Lunar and Martian agriculture will need to know which plant traits change under galactic cosmic radiation. Floral scent underlies pollination and is one of the most biochemically well-mapped plant traits, yet its response to radiation is essentially untested. This project builds a reusable transcriptomic framework to ask the question in Brassica rapa (Wisconsin Fast Plant), a fast-cycling model crop, and reports a first, deliberately modest test. The aim is a resource + method + a specific, falsifiable prediction — a foundation for a properly powered follow-up, not a definitive answer.
Does space radiation alter floral scent? Building and testing the question in Brassica rapa
RNA-seq analysis code and data for a Brassica rapa (Wisconsin Fast Plant) project asking whether galactic-cosmic-ray (GCR) radiation changes floral scent — part of the Lunar LEAF (Life sciences & Engineering for lunar Agriculture and Flight) effort.
CC0-1.0Lunar LEAF
RNA-seqNASA OSDR / GeneLab-style
🚧 in development
🚧 Status — work in progress. This repository is an analytical framework and a preliminary, testable signal — not a finished study or a claimed discovery. The two RNA-seq datasets are still being reconciled, the manuscript is a draft outline with open placeholders, and the low-dose radiation effect described below is small and awaits higher-power counts from collaborators to confirm. Treat everything here as provisional.
Overview
What's in this repository
The repo brings together two separate RNA-seq experiments in the same species. They use
different samples and different genome annotations, so their gene-ID namespaces
(Bra… Chiifu/Ensembl vs BRA… FPsc/RefSeq) do not join directly —
reconciling them is the first analytical step.
- Scent dataset — 8 samples, High- vs Low-scent B. rapa lines
(SRA
SRR4417237–SRR4417244), processed through NASA OSDR/GeneLab-style tooling. - Radiation / GCR dataset — 39 GeneLab-style libraries; factors: dose (0 / 40 cGy), genotype (WT / anthocyaninless), preservative (DRS / RL); analysed with iDEP-generated DESeq2 models. This is an exploratory re-analysis; the primary radiation study is being carried forward separately by collaborators, with OSDR as the source of record.
Preliminary signal — no significant effect at 40 cGy
Stated as a hypothesis to test, not a finding. At this low dose the result is a non-significant trend; it needs the collaborators' higher-power counts to confirm or refute.
Working from a curated, tiered floral-volatile gene set (~363 genes across the terpenoid, benzenoid/phenylpropanoid, fatty-acid/green-leaf-volatile and apocarotenoid routes), the core volatile synthase enzymes are unaffected by 40 cGy. A correlation-aware permutation test (5,000 sample-label shuffles, stratified by genotype and preservative) with Benjamini–Hochberg correction finds no route significant at FDR<0.10 — the naïve competitive test (p ≈ 0.004) was inflated roughly ten-fold by inter-gene correlation. The strongest remaining trend is a mild relative down-shift of the ester/methyltransferase "tailoring" route (permutation p ≈ 0.07, BH q ≈ 0.16 — not significant). That is enough to motivate a specific, falsifiable prediction: if radiation alters scent, it should act on the tailoring methyltransferases, not the core synthases — the same gene family that is lineage-specifically expanded and scent-defining across flowering plants (see Fig 3–4 and the tables). Confirming or refuting this needs higher-powered radiation counts.
Data & code
- Plan & current state:
README_PLAN.md— read first if picking this up - Manuscript outline:
docs/MANUSCRIPT_OUTLINE.md(draft scaffold, bracketed placeholders) - Scent gene-set & orthology:
annotation/(scent_geneset.tsv, orthology matrix, curation scripts) - Analysis notebooks:
01/02; radiation models inRadiation model/ - Figures: per-gene expression and pathway plots in
images/,images_pathways/(exploratory outputs, not curated manuscript figures)
Sequencing data trace to SRA/NASA OSDR (accessions/DOI to be linked); OSDR data remain subject to the NASA Open Data policy. Part of the Lunar LEAF effort.