Plant Biology — Photosynthesis, Hormones, Stress, Crop Improvement

Plant biology spans the molecular mechanisms of photosynthesis, the hormonal control of growth, the immune and stress-response systems that determine survival in a variable environment, and the breeding and engineering programs that feed roughly 8 billion humans. Plants are autotrophs whose evolution onto land ~470 Ma (megaannum, million years ago) reshaped Earth’s atmosphere, climate, and biogeochemistry. The Calvin cycle remains the dominant route of inorganic carbon fixation on the planet, and a single enzyme — RuBisCO — accounts for an estimated 50% of soluble leaf protein and is by mass the most abundant enzyme on Earth. This note covers the plant kingdom, cell and tissue biology, photosynthesis, phytohormones, pathology and immunity, symbioses, stress responses, photoreceptors, reproduction, and crop improvement from the Green Revolution to CRISPR.

The Plant Kingdom

Land plants (Embryophyta) descend from charophyte green algae and split into bryophytes (non-vascular) and tracheophytes (vascular). Tracheophytes diverge into lycophytes plus ferns (seedless vascular) and seed plants (spermatophytes), with seed plants splitting into gymnosperms and angiosperms. Land-plant origin is dated to ~470 Ma in the Ordovician based on spore microfossils; embryophyte synapomorphies include the cuticle, stomata, multicellular sporangia, and the protected embryo.

• Angiosperms (flowering plants) — Roughly 350,000+ described species.
  • About 90% of plant biomass on land.
  • Produce flowers with enclosed ovules and fruits derived from the ovary wall.
  • Monocots (~70k species — grasses, palms, orchids, lilies) vs eudicots (~210k species — legumes, roses, asters, mints, Brassicaceae).
  • ~130 Ma rapid radiation puzzled Darwin (“abominable mystery”).
  • ANA grade (Amborella, Nymphaeales, Austrobaileyales) at base of the angiosperm tree.
• Gymnosperms — Naked-seeded plants in four lineages.
  • Conifers (~615 species — Pinus, Picea, Sequoia sempervirens tallest tree 116 m, Sequoiadendron giganteum most massive single-stem organism).
  • Cycads (~300 species, dioecious, ancient).
  • Ginkgo biloba (sole survivor of Ginkgophyta, 270 Ma lineage).
  • Gnetophyta (Welwitschia mirabilis, Ephedra, Gnetum).
• Ferns + lycophytes — ~12,000 fern species.
  • Seedless vascular plants with alternation of generations and dominant sporophyte.
  • Carboniferous (359–299 Ma) coal forests dominated by Lepidodendron lycopsids and tree ferns.
• Bryophytes — Non-vascular embryophytes.
  • Mosses (~12,000 species), liverworts (~9,000), hornworts (~200).
  • Gametophyte-dominant life cycle.
  • Ecologically critical in tundra and peatlands (Sphagnum ~30% of terrestrial soil carbon).
• Charophyte green algae — Sister group to land plants.
  • Chara, Coleochaete, Spirogyra; mostly freshwater.
  • Multicellularity, plasmodesmata, and apical growth evolved here.

Model species

• Arabidopsis thaliana — The plant E. coli.
  • Thale cress (Brassicaceae).
  • 5 chromosomes; ~135 Mb genome (smallest among flowering plants); ~27,400 genes.
  • First plant genome sequenced (Arabidopsis Genome Initiative, Nature 2000) with Elliot Meyerowitz, Maarten Koornneef, Chris Somerville, Joe Ecker, and collaborators.
  • 6-week life cycle; thousands of mutants and T-DNA insertion lines (SALK, GABI-Kat).
  • Reference for nearly all plant molecular biology.
• Oryza sativa (rice) — Two subspecies (indica, japonica).
  • ~430 Mb genome; feeds half of humanity.
  • Sequenced 2002 (IRGSP Nature 2005); MSU + RAP databases.
• Zea mays (maize) — ~2.3 Gb genome with ~85% transposable elements.
  • B73 reference inbred line.
  • Key for hybrid vigor research and the classical genetics of Barbara McClintock and George Beadle.
• Glycine max (soybean) — Major oilseed and protein crop.
  • Paleopolyploid genome.
  • Nitrogen-fixing nodules with Bradyrhizobium japonicum.
• Solanum lycopersicum (tomato) — Model fruit-ripening system.
  • Ethylene biology and climacteric ripening.
• Populus trichocarpa (black cottonwood) — First tree genome sequenced (2006).
  • Model for woody perennials, lignin biology, and bioenergy.
• Brachypodium distachyon — Small grass model.
  • Bridge between rice and wheat/temperate cereals.

Cell + Tissue Biology

Cell wall

Cell walls distinguish plants from animals and constrain cell shape, growth, and water relations. They also determine wood density, fiber length for textiles and pulp, and recalcitrance of plant biomass to enzymatic digestion in biofuel and ruminant nutrition contexts.

• Cellulose (~30–40% of dry wall mass).
  • β-1,4-linked D-glucose polymer.
  • Synthesized at the plasma membrane by Cellulose Synthase (CESA) rosette complexes guided along cortical microtubules.
  • Forms microfibrils ~3 nm wide and several μm long.
• Hemicelluloses (~20–30% of wall).
  • Xyloglucan in dicots; xylan and mixed-linkage glucan in grasses; mannan in some gymnosperms.
  • Cross-link cellulose microfibrils into a load-bearing network.
• Pectin (~30% in primary walls).
  • Homogalacturonan, rhamnogalacturonan I, and rhamnogalacturonan II.
  • Ca²⁺-mediated egg-box gels.
  • Cell adhesion through the middle lamella.
• Lignin (in secondary walls).
  • Phenylpropanoid polymer of monolignols: p-coumaryl, coniferyl, and sinapyl alcohols giving H, G, and S units.
  • Waterproofs xylem conduits and provides compressive strength.
  • ~30% of woody biomass.
  • Recalcitrant to enzymatic degradation, a key challenge for cellulosic biofuels.
• Expansins — Wall-loosening proteins active at low pH; mediate acid growth driven by auxin-induced proton pumping.

Organelles

• Chloroplasts
  • Derived by primary endosymbiosis from a cyanobacterium ~1.5 Ga (Lynn Margulis J. Theor. Biol. 1967).
  • Contain their own circular genome (~100–200 kb, ~120 genes).
  • Double envelope membrane plus an internal thylakoid system.
  • Site of photosynthesis, starch synthesis, fatty acid synthesis, much amino acid biosynthesis, and isoprenoid synthesis via the MEP pathway.
• Mitochondria
  • Higher cristae density in C4 bundle-sheath cells.
  • Site of the photorespiratory glycine decarboxylase complex.
• Vacuole
  • Often >90% of cell volume in mature cells.
  • Turgor maintenance against the cell wall.
  • Storage of secondary metabolites, anthocyanins, defense compounds, and ions.
  • Tonoplast contains aquaporins of the PIP and TIP families.
• Plasmodesmata
  • Cytoplasmic channels ~40 nm wide that traverse cell walls.
  • Allow symplastic transport of small molecules, RNAs, transcription factors, and viral movement proteins between adjacent cells.

Meristems + tissues

• Apical meristems
  • SAM (shoot apical meristem) at the shoot tip produces leaves and stem tissues.
  • CLV3-WUS feedback maintains the stem-cell population (Laux, Jürgens, Meyerowitz).
  • RAM (root apical meristem) at the root tip produces all root tissues.
  • Quiescent center surrounded by stem-cell initials.
• Lateral (cambial) meristems
  • Vascular cambium produces secondary xylem (wood) inward and secondary phloem outward.
  • Cork cambium (phellogen) produces bark (phellem + phelloderm).
• Xylem
  • Water and mineral transport upward.
  • Tracheids in all vascular plants; vessel elements mainly in angiosperms.
  • Dead at maturity; lignified secondary walls.
  • Transpiration-cohesion-tension drives flow (Dixon-Joly cohesion-tension theory, 1894).
  • Xylem column normally under tension of –1 to –2 MPa under transpiration.
• Phloem
  • Bidirectional transport of sucrose, amino acids, and signaling molecules (small RNAs, FT protein, peptides).
  • Sieve tube elements alive but lack nuclei; companion cells provide proteins and metabolites.
  • Pressure-flow hypothesis (Münch 1930).
  • Loading via SUT/SUC sucrose transporters (apoplastic) or symplastic via plasmodesmata.
• Epidermis
  • Cuticle (cutin polyester + waxes) limits water loss.
  • Stomata (paired guard cells) regulate gas exchange and transpiration.
  • Trichomes for defense, UV protection, water capture, and secondary metabolite storage.
• Mesophyll
  • Palisade parenchyma — densely packed cells in the upper leaf optimized for light capture.
  • Spongy parenchyma — loosely packed cells for gas exchange between intercellular air space and chloroplasts.

Photosynthesis

Light reactions

The light reactions convert photons into chemical energy (ATP and NADPH) at the thylakoid membrane. Linear electron flow runs from H₂O at PSII to NADP⁺ at PSI, producing both NADPH and a proton gradient that drives ATP synthesis. Cyclic electron flow around PSI produces only ATP and is engaged when the ATP:NADPH ratio supplied by linear flow is insufficient for downstream demand, particularly in C4 bundle-sheath chloroplasts.

• Photosystem II (PSII)
  • P680 reaction center splits water at the Mn₄CaO₅ oxygen-evolving complex (OEC).
  • Releases O₂ to the atmosphere and protons into the thylakoid lumen.
  • Joliot-Kok S-state cycle through five oxidation states S₀–S₄.
  • Chlorophyll absorption peak near 680 nm.
  • Crystal structure determined to 1.9 Å by Umena, Kawakami, Kamiya, Shen 2011 Nature.
• Cytochrome b₆f complex
  • Plastoquinone-to-plastocyanin electron transfer.
  • Q cycle pumps additional protons across the thylakoid membrane.
• Photosystem I (PSI)
  • P700 reaction center.
  • Reduces ferredoxin, which reduces NADP⁺ to NADPH via ferredoxin-NADP⁺ reductase (FNR).
• Z-scheme — Hill-Bendall 1960.
  • Two photosystems operate in series.
  • Redox spans from +0.8 V at P680⁺ to –1.2 V at P700⁻.
• ATP synthase — Uses the proton gradient (ΔpH plus ΔΨ) across the thylakoid membrane to produce ATP.
  • Reflects Peter Mitchell’s chemiosmotic theory (Nobel 1978).

Calvin cycle (Calvin-Benson-Bassham cycle)

• Carboxylation
  • RuBisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase; EC 4.1.1.39) condenses CO₂ with ribulose-1,5-bisphosphate (RuBP).
  • Yields two molecules of 3-phosphoglycerate (3-PGA).
• Reduction
  • 3-PGA phosphorylated to 1,3-bisphosphoglycerate (1,3-BPG) by phosphoglycerate kinase using ATP.
  • 1,3-BPG reduced by NADPH to glyceraldehyde-3-phosphate (G3P).
• Regeneration
  • G3P recycled through transketolase, aldolase, sedoheptulose-1,7-bisphosphatase (SBPase), and ribulose-5-phosphate kinase.
  • Restores RuBP at the cost of 1 ATP per RuBP regenerated.
• Stoichiometry
  • Net fixation of 1 CO₂ uses 3 ATP and 2 NADPH.
  • One G3P exits the cycle per 3 turns; remaining 5 G3P regenerate 3 RuBP.
• RuBisCO limits
  • Slow kcat of roughly 3 s⁻¹ per active site.
  • ~25% oxygenase side reaction at current atmospheric O₂/CO₂ ratios in C3 plants.
  • Up to 50% of soluble leaf protein in C3 plants is RuBisCO.
  • Melvin Calvin received Nobel Chemistry 1961 for the cycle.

C4 and CAM photosynthesis

C4 and CAM evolved repeatedly as biochemical CO₂-concentrating mechanisms (CCMs) that suppress photorespiration. C4 photosynthesis has independently evolved more than 60 times across angiosperms; CAM has evolved at least as many times.

• C4
  • First fixation in mesophyll by PEP carboxylase (PEPC), forming oxaloacetate and then malate (or aspartate).
  • C4 acid transported to bundle-sheath cells and decarboxylated to release CO₂ at high concentration around RuBisCO.
  • Kranz anatomy provides the spatial separation.
  • ~3% of plant species but ~25% of terrestrial productivity.
  • Includes Zea mays (maize), Saccharum officinarum (sugar cane), Sorghum bicolor, Panicum virgatum (switchgrass), Miscanthus, Amaranthus.
  • Discovered by Marshall Hatch and Roger Slack 1966.
• CAM (Crassulacean Acid Metabolism)
  • Stomata open at night to limit transpiration in hot, dry climates.
  • PEPC fixes CO₂ at night as malate stored in vacuole.
  • Daytime stomata closed; malate decarboxylated to deliver CO₂ to RuBisCO.
  • Conserves water in arid habitats.
  • Found in Crassulaceae, Cactaceae, Agave, pineapple (Ananas comosus), and many epiphytic orchids and bromeliads.
• C3 — Direct fixation by RuBisCO in mesophyll without spatial or temporal pre-fixation.
  • ~85% of vascular plant species.
  • Includes rice, wheat, soybean, cotton, potato, and essentially all trees.

Photorespiration

When RuBisCO uses O₂ instead of CO₂, it forms 2-phosphoglycolate, which is metabolized through the photorespiratory pathway. The pathway shuttles intermediates through three organelles in the cycle chloroplast → peroxisome → mitochondrion → back to chloroplast. The cycle releases previously fixed CO₂ as well as NH₃ that must be reassimilated, and it consumes additional ATP and reducing equivalents. Net loss is 25–50% of fixed carbon in C3 plants under hot, dry, high-light conditions where Rubisco oxygenation competes more strongly.

• RIPE Project (Realizing Increased Photosynthetic Efficiency).
  • University of Illinois plus partners; led by Donald Ort and Stephen Long.
  • Engineered alternative photorespiration bypasses through synthetic shunts in the chloroplast.
  • Field trial of tobacco showed ~40% biomass gain (South et al. Science 2019).
  • Now being introgressed into soybean, cowpea, rice, and cassava.
• Cyanobacterial CCM in C3 plants — Engineering carboxysome + bicarbonate transporters into chloroplasts.
  • Maureen Hanson (Cornell) and Martin Hagemann (Rostock) groups; CAPP / RIPE collaborations.
• RuBisCO engineering — Faster but lower-specificity variants from cyanobacteria.
  • Chimeric L8S8 holoenzymes; directed evolution; chaperone (RAF1, RAF2, Bsd2) requirements complicate transplantation.

Photosynthesis Nobels

• 1961 Chemistry — Melvin Calvin (Calvin cycle).
• 1978 Chemistry — Peter Mitchell (chemiosmosis).
• 1988 Chemistry — Johann Deisenhofer, Robert Huber, Hartmut Michel (first crystal structure of a membrane-protein photosynthetic reaction center, from Rhodopseudomonas viridis).

