From magnetic environment to plant phenotype. The flagship map, and the one that has to be read most carefully. The review states that its Figure 7 is designed for hypothesis generation and experimental planning rather than as a proven causal network, and the tiers here preserve that distinction: the input perturbation and the developmental outputs carry real evidence, while the molecular route between them does not. Read the border styles from left to right and the shape of the field's problem is visible — the evidence is concentrated at the two ends, on the perturbation and on the phenotypes, while the middle, where the mechanism would have to live, is almost entirely dashed. Primary metabolism, the review's central thesis, is drawn as T4 on purpose: the metabolic route is argued rather than demonstrated, and the map should not let it borrow credibility from the developmental evidence beside it. The model is explicitly modular — cryptochrome may dominate in blue-light-grown seedlings, mitochondria in dark-imbibed seeds, plastids in greening tissue, and nutrient uptake in roots — so a single phenotype may be produced by different weightings of the same components depending on tissue, stage and light regime. Derived from: Figure 7 of Porterfield & Barker, "Plant Responses to Near-Null Magnetic Fields" — expanded and tier-annotated structural_context structural_context radical_pair_acceptor flavin_semiquinone triplet_yield_sensitive 1H 14N CHEBI:57692 AT4G08920 GO:0005634 Magnetic intensity affects cryptochrome-dependent responses in Arabidopsis thaliana. Theoretical analysis of Arabidopsis cryptochrome-1 shows magnetic fields could alter activation yields through radical-pair spin dynamics. Under blinded conditions, cryptochrome-dependent magnetic-field effects in Arabidopsis were NOT reproduced. Magnetic sensitivity mediated by Arabidopsis cryptochrome occurs during flavin reoxidation in the dark, not during photoreduction. Blue-light-dependent phosphorylation of cryptochromes is affected by magnetic fields in Arabidopsis. The reference case for the radical-pair mechanism in biology, and the entity from which the review's whole argument is generalised outward. Direction of effect is not consistent across the literature, and one blinded replication attempt failed (see Harris2009 below). Treat the magnitude as unsettled even though the mechanism is well characterised. flavin_semiquinone iron_sulfur_4Fe4S iron_sulfur_2Fe2S ros_leak_site 1H 14N 57Fe 33S CHEBI:58210 AT5G37510 AT5G08530 AT4G02580 AT5G11770 GO:0005747 7.1.1.2 The FMN site forms a flavin semiquinone during turnover and is a known superoxide-producing leak site, and the Fe/S chain performs sequential one-electron transfers — both of the physical routes the radical-pair and hyperfine arguments require. No published experiment has applied a near-null field and measured plant complex I activity, so this is a hypothesis with a mechanism, not a result. Electron transfer along the Fe/S chain is fast relative to plausible singlet-triplet mixing times, so a coherent radical-pair effect here is harder to argue than at the flavin. Treat the flavin and the cluster chain as separate hypotheses rather than one. rieske_2Fe2S semiquinone_radical ros_leak_site 57Fe 33S 1H AT5G13430 AT5G13440 GO:0005750 The Qo site generates a kinetically stabilised ubisemiquinone — a genuine, comparatively long-lived organic radical in a defined protein pocket, which is the most favourable setting for a field-dependent branching effect anywhere in the respiratory chain. Qo-site semiquinone is short-lived and its occupancy is debated; a field effect here would be easier to argue if lifetime were measured under the relevant conditions. iron_sulfur_4Fe4S radical_pair_acceptor triplet_yield_sensitive 57Fe 33S 1H ATCG01060 GO:0009522 1.97.1.12 The geomagnetic field is required for normal lima bean photosynthesis, PSI/LHCI content and ROS production; near-null field conditions altered photosynthetic electron transport. PSI is the strongest structural case in the whole atlas. Charge separation at P700 produces a genuine spin-correlated radical pair (P700·+ A1·−), which is the textbook example of the species the radical-pair mechanism describes — it is studied by exactly that formalism in photosynthesis spectroscopy. Three [4Fe-4S] clusters then carry the electron onward. The P700·+ A1·− pair is extremely short-lived, and the well-characterised magnetic-field effects on it are seen in isolated preparations at fields far above geomagnetic. Structural plausibility is high; relevance at 50 uT is not established. structural_context CHEBI:29033 CHEBI:29034 CHEBI:16189 The geomagnetic field contributes to efficient iron uptake in Arabidopsis; reducing it to near-null affects root metal reductase activity. Geomagnetic-field-dependent modulation of iron-sulfur interplay in Arabidopsis, most pronounced under combined Fe and S deficiency. Reduction of the geomagnetic field to near-null affects Arabidopsis root mineral nutrition. Note carefully what the cited work does and does not show. Islam 2020 and Vigani 2021 measured iron uptake and Fe-S interplay under altered field conditions — nutritional physiology. Neither measured cluster assembly. This entity is T2 because the field effect is demonstrated for the process it names; the assembly entities above remain T3 because that evidence does not reach them. triplet_yield_sensitive spin_correlated_pair hyperfine_coupled 1H 14N A photoreceptor-based radical-pair model can in principle