3 plant pathogens
- Agrobacterium tumefaciens
Soil bacterium, causes crown gall disease, manifests as tumour-like growth primarily at the crown of plant
Bacterium has large TI (tumor-inducing) plasmid, central to pathogenicity
T-DNA of ti plasmid is transferred into plant genome, and cause plant cells to produce auxin and cytokinin, this cause incontrollable proliferation and auxin supress defence , also plant cells to produce opines which act as nutrient source for bacterium- Rhodococcus fascians
Bacterium that causes fasciation or leafy gall disease, disrupts plants normal development and can severely impact its growth- this is because it makes the plant has fas genes which lead to biosynthesis of 6 acting cytokinins that overwhelm plants homeostatic mechanism, leading to uncontrolled differentiation into shoot meristems, that remain immature ( and so form nutrient rich niche). the mixture of cytokinins reduce plants cytokinin-degradation ability - Root-knot and cyst nematodes
Root-knot
Form galls or knots, these galls are swellings where nematodes feed and develop- cause stunted growth and reduced yield
Cyst
Affected plants exhibit yellowing, poor growth and reduced yeild, roots are less efficient at nutrient uptake due to damage by nematode feeding
- Rhodococcus fascians
what is the hormonal signalling pathway
There are
Biotrophic- pathogens that live within cells parasitically
Biotrophic pathogen triggers microbe (pathogen)-associated molecular pattern (PAMPS), triggers PRR (pattern recognition response), recognise a protein in flagella of pathogen, this activates transcription factors that activate genes for salicylic acid, once the hormone reaches certain threshold cause rapid fluctuations in the redox state, this changes the NPR1 proteins from an oxidised to reduced state through SA response, this then breaks down sulphate bridges that allow it to enter nucleus to activate defence genes
Necrotrophic- pathogens that kill cell and feed off it
Necrotrophic pathogens trigger damage associated molecular patterns (DAMPS), trigger PRR (pattern recognition receptors), this causes transcription factors to trigger expression of JA biosynthesis (these enzymes are usually already present just need to be turned on, faster for necrotrophic attack), JA conjugates with amino acid isoleucine, this then causes complex downstream pathway, COI1 releases MYC2 by taking the JAZ repressor proteins away for proteasomal degradation, liberated MYC2 activates defence genes in promoter regions
both these pathways can trigger creation of P-R (pathogenesis related) gene
steps of innate immunity
physical and chemical defence- cell wall/cuticle/antimicrobial compounds
plant cells have PRR, pattern recognition receptor, this recognises PAMP, pathogen association molecular pattern (or MicrobeAMP)
- cell will then go through PTI (pattern triggered immunity) and then ETI (effector triggered immunity)
- PTI, pattern (or pamp) triggered immunity
Pathogen-Associated Molecular Patterns are found in a broad range of pathogens, pattern recognition receptors trigger MAPK cascade forming transcriptional factor proteins that turn on defence gene
- PTI, pattern (or pamp) triggered immunity
- pathogen can release effectors- reception of effector triggers effector triggered immunity.
- ETI, effector triggered immunity
Is response to pathogens secreting effectors (protein that suppress PTI), the NB-LRR protein recognises specific pathogen effector, and the R (resistant ) gene is expressed this triggers localised immune response such as stimulating iron flux protein that binds with cytoplasm of cell triggering the hypersensitive response (leads to ell death at site of infection). does this by an oxidative burst that produce ROS (reactive oxygen species) that cause cell death. it also produces lignin and callose for other cells to prevent infection of surrounding cell
plants defence against herbivores
Structural Defenses:
- Thorns and Spines: sharp structures like thorns and spines that physically deter herbivores from feeding.
- Trichomes (Hair-like Structures): They can create a physical barrier, produce toxic or sticky substances, or cause discomfort to herbivores.
- Toughened Tissues: Some plants increase the toughness of their leaves or stems, making them harder to chew.
Chemical Defences:
Secondary Metabolites: chemical compounds that are toxic, repellent, or anti-nutritive to herbivores. These include:
- Alkaloids (e.g., nicotine, caffeine) that can poison or deter herbivores.
- Terpenoids (e.g., menthol, pyrethrins) that have various toxic effects on insects.
- Phenolics (e.g., tannins, flavonoids) reduce digestibility and inhibit the growth of herbivores.
