Results — figures & tables

Draft manuscript figures and tables, generated from the committed analysis (annotation/). All values regenerate via the scripts.

Read the effect honestly. At 40 cGy there is no statistically significant effect of radiation on the scent gene set after correlation-aware permutation and multiple-testing correction (Fig 3). The tables list a validated gene set and individual candidates — not a confirmed radiation-responsive hit list.

Figures

Fig 1. Two-experiment design and the Bra↔BRA gene-ID join.
Fig 1. Two-experiment design and the Bra↔BRA gene-ID join.
Fig 2. (A) The 363-gene scent set by route and tier. (B) Scent-axis validation: % of each route's genes differentially expressed between High- and Low-scent lines.
Fig 2. (A) The 363-gene scent set by route and tier. (B) Scent-axis validation: % of each route's genes differentially expressed between High- and Low-scent lines.
Fig 3. Radiation dose effect (40 vs 0 cGy) by scent route vs genomic background. No route is significant after correlation-aware permutation and BH correction; the ester/methyltransferase route gives the strongest (still non-significant) trend.
Fig 3. Radiation dose effect (40 vs 0 cGy) by scent route vs genomic background. No route is significant after correlation-aware permutation and BH correction; the ester/methyltransferase route gives the strongest (still non-significant) trend.
Fig 4. Cross-species conservation of an Arabidopsis-anchored scent panel (Ensembl Compara ortholog counts). Note the Brassicaceae-specific expansion of COMT1 and the terpene-synthase expansions in grape/tomato.
Fig 4. Cross-species conservation of an Arabidopsis-anchored scent panel (Ensembl Compara ortholog counts). Note the Brassicaceae-specific expansion of COMT1 and the terpene-synthase expansions in grape/tomato.
Fig S1. Sensitivity of the gene-set test: power to detect a coordinated shift δ in the scent set's dose response. The set-level test is well-powered (~3–4% detectable at 80% power); observed effects (dashed) fall below, so the null is informative, not merely under-powered.
Fig S1. Sensitivity of the gene-set test: power to detect a coordinated shift δ in the scent set's dose response. The set-level test is well-powered (~3–4% detectable at 80% power); observed effects (dashed) fall below, so the null is informative, not merely under-powered.

Tables

Table 1. Composition of the curated floral-scent gene set in B. rapa (363 genes).

Biosynthetic routeTier 1 (core enzymes)Tier 2 (supporting)TotalExample families
Terpenoid391352terpene synthases (TPS)
Benzenoid / phenylpropanoid09797PAL, O-methyltransferases
Ester / methyltransferase39135174SABATH MTs, BAHD acyltransferases
Fatty-acid / GLV143852lipoxygenase (LOX), HPL
Apocarotenoid16016carotenoid cleavage dioxygenases (CCD)
All routes108255363—

Table 2. Candidate genes: scent-associated (High vs Low, adjP<0.1) and their radiation dose effect. Note: the scent set as a whole is NOT significantly radiation-responsive after correction (see Fig 3); these are individual candidates, not a validated hit list.

Gene (Bra)RouteTierRadiation dose effect (40 vs 0 cGy, log2)Scent High/Low log2FCScent adjPEnzyme evidence
Bra028893Ester / methyltransferase2-0.56+1.210.014T2 Pfam:PF02458 BAHD acyltransferase (vola
Bra012779Terpenoid2+0.37-0.470.0028T2 GO:0016114 terpenoid biosynthetic proce
Bra009460Ester / methyltransferase1-0.23-1.700.0089T1 Pfam:PF03492 SABATH methyltransferase (
Bra012138Ester / methyltransferase2-0.22+0.370.033T2 Pfam:PF02458 BAHD acyltransferase (vola
Bra014354Benzenoid / phenylpropanoid2-0.11+0.690.078T2 GO:0009699 phenylpropanoid biosynthetic
Bra028224Ester / methyltransferase2+0.10+0.720.03T2 Pfam:PF02458 BAHD acyltransferase (vola
Bra020970Apocarotenoid1+0.09+1.500.016T1 Pfam:PF03055 carotenoid cleavage dioxyg
Bra013161Fatty-acid / GLV2+0.09+0.500.01T2 GO:0009695 jasmonic acid biosynthetic p
Bra019582Ester / methyltransferase2-0.08+1.770.088T2 Pfam:PF02458 BAHD acyltransferase (vola
Bra040746Ester / methyltransferase2+0.08-0.940.042T2 GO:0080032 methyl jasmonate esterase ac
Bra032359Apocarotenoid1-0.07+2.290.00054T1 Pfam:PF03055 carotenoid cleavage dioxyg
Bra039556Ester / methyltransferase2-0.06-2.730.00023T2 Pfam:PF02458 BAHD acyltransferase (vola

Table 3. Characterised floral-scent genes in model scent species absent from Ensembl Plants (literature-curated; NCBI/UniProt accessions verified where fetched).

