

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