- protease inhibitors, prevents digestion
Volatile Organic Compounds (VOCs): Plants can release VOCs when damaged, which can directly deter herbivores or attract predators and parasitoids of the herbivores.
acquired immunity to pathogens, herbivores, microbes and BABA
defence mechanisms that resemble “acquired immunity,” offering enhanced resistance after an initial exposure to pathogens, herbivores, soil microbes, and certain chemical compounds like BABA (β-aminobutyric acid). Although plants do not have an adaptive immune system like animals, they can “prime” their defenses, leading to a heightened state of readiness against future attacks
pathogens
Triggering Event: SAR (systemic acquired immunity) is typically activated by an initial infection with a pathogen, often involving a localized hypersensitive response (HR) where infected cells undergo programmed cell death to limit the pathogen’s spread.
After the initial infection, signaling molecules like salicylic acid (SA) accumulate and move through the plant, leading to the activation of defence-related genes in distant, uninfected tissues.
The activation of SAR leads to the production of pathogenesis-related (PR) proteins that have antimicrobial properties, providing broad-spectrum resistance against a variety of pathogens.
SAR confers long-lasting, broad-spectrum resistance, making the plant more resistant to subsequent pathogen attacks.
herbivore/microbe
Induced Systemic Resistance (ISR) is a similar phenomenon to SAR but is typically activated in response to herbivory or beneficial soil microbes.
ISR is often associated with the JA and ET signaling pathways, which are activated in response to herbivory or colonization by beneficial microbes like rhizobacteria.
ISR primes the plant to respond more robustly to herbivore attacks, leading to the production of anti-herbivore defenses such as toxic secondary metabolites, protease inhibitors, and volatile organic compounds (VOCs)
(In addition to ISR, beneficial soil microbes can enhance plant growth and resistance by improving nutrient uptake, producing antimicrobial compounds, and competing with pathogenic microbes in the rhizosphere)
BABA
BABA (β-Aminobutyric Acid) is a synthetic compound that induces a state of heightened immunity in plants, known as BABA-induced resistance (BABA-IR).
Priming Effect: BABA does not directly act as an antimicrobial agent but primes the plant’s immune system. This priming effect means that the plant can respond more rapidly and strongly when it encounters a pathogen or stress.
BABA-IR
**1mutant
enhanced **1
BABA-IR in Arabidopsis
- Shows priming effect on increased effectiveness of innate immunity, like a plant vaccine
- Two ways- 1 priming of early acting cell wall defence, 2 priming of late acting SA-dependent defences
hOWEVER shows side effects which reduces its ability to be used for crops widely, the plants that are heavily primed have reduced growth, also cant be sprayed on leaves due to the wax layer
Ibi1 mutant
- iBi1 mutant: impaired in Baba-IR, these plants are more greatly negatively effected by BABA priming, they also do not show the benefits of BABA priming
- Hypersensitive to side effects with no benefit of priming, this is because IBI1 disrupts defence pathways
- It might be more susceptible to BABA negatives because it prevents BABA binding, this could cause upstream accumulation of uncharged tRNA, means amino acid homeostasis is unbalanced
Enhanced IBI1
- Enhancing ibi1 boosts induced resistance and increased tolerance to BABA-induced stress (negatives of BABA), tests show increased IBI1 mutants will grow more then wildtype after being treated with BABA under no disease pressure, there is very increased resistance in mutants then in wt when treated with BABA under disease pressure
what does downy mildew do
downy mildew pathogen activates the ABA pathway so plant thinks it is under abiotic stress, however VOZ1/2 gene counteracts this signal and instead activates early PTI and callose defence
RBH strain
- less toxic R-BABA still induce resistance RHB, induces resistance without toxic effect on growth
RBH is not perceived by IBI1 and operated through different pathways potentially working through the JA/ET dependent defence pathway- Through an IR assay found RBH immune mutants had mutant LHT1 gene- these mutant could not use RBH and so had no resistance to pathogens
- Mutants that overexpressed LHT1 had increased resistance, these are cellular transporters for RBH
- LHT1 knockouts had reduced accumulation of RBH and so no induced resistance, overexpressed LHT1 more accumulation of RBH
- Despite structural similarity in BABA and RBH and that they share transporter they act through completly different pathways, this could be used via combined vaccines
maintanence of acquired immunity
methylation
effect of ROS1
the ROS1 enzyme is responsible for removing methylation
he comparison between hypomethylated and hypermethylated progeny of diseased plants revolves around how DNA methylation states impact the inheritance of traits, particularly in response to stress or disease. Here’s an overview of the differences between hypomethylated and hypermethylated progeny and how these states might influence disease resilience or susceptibility.