SpeciesGeneEnzyme / roleRouteVolatile productFamilyNCBI/UniProtReference
Petunia hybridaPhPAL1/PhPAL2phenylalanine ammonia-lyasebenzenoid phenylpropanoid(pathway entry)PALVerdonk 2005 Plant Cell (PMID 15805488)
Petunia hybridaPhPAASphenylacetaldehyde synthasebenzenoid phenylpropanoid2-phenylacetaldehydearomatic AAADKaminaga 2006 JBC
Petunia hybridaPhBPBTbenzoyl-CoA:benzyl/phenylethanol benzoyltransferaseesterbenzylbenzoate/phenylethylbenzoateBAHD acyltransferasesp|Q6E593.1|BEBT1_PETHYBoatright 2004 Plant Physiol
Petunia hybridaPhBSMT1/2benzoic/salicylic acid carboxyl methyltransferaseestermethylbenzoateSABATH methyltransferasesp|A4ZDG8.1|BSMT3_PETHYNegre 2003 Plant Cell; Underwood 2005
Petunia hybridaPhCFATconiferyl alcohol acyltransferasebenzenoid phenylpropanoid(isoeugenol precursor)BAHD acyltransferaseDexter 2007 Plant J
Petunia hybridaPhIGS1isoeugenol synthasebenzenoid phenylpropanoidisoeugenolPIP/NADPH reductaseKoeduka 2008
Petunia hybridaPhODO1R2R3-MYB regulatorregulator(activates benzenoid genes)MYB TFsp|Q50EX6.1|ODO1_PETHYVerdonk 2005 Plant Cell (PMID 15805488)
Petunia hybridaPhEOBI/PhEOBIIR2R3-MYB regulatorsregulator(activate ODO1 + scent genes)MYB TFSpitzer-Rimon 2010/2012 Plant Cell
Antirrhinum majusAmNES/LIS-1,-2nerolidol/linalool synthaseterpenoidlinalool, (E)-nerolidolterpene synthase (TPS)ABR24418.1Nagegowda 2008 Plant J (PMID 18363779)
Antirrhinum majusAmMYSmyrcene synthaseterpenoidmyrceneterpene synthase (TPS)Dudareva 2003 Plant Cell
Antirrhinum majusAmOCS(E)-beta-ocimene synthaseterpenoid(E)-beta-ocimeneterpene synthase (TPS)Dudareva 2003 Plant Cell
Antirrhinum majusAmBAMTbenzoic acid carboxyl methyltransferaseestermethylbenzoateSABATH methyltransferasesp|Q9FYZ9.1|BAMT_ANTMADudareva 2000 (seminal floral SABATH)
Rosa x hybridaRhNUDX1Nudix hydrolase (GPP diphosphohydrolase)terpenoidgeraniol (non-canonical route)Nudix hydrolasesp|M4I1C6.1|NUDT1_ROSHCMagnard 2015 Science (PMID 26138978)
Rosa x hybridaRhLINS/RhNESlinalool / nerolidol synthaseterpenoidlinalool, nerolidolterpene synthase (TPS)Conart 2019 Plant Physiol
Rosa x hybridaRhOMT1/2orcinol O-methyltransferasebenzenoid phenylpropanoid3,5-dimethoxytolueneO-methyltransferaseAAM23005.1Lavid 2002 Plant Physiol
Rosa x hybridaRhAAT1alcohol acyltransferaseestergeranyl/2-phenylethyl acetateBAHD acyltransferaseGuterman 2006

Sources: scent_geneset.tsv, phase3_robust_results.tsv, scent_orthology_matrix.tsv, scent_reference_species.tsv, scent_query_accessions.tsv. Markdown: docs/TABLES.md; CSV: annotation/tables/. Supplementary (Fig S1, Tables S1–S2): docs/SUPPLEMENTARY.md; reproduce all: annotation/reproduce.sh.