Plant Hormones (Phytohormones)

Auxin

• Primary native auxin is indole-3-acetic acid (IAA); typical tissue concentrations are nanomolar to micromolar.
• Frits Went 1928 — Avena coleoptile bioassay; named “auxin” from Greek auxein, to grow.
• Polar transport — Strict basipetal (downward in shoots, away from the apex) flow.
  • Mediated by PIN-FORMED (PIN) efflux carriers polarized in the plasma membrane.
  • AUX1/LAX influx carriers; ABCB/PGP ABC-type transporters add a second layer.
  • Rotation of PIN polarity drives lateral redistribution in tropic responses.
• TIR1/AFB receptor — F-box protein that forms an SCF E3 ligase complex.
  • Binds auxin and triggers ubiquitination and degradation of Aux/IAA repressors.
  • Freeing ARF transcription factors to activate auxin-responsive genes (Tan et al. Nature 2007).
• Functions — Phototropism (Cholodny-Went hypothesis), gravitropism, apical dominance, vascular differentiation, lateral root initiation, fruit development, embryo polarity.
• Synthetic auxins — 2,4-D (2,4-dichlorophenoxyacetic acid) selective broadleaf herbicide.
  • Dicamba, picloram, fluroxypyr — additional auxinic herbicides.
  • NAA (1-naphthaleneacetic acid) — rooting compound in horticulture.
  • Agent Orange was 2,4-D + 2,4,5-T contaminated with TCDD dioxin.

Cytokinins

• Adenine derivatives such as zeatin, isopentenyl adenine, and dihydrozeatin.
• First cytokinin “kinetin” identified by Carlos Miller in Folke Skoog’s lab 1955 from autoclaved herring-sperm DNA.
• Functions
  • Promote cell division (in combination with auxin).
  • Shoot induction in tissue culture; the Skoog-Miller ratio of auxin:cytokinin determines shoot vs root vs callus.
  • Delay senescence of leaves and detached organs.
  • Promote chloroplast development and greening.
• Receptors — AHK histidine kinases at the ER and plasma membrane.
  • Phosphorelay through AHPs to type-B ARRs (response regulators) for transcriptional output.
  • Type-A ARRs provide negative feedback.

Gibberellins (GAs)

• Tetracyclic diterpenoid hormones.
• ~136 GAs identified; only ~5 bioactive in plants (GA₁, GA₃, GA₄, GA₇).
• Discovered by Eiichi Kurosawa 1926 and Teijiro Yabuta 1934 from rice “bakanae” (foolish seedling) disease.
• Causal organism is Gibberella fujikuroi (now Fusarium fujikuroi); the fungal toxin overdoses host gibberellin response and produces spindly seedlings.
• Functions — Bolting (stem elongation), breaking of seed dormancy, flowering, fruit growth, induction of α-amylase in barley aleurone.
• GID1 receptor — Soluble nuclear receptor.
  • Bound GID1-GA complex recruits DELLA repressors for SCF-SLY1 ubiquitination and proteasomal degradation.
• Green Revolution dwarfing genes
  • Rht1 and Rht2 in wheat (Reduced height) are GA-insensitive DELLA gain-of-function alleles.
  • sd1 in rice is a loss-of-function GA20ox biosynthesis gene.
  • Both reduce stem elongation, allowing higher nitrogen application without lodging.

Abscisic acid (ABA)

• Sesquiterpenoid stress hormone derived from the carotenoid pathway.
• Functions
  • Stomatal closure under drought via the SLAC1 anion channel activated by the OST1/SnRK2.6 kinase.
  • Seed dormancy maintenance.
  • Activation of LEA proteins and other ABA-responsive genes during dehydration and seed maturation.
• PYR/PYL/RCAR receptors
  • Identified by Sean Cutler, Julian Schroeder, Pedro Rodriguez and the Erwin Grill lab in two papers in 2009.
  • ABA-bound receptor inhibits PP2C phosphatases (ABI1, ABI2, HAB1).
  • Inhibition of PP2Cs releases SnRK2 kinases.
  • SnRK2s phosphorylate downstream targets including SLAC1 and AREB/ABF bZIP transcription factors.

Ethylene

• Gaseous hormone (C₂H₄).
• First plant hormone identified, by Dimitry Neljubow 1901 from observing gas-leak effects on pea seedlings in greenhouses.
• Functions
  • Fruit ripening in climacteric fruits — tomato, banana, apple, avocado, mango, pear.
  • Leaf and flower senescence.
  • Abscission of leaves and fruit.
  • Triple response in dark-grown seedlings (shortened hypocotyl, radial swelling, exaggerated apical hook).
• Biosynthesis — SAM → ACC (1-aminocyclopropane-1-carboxylic acid) by ACS → ethylene by ACO.
• Signaling — ETR1 and the ETR family of receptors localize at the endoplasmic reticulum (Bleecker, Chang).
  • CTR1 Raf-like kinase active in the absence of ethylene.
  • EIN2 C-terminal cleavage upon ethylene perception.
  • EIN3/EIL1 master transcription factors.
  • Harry Klee and Tony Bleecker were key contributors to the molecular dissection.
• Industrial — Ethylene scrubbers in shipping containers extend banana shelf-life.
  • 1-MCP (1-methylcyclopropene; SmartFresh) blocks the ETR receptor and is widely used for apple storage.
  • Ethephon (Ethrel) sprays release ethylene in planta for uniform ripening of fruit and rubber latex flow.

Brassinosteroids

• Polyhydroxylated steroidal hormones.
• Identified 1979 from rapeseed (Brassica napus) pollen by Mitchell and Mandava (USDA Beltsville).
• Functions
  • Cell elongation.
  • Vascular differentiation.
  • Response to environmental stress including heat and oxidative stress.
• BRI1 receptor
  • Leucine-rich-repeat receptor kinase (LRR-RK) at the plasma membrane.
  • Co-receptor BAK1 (shared with PRR pathways).
  • BSK1 substrate phosphorylated by activated BRI1.
  • BIN2 GSK3-like kinase represses TFs in the absence of BR.
  • BZR1/BES1 transcription factors mediate downstream gene expression.

Salicylic acid (SA), Jasmonate (JA), Strigolactones

• SA (salicylic acid)
  • Aromatic phenolic; aspirin (acetylsalicylic acid) is a derivative.
  • Mediates systemic acquired resistance (SAR) against biotrophic pathogens.
  • NPR1 receptor; perceived in part through thiol redox state changes.
  • Drives expression of PR (pathogenesis-related) genes.
• JA / methyl-JA (jasmonate)
  • Oxylipin derived from α-linolenic acid via the octadecanoid pathway.
  • Mediates wounding and herbivory responses, defense against necrotrophic pathogens, and pollen viability.
  • COI1 F-box receptor recruits JAZ repressors for degradation in the presence of JA-Ile conjugate.
  • MYC2 bHLH master transcription factor.
• Strigolactones
  • Carotenoid-derived terpenoid lactones.
  • Named from Striga parasitic-plant germination cue (Cook and Egley 1966).
  • Root-exuded; signal to arbuscular mycorrhizal (AM) fungi.
  • Shoot-branching inhibitors identified in 2008 (Gomez-Roldan Nature, Umehara Nature, Akiyama Nature).
  • Key genes: MAX1 (cytochrome P450), MAX2 (F-box), D14 (α/β-hydrolase receptor), D27, CCD7/8 carotenoid cleavage dioxygenases.

Peptide hormones

• CLE peptides — CLAVATA3 (CLV3) in SAM; binds CLV1, CLV2 receptor complex; restricts stem cell pool size.
• EPF/EPFL — Epidermal patterning; stomatal density control.
• PSK, PSY1 — Sulfated tyrosine peptides; cell division and elongation.
• CIF / CASPARIAN STRIP — Schengen pathway in root endodermis.
• RGF / GLV / CLE40 — Root meristem maintenance.

Plant Pathology + Immunity

Two-tiered immune system (Jones-Dangl 2006 Nature zigzag model)

• PTI (PAMP-Triggered Immunity) — Pattern Recognition Receptors (PRRs) at plasma membrane detect microbe-associated molecular patterns (MAMPs); examples: FLS2 (LRR-RK) binds bacterial flagellin epitope flg22 (Felix-Boller 1999, Gomez-Gomez-Boller 2000); EFR binds bacterial EF-Tu epitope; LYK5/CERK1 binds fungal chitin; co-receptor BAK1.
• ETI (Effector-Triggered Immunity) — Intracellular NLR (nucleotide-binding leucine-rich repeat) immune receptors detect pathogen-secreted effectors; gene-for-gene relationship described by Harold Flor 1942 in flax-flax rust system; triggers hypersensitive response (HR) — programmed cell death restricting pathogen spread.
• SAR (Systemic Acquired Resistance) — Long-distance immune memory; SA-dependent; activated days after local infection.

Major crop pathogens

• Magnaporthe oryzae (rice blast).
  • Filamentous ascomycete with appressorium-mediated penetration.
  • ~30% of global rice yield lost annually.
  • Pi-resistance gene catalog widely deployed.
• Phytophthora infestans (potato + tomato late blight).
  • Oomycete (not a true fungus, in the SAR clade with diatoms and brown algae).
  • Cause of the Irish Potato Famine 1845–1849, ~1 million dead and ~1 million emigrated.
  • HZ1A1 lineage in the 19th century; modern lineages 13_A2 and US-23 dominant.
• Fusarium graminearum (wheat head blight, Fusarium head blight / scab).
  • Produces deoxynivalenol (DON) mycotoxin; major food-safety concern in temperate cereals.
• Puccinia graminis (wheat stem rust).
  • Race Ug99 / TTKSK emerged Uganda 1998, threatening ~80% of world wheat cultivars.
  • Borlaug Global Rust Initiative (BGRI) and Durable Rust Resistance in Wheat (DRRW) monitor and respond.
  • Resistance genes Sr2, Sr31, Sr35, Sr50, Sr55 widely deployed.
• Xanthomonas oryzae pv. oryzae (rice bacterial blight); Pseudomonas syringae pv. tomato (model); Erwinia amylovora (fireblight of pear, apple).
• Viruses
  • Tobacco mosaic virus (TMV; Beijerinck 1898 — first virus identified).
  • Banana bunchy top virus (BBTV), Maize streak virus (MSV), Cassava mosaic virus (CMV — both cassava brown streak and cassava mosaic), Cucumber mosaic virus.
• Nematodes — Meloidogyne (root-knot), Heterodera, Globodera (potato cyst nematodes).
• Insects
  • Helicoverpa armigera / Helicoverpa zea (cotton bollworm, corn earworm).
  • Spodoptera frugiperda (fall armyworm — invasion of Africa 2016, Asia 2018).
  • Schistocerca gregaria (desert locust).
  • Drosophila suzukii (spotted wing drosophila on soft fruit).

Symbioses

Legume-rhizobium nitrogen fixation

Legumes (Fabaceae) host nitrogen-fixing bacteria in root nodules. Symbionts include Rhizobium, Bradyrhizobium, Sinorhizobium, and Mesorhizobium species.

• Nod factors
  • Lipo-chito-oligosaccharides (LCOs) secreted by rhizobia in response to flavonoid signals from the host.
  • Recognized by LysM receptor kinases — NFR1/NFR5 in Lotus japonicus, NFP/LYK3 in Medicago truncatula.
• Nodule organogenesis
  • Cortical cell divisions produce the nodule primordium.
  • Bacteroid differentiation occurs inside symbiosome membrane compartments.
  • Nitrogenase (Fe-Mo cofactor) catalyzes N₂ + 8 H⁺ + 8 e⁻ + 16 ATP → 2 NH₃ + H₂ + 16 ADP + 16 Pi.
• Leghemoglobin
  • Plant-encoded oxygen-binding protein.
  • Creates the microaerobic environment required by O₂-sensitive nitrogenase.
  • Gives functional nodules their characteristic pink color.
• Frankia — Actinorhizal symbiont of Alnus, Casuarina, Myrica, and other woody non-legumes.
• Engineering nitrogen fixation in cereals
  • Long-running effort by Giles Oldroyd (Cambridge SLCU) and others.
  • Funded in part by the Bill and Melinda Gates Foundation through the ENSA project.
  • Transferring the SymRK pathway and re-establishing the ancient mycorrhizal-symbiosis genetic toolkit.
  • Cereal-rhizobia symbiosis remains a long-term goal.

Mycorrhizae

~80% of land plants form mycorrhizal symbioses.

• Arbuscular mycorrhizae (AM)
  • Fungal partners in the phylum Glomeromycota.
  • Coenocytic intra-radical hyphae.
  • Arbuscules form within cortical cells and are the exchange interface.
  • Deliver phosphate, water, and micronutrients in exchange for plant sugars and lipids.
  • ~20% of plant net carbon assimilation can be allocated to AM partners.
  • Rhizophagus irregularis is the principal model species.
• Ectomycorrhizae (ECM)
  • Mainly Basidiomycota and Ascomycota.
  • Hartig net around cortical cells and a mantle around the root tip.
  • Common with conifers, oaks, beech, birch.
  • Tuber melanosporum (black truffle) and Boletus edulis are well-known ECM fungi.
• Ericoid mycorrhizae — Specialized symbiosis with Ericaceae in acidic, organic-rich soils.

Stress Responses

• Heat
  • Heat shock proteins (HSPs) function as molecular chaperones.
  • HSP70, HSP90, HSP100, and small HSPs all contribute.
  • HSF transcription factors regulate the heat-shock response.
• Cold
  • CBF/DREB1 transcription factor cascade is activated by ICE1.
  • Downstream COR (cold-regulated) genes encode cryoprotectants and dehydrins.
• Drought
  • ABA accumulation drives stomatal closure.
  • Osmotic adjustment via accumulation of proline, glycine betaine, and soluble sugars.
  • LEA (Late Embryogenesis Abundant) proteins protect cellular machinery during dehydration.
• Salt
  • SOS (Salt Overly Sensitive) pathway: SOS3 Ca²⁺ sensor → SOS2 kinase → SOS1 plasma-membrane Na⁺/H⁺ antiporter.
  • Vacuolar NHX antiporters sequester Na⁺ into the vacuole.
  • HKT1 controls root-to-shoot Na⁺ partitioning.
• Heavy metals
  • Phytochelatins (PCs) synthesized from glutathione and metallothioneins (MTs) chelate Cd, Zn, Cu, and other metals.
  • Vacuolar sequestration of chelated complexes via ABC transporters.
• Oxidative
  • Reactive oxygen species (ROS) include H₂O₂, O₂⁻, and ·OH.
  • Detoxified by superoxide dismutase (SOD), catalase, ascorbate peroxidase, and the ascorbate-glutathione (Foyer-Halliwell-Asada) cycle.
• UV-B
  • UVR8 photoreceptor identified by Brown et al. Science 2005; structure by Christie et al. 2012.
  • Homodimer monomerizes upon UV-B absorption.
  • Monomer binds COP1 and stabilizes HY5 to drive UV-protective gene expression.