- DNA Methylation in Plants:
Hypomethylation:
Hypomethylation refers to a reduction in the normal level of DNA methylation. This can lead to the activation of genes that are typically repressed, including Transopable elements and stress-responsive genes.
Effects:
Increased Genetic Variability: Activation of TEs can lead to genetic variability, which might be beneficial under stress by providing a broader range of responses.
Stress Response Genes: Hypomethylation may activate genes involved in stress responses, potentially enhancing the plant’s ability to cope with environmental challenges.
Hypermethylation:
Hypermethylation is the increased addition of methyl groups to DNA, typically leading to gene silencing.
Effects:
Gene Silencing: Critical genes, including those involved in stress responses, may be silenced, which could either be beneficial or detrimental, depending on the context.
Transcriptional Stability: Hypermethylation may contribute to the stability of gene expression by silencing potentially deleterious genes or TEs.
- Impact on Progeny of Diseased Plants:
Hypomethylated Progeny:
Advantages:
Enhanced Stress Resilience: Progeny with reduced DNA methylation may exhibit enhanced resilience to diseases or environmental stress due to the activation of stress-response genes.
Increased Plasticity: Hypomethylation can lead to a more plastic genome, allowing progeny to adapt more rapidly to changing environments or stress conditions.
Disadvantages:
Genomic Instability: Activation of TEs and other normally repressed sequences can lead to mutations and genomic instability, potentially reducing fitness in stable environments.
Potential Disease Susceptibility: If stress-response genes are activated without actual stress, it might lead to unnecessary energy expenditure or inappropriate responses, making the plants more vulnerable in some contexts.
Hypermethylated Progeny:
Advantages:
Genomic Stability: Increased methylation typically leads to the suppression of TEs and other potentially harmful sequences, contributing to greater genomic stability.
Consistent Gene Expression: The silencing of stress-responsive or disease-related genes might be beneficial in stable environments, preventing unnecessary activation of stress pathways.
Disadvantages:
Reduced Adaptability: Silencing of stress-response genes might limit the progeny’s ability to respond effectively to disease or environmental changes, potentially making them more susceptible to new or unexpected stressors.
Potential Disease Persistence: If the disease-associated genes are hypermethylated and silenced, this might allow for the persistence of the disease within the plant or its progeny without an adequate response.
- Ecological and Evolutionary Implications:
Selection Pressure:
In environments where disease or stress is prevalent, hypomethylated progeny may have an advantage due to their increased adaptability and activation of defense mechanisms. However, in stable environments, hypermethylated progeny might be favored for their genomic stability and consistent expression profiles.
Transgenerational Inheritance:
Methylation patterns can be inherited, and the progeny of plants that experienced disease may carry forward the epigenetic marks that influenced their parents’ response to stress. This can lead to an epigenetic memory of stress, potentially affecting the resilience or susceptibility of future generations.
Conclusion:
The methylation state of progeny in diseased plants can have significant effects on their ability to handle stress and disease. Hypomethylated progeny may be more adaptable and resilient to environmental challenges but at the cost of potential genomic instability. In contrast, hypermethylated progeny might enjoy genomic stability but could be less adaptable to new stresses. The balance between these states can influence the long-term survival and fitness of plant populations in changing environments.- knockout mutation in ros1 did not effect experiment via growth so was tested for disease resilience, it was found mutant progeny had high levels of infection this is due to hyper-methylation (ROS1 prevents methylation so without it get more)
- epigenetic recombinant inbred lines (epiRILs) varying in DDM1(dwarf plant mutant, reduced methylation at transposons). they had 123 identical lines that varied in dna demethylation, reduced methylation correlated with heritable resistance, lines that were very resistance, showed normal growth phenotype compared to parent that was stunted
Crop epigenetics
-lettuce has 50x more transposable elements (DNA that can change their position) then Arabidopsis this means there is greater genomic flexability, mutants in DNA methylation machinery are more likely to be lethal and/or more sterile in lettuce, generation of crops epiRILS require fine tuning of the level of DNA hypo-methylation. Active removal of DNA demethylation by ros1 is important for induced resistance
what is estradiol-inducible system
The estradiol-inducible system for ROS1 is a tool used in plant research to precisely control the expression of the ROS1 (Repressor of Silencing 1) gene. This system allows scientists to study the effects of ROS1 in plants by turning its expression on or off using estradiol, a synthetic hormone.
Key Components:
Estradiol: A synthetic hormone used to activate the system. In this context, estradiol acts as a switch that turns on the expression of the ROS1 gene.