transduce a geomagnetic-strength field into a change in signalling yield. Review of magnetic field effects in biology from the radical-pair perspective, covering the lifetime and hyperfine conditions required. This is the mechanism itself rather than a molecule. It is on the map because the review's argument is that this step, not the protein, is what generalises to other flavoproteins and Fe/S centres. For a field of geomagnetic magnitude to compete, the radical pair must live long enough for mixing to accumulate — roughly the microsecond scale. That lifetime requirement is what most candidate sites elsewhere in this atlas have not been shown to meet. iron_sulfur_4Fe4S iron_sulfur_2Fe2S 57Fe 33S AT4G35830 AT5G66760 AT5G13430 AT4G03280 AT1G10960 AT2G20860 AT2G21790 Collected here so the map can show, in one edge, that a single assembly defect reaches respiration, photosynthesis, the TCA cycle, nitrogen and sulfur assimilation and DNA replication simultaneously. That breadth is the review's argument for why Fe/S biology deserves attention ahead of cryptochrome. ros_leak_site CHEBI:18421 CHEBI:16240 AT3G10920 Near-null magnetic field exposure alters ROS-associated transcriptomic and metabolomic programmes in Arabidopsis. Reactive oxygen species and mitochondria jointly regulate seed germination, establishing the route from mitochondrial ROS to a developmental outcome. Not a magnetosensitive mechanism itself — it is the amplifier. A field effect too small to measure as a rate change can still register here, because ROS signalling is threshold-like. structural_context structural_context Transcriptomics and metabolomics of ROS modulation in near-null magnetic field-induced Arabidopsis: field reduction alters ROS-associated transcriptional and metabolic programmes. Arabidopsis PPR40 connects abiotic stress responses to mitochondrial electron transport, establishing a route from respiratory state to stress signalling. This entity carries demonstrated near-null-field evidence but NO proposed quantum route, and is classed structural_context to say so explicitly. It is the amplifier's output: threshold-like signalling turns an upstream change too small to measure directly into a transcriptional response. That sensitivity is what makes it the best-evidenced node in the atlas and simultaneously a poor discriminator — it reports that something moved upstream, never what. structural_context AT1G15550 AT4G25420 AT2G01570 AT1G14920 AT3G03450 Gibberellins are involved in the effect of a near-null magnetic field on Arabidopsis flowering. Demonstrated field evidence with no proposed quantum route. Xu et al. showed gibberellins are involved in the near-null-field effect on flowering, which makes this a real link in the causal chain — but GA signalling is ubiquitin-proteasome chemistry with no radical or metal centre, so no mechanism is claimed. structural_context AT1G73590 AT5G57090 AT1G70940 AT2G38120 AT3G62980 AT5G20730 Suppression of Arabidopsis flowering by a near-null magnetic field is mediated by auxin. A near-null magnetic field suppresses fruit growth in Arabidopsis. As with gibberellin: a demonstrated field effect with no proposed spin route. Xu et al. showed auxin mediates near-null-field suppression of flowering. structural_context AT2G46830 AT1G01060 AT5G61380 AT5G24470 AT5G02810 AT2G46790 AT1G22770 AT2G40080 No spin route of its own, and no direct field measurement on clock components in the bibliography. It is on the map because cryptochrome is a clock input, so a field effect at CRY would necessarily arrive here — and because a clock is a gate, meaning the same perturbation can produce opposite outcomes depending on when it is applied. That alone could explain some of the inconsistency in near-null-field results, and it is testable. This is the atlas's most speculative causal claim and is flagged as such. It is offered as an experimental design consideration, not a finding. structural_context Reactive oxygen species and mitochondria jointly regulate seed germination, defining the window in which a respiratory lesion would have most leverage. Peroxisomal citrate synthase provides the exit route from fatty acid metabolism in oilseeds, linking reserve mobilisation to the TCA cycle. structural_context Reduction of the geomagnetic field to below 100 nT delayed Arabidopsis flowering and downregulated flowering-related genes. Suppression of Arabidopsis flowering by a near-null magnetic field depends on the light conditions. Removal of the local geomagnetic field affected reproductive growth, including silique number and seed yield. structural_context Removal of the local geomagnetic field affects reproductive growth in Arabidopsis, reducing silique number and seed yield. Near-null magnetic field suppresses fruit growth in Arabidopsis. A phenotype with demonstrated field evidence and, necessarily, no quantum route of its own. It is the accumulated consequence of everything upstream, which is what makes it reproducible and also what makes it uninformative about mechanism. structural_context direct_influence direct_influence direct_influence direct_influence direct_influence indirect_influence direct_influence direct_influence direct_influence direct_influence cofactor_insertion direct_influence redox_feedback indirect_influence direct_influence energy_feedback energy_feedback indirect_influence energy_feedback hormonal_feedback hormonal_feedback hormonal_feedback circadian_feedback indirect_influence direct_influence indirect_influence indirect_influence