Photoreceptors

• Phytochromes — Red (660 nm) and far-red (730 nm) sensors.
  • Biliprotein chromophore phytochromobilin (PΦB).
  • Pr → Pfr photoconversion drives nuclear translocation and signaling.
  • Detect light quality, mediate shade avoidance and photoperiodism.
  • PHYA–E in Arabidopsis thaliana.
  • Identified by H.A. Borthwick and S.B. Hendricks 1952 at USDA Beltsville.
• Cryptochromes — Blue and UV-A (320–500 nm) sensors.
  • Flavin (FAD) chromophore.
  • CRY1 and CRY2 in Arabidopsis.
  • Drive photomorphogenesis, circadian entrainment, and flowering time.
  • Structurally homologous to DNA photolyases.
• Phototropins — Blue light receptors.
  • FMN-binding LOV (Light-Oxygen-Voltage) domains.
  • PHOT1 and PHOT2 in Arabidopsis.
  • Drive phototropism, stomatal opening, and chloroplast movement.
• UVR8 — UV-B (280–315 nm) sensor.
  • Homodimer stabilized by a tryptophan pyramid that absorbs UV-B.
  • Monomerizes upon UV-B absorption to engage COP1.
• ZTL/FKF1/LKP2 — Blue-light-sensing F-box LOV proteins.
  • Couple light input to the circadian clock and the floral transition.

Reproduction

• Flower development
  • ABCDE model of floral organ identity (Coen and Meyerowitz 1991; Pelaz, Ditta, Yanofsky 2000 extended to E class).
  • A class (APETALA1, APETALA2) + B class (APETALA3, PISTILLATA) + C class (AGAMOUS) + D class (SEEDSTICK) + E class (SEPALLATA1–4) MADS-box transcription factors.
  • Floral quartet model (Theißen) describes tetrameric MADS complexes specifying each whorl.
• Florigen
  • FT (FLOWERING LOCUS T) protein moves from leaf phloem to the SAM.
  • Binds FD bZIP TF to activate floral meristem identity genes.
  • Florigen molecular identity established ~2005 by Corbesier (Arabidopsis) and Tamaki (Oryza sativa Hd3a).
• Pollination
  • Wind (anemophily) — grasses and conifers.
  • Insect (entomophily) — bees (especially Apis mellifera), butterflies, beetles, flies.
  • Bird (ornithophily) — hummingbirds and sunbirds.
  • Bat (chiropterophily) — many tropical species.
  • Colony collapse disorder (CCD) since ~2006 in honeybees; ongoing concerns about neonicotinoid pesticides and Varroa destructor mite.
• Self-incompatibility
  • Gametophytic system in Solanaceae, Rosaceae, and Plantaginaceae via S-RNase and pollen F-box proteins.
  • Sporophytic system in Brassicaceae via SCR/SP11 ligand and SRK receptor kinase.
• Seed and fruit
  • Double fertilization (Nawaschin 1898): one sperm fuses with the egg to produce the diploid embryo.
  • The second sperm fuses with the central cell to produce the triploid endosperm.
  • Fruit develops from the ovary wall (pericarp), accessory tissues, or floral receptacle depending on species.

Crop Improvement

Green Revolution (1940s–1970s)

• Norman Borlaug
  • Wheat breeding at CIMMYT (Mexico).
  • Semi-dwarf high-yielding varieties combining Rht dwarfing alleles with rust resistance.
  • Awarded Nobel Peace Prize 1970.
  • Credited with saving an estimated 1 billion lives.
• IR8 “miracle rice”
  • Released 1966 by IRRI (Philippines).
  • Semi-dwarf variety carrying sd1.
  • Doubled rice yields across much of Asia within a decade.
• Yuan Longping
  • “Father of Hybrid Rice” in China.
  • Developed three-line hybrid rice system in 1973.
  • Yields 20–30% above conventional inbred lines.
  • Died May 2021; no Nobel but received the World Food Prize 2004.
• Maize hybrids
  • Single-cross hybrids commercialized in the U.S. from the 1930s.
  • Henry A. Wallace and Pioneer Hi-Bred pioneered commercial production.
  • Heterosis (hybrid vigor) underlies the yield advantage.
  • U.S. yields rose from ~25 bu/acre (1930) to >180 bu/acre (2024).
• Cereal yields tripled globally 1960–2000.
  • Required massive synthetic-fertilizer (Haber-Bosch) and irrigation expansion.
  • Associated with environmental costs including eutrophication, soil degradation, and groundwater depletion.

Transgenic crops (1996–present)

• Bt crops — Express Bacillus thuringiensis Cry proteins.
  • Cry1Ab/c, Cry2A, Cry3A, Vip3A toxic to specific insect orders (mainly Lepidoptera, Coleoptera).
  • Commercial brands include Monsanto/Bayer YieldGard and Bollgard.
  • Bt cotton dominant in India, China, Pakistan, USA, Brazil.
  • Bt brinjal commercialized in Bangladesh 2013 (BARI + Cornell collaboration).
  • Bt corn covers 80%+ of U.S. corn acreage.
• HT (herbicide tolerance)
  • Roundup Ready (glyphosate tolerance via CP4 EPSPS).
  • LibertyLink (glufosinate via PAT).
  • Enlist (2,4-D + glyphosate via AAD-12).
  • Dicamba-tolerant Xtend (DMO).
• Stacked traits — SmartStax, VT Triple Pro, Optimum Intrasect combine multiple Bt + HT genes.
• DroughtGard — Bacterial cold-shock protein CSPB confers modest drought tolerance under mild water deficit.
• Biotech crops cover ~200 Mha globally in 2024 (ISAAA / USDA reports).

Genome editing (CRISPR + base/prime editing)

• CRISPR-Cas9
  • Doudna-Charpentier Science 2012; Nobel Chemistry 2020.
  • Programmable double-strand break followed by NHEJ for knockouts or HDR for knock-ins.
• USDA regulatory clarity since 2016
  • SECURE rule (2020) exempts most CRISPR-edited plants that lack foreign DNA from GE regulation.
• Commercial CRISPR crops
  • Yinong/Calyxt high-oleic soybean (Calyno, launched 2019).
  • Pairwise leafy greens (Conscious Greens mustard-greens, 2023).
  • Inari (genome-edited soy and corn pipeline).
  • Tropic Biosciences (non-browning banana, decaffeinated coffee Robusta).
  • Greenlight Biosciences Calantha dsRNA spray for Colorado potato beetle (2022 EPA approval).
  • J.R. Simplot Innate potatoes (RNAi-based bruise resistance plus acrylamide reduction).
  • Wageningen non-browning white-button mushroom (Agaricus bisporus, CRISPR-edited 2016; USDA cleared as non-regulated).
• PINPOINT / base editors
  • Cytosine and adenine base editors developed in David Liu’s lab.
  • Pairwise holds an agricultural license; Verve and Beam Therapeutics develop medical applications.
  • Applied to wheat, maize, and rice for targeted amino-acid substitutions and herbicide-tolerance edits.
• Prime editing
  • Anzalone and Liu Nature 2019.
  • Search-and-replace genome editing; deployment in cereals and tomato ongoing.

Modern breeding methods

• Marker-Assisted Selection (MAS)
  • DNA markers linked to QTLs (quantitative trait loci).
  • Marker types include SSRs, SNPs from genotyping arrays, and KASP assays.
• Genomic Selection (GS)
  • Meuwissen, Hayes, Goddard 2001 Genetics.
  • Whole-genome marker-based prediction model trained on a phenotyped reference panel.
  • Widely used by dairy industry and by wheat (CIMMYT) and maize breeders (Corteva, Bayer, KWS, BASF Innogen, Limagrain).
• Speed breeding
  • Watson et al. Nature Plants 2018.
  • 22-h LED photoperiod plus controlled temperature.
  • 6 wheat generations per year vs 2–3 conventional.
  • Adopted at NIAB Cambridge, CIMMYT, John Innes Centre, and many private breeding programs.
• Doubled haploids
  • Produced via wide-crossing (maize-pollinated wheat) or anther/microspore culture.
  • Yields instant homozygosity in a single generation.
• Wide hybridization / synthetic wheats
  • Triticum aestivum × Aegilops tauschii recreations expand D-genome diversity for disease resistance.

Carbon, Climate, and Plants

• Terrestrial sink
  • Tracked by the Global Carbon Project (Le Quéré, Friedlingstein, Peters et al., annual budgets).
  • Forests absorb roughly 3 GtC/yr (gigatonnes of carbon per year).
  • Land sink currently offsets ~30% of anthropogenic fossil-fuel emissions.
• Deforestation
  • Emissions ~1 GtC/yr; mostly tropical (Amazon, Congo, Southeast Asia).
  • Net land-use change emissions remain the most uncertain component of the global carbon budget.
• CO₂ fertilization
  • Elevated CO₂ enhances C3 photosynthesis ~30% at doubled CO₂ in FACE experiments (Free-Air CO₂ Enrichment).
  • Key sites included ORNL FACE, Duke FACE, and SoyFACE in Illinois.
  • Benefit appears to saturate over time as plants acclimate or become nutrient-limited.
  • Elevated CO₂ produces nutrient dilution with lower protein and micronutrients (Zn, Fe) in cereals (Loladze 2014; Myers Nature 2014).
• Range shifts
  • Boreal forest northward expansion.
  • Alpine treeline rise.
  • Pollinator and seed-disperser mismatch can decouple plant range expansion from suitable climate.
• Amazon tipping point
  • Estimated 20–25% deforestation threshold beyond which large portions of the forest could flip to savanna (Lovejoy and Nobre 2018 Sci. Adv.).
  • Current cumulative deforestation in the Brazilian Amazon is ~17%.
• Drought and heat impacts
  • 2003 European, 2010 Russian, and 2018 Central European heatwaves each cut crop yields by 10–30% (Zampieri et al.).
  • 2022 Indo-Gangetic Plain heat affected wheat yields, with India temporarily banning wheat exports.

Adjacent

• cell-molecular-biology — Cell wall biosynthesis, chloroplast biology, plasmodesmatal transport, and the molecular machinery underlying plant cell organization.
• genetics-and-genomics — Quantitative trait loci, genomic selection, polyploidy, and the genomic basis of crop improvement.
• ecology-and-evolution — Plant community assembly, mycorrhizal networks, and plant-herbivore-pathogen coevolution.
• microbiology-foundations — Rhizobium nitrogen fixation, plant-pathogenic bacteria and oomycetes, and rhizosphere microbiome.
• biochemistry — RuBisCO mechanism, Calvin cycle stoichiometry, secondary metabolism (phenylpropanoids, terpenoids, alkaloids).
• carbon-cycle — Terrestrial carbon sinks, photosynthesis under elevated CO₂, and forest-climate feedbacks.
• biotech-engineering — Industrial crop biotechnology, CRISPR delivery in plants, and the agricultural input value chain.