ROS1 Gene: The gene of interest, which plays a crucial role in DNA demethylation in plants. ROS1 helps to remove methyl groups from DNA, which can activate certain genes that are otherwise silenced.
Inducible System: This is a genetic system designed to control when the ROS1 gene is turned on or off in the plant.
How It Works:
Gene Control: In the absence of estradiol, the ROS1 gene is not expressed or is expressed at very low levels, so its activity in the plant is minimal or non-existent.
Adding Estradiol: When researchers add estradiol to the plant, the inducible system is activated. This causes the ROS1 gene to be expressed, leading to the production of ROS1 protein.
Reversible and Controlled Expression: By removing estradiol, the expression of the ROS1 gene can be turned off again. This allows researchers to control the timing and extent of ROS1 activity, enabling them to study its effects on the plant at specific times or under certain conditions.
Why It’s Useful:
Precision: Researchers can study the function of the ROS1 gene without it being constantly active, allowing for more precise experiments.
Reversibility: The system is reversible, meaning gene expression can be turned on or off as needed by adding or removing estradiol.
Timing: Scientists can investigate how ROS1 affects processes like DNA methylation, gene expression, and plant development at specific stages or in response to environmental changes.
Application Example:
If a researcher wants to understand how ROS1 influences a plant’s response to stress, they can use the estradiol-inducible system to activate ROS1 only during stress conditions. This helps them see the direct effects of ROS1 activation on the plant’s ability to manage or recover from stress.
In summary, the estradiol-inducible system for ROS1 provides a powerful, controllable way to study the function of the ROS1 gene in plants by using estradiol as an on/off switch. This system is invaluable for understanding the role of ROS1 in plant development and stress responses.
indirect ecological defences of maize
Maize
Above ground
- in maize when it is attacked by larvae of Egyptian cotton wool, they release volatile blend- this includes green leaf volatiles, aromatic volatiles and terpenoid volatiles
- volatiles play important role in recruiting parasitic wasps that lay eggs in caterpillar that kills them off
Below ground
when maize is attacked by western corn rootworm, root emit e-beta-carboline (alkaloids), this recruits pathogenic nematodes that infect the larvae of rootworm
DIMBOA experiment
Experiment
- Young maize roots produced high quantities of the benzoxazinoid DIMBOA, around day 7 of maize growth had super high quantities of DIMBOA the secondary metabolite.
- DIMBOA is exuded from the leaf cells into intercellular space upon attack by aphids or colonisation of necrotising fungi northern leaf blight, it acts as an aboveground defence metabolite against pests and disease, when under attack compounds are hydrolysed to form toxic compounds
- DIMBOA when under such high quantities in root, gave beneficial rise in rhizobacterium called pseudomonas k24 that loves rhizophore of wheat
- looked into cells of pseudomonas k24 that had biologically realistic conc of DIMBOA added and then looked at the effect on genes, small faction of genes were highly uprated, found the group of genes evolved to break down aromatic compounds, this explains how it is so tolerant and colonised rhizophere to maize. found three genes that were highly upregulated were critical for positive chemotaxis in pseudomonas putida (moving towards a specific chemical), this suggested that maize was crying out for help from p.putida,
DIMBOA experiment
- looked at 4 maize strains;
wild type, igl single mutant (produces 90% DIMBOA),single bx mutant (strongly reduced DIMBOA), double mutant (completely impacted DIMBOA )
- found that pseudomonas putida strongly colonised in the wild type, igl single mutant (nearly wildtype) showed substantial colonisation, in single bx mutant there was very little colonisation, double mutant could barely find any presence of species - the results of this experiment was replicated by using non-sterile agri soil and introducing P.putida, found that double mutant caused signifcant difference in P.putida colonisation specifically. - looked at wildtype maize, bx1 (complete knockout of downstream benzoxazinoid components, bx2 (upstream mutation), and bx6 (downstream mutation which is responsible for the conversion of DIBOA into DIMBOA) - found bx6 accumulate more DIBOA then DIMBOA, subtle change in composition of benzoxazinoids. - bx1 and bx2 accumulated little benzoaxazinoids. - very few operational taxonomic units differed between wt and Bx6 so, DIBOA (accumulate in bx6 mutant) has a similar function is DIMBOA, led to finding of MBOA which is a resilient stable compound, release of MBOA had a legacy effect of pest suppression- natural biocontrol agent
phylochip experiemnt
- the phylochip (glass device with taxonomic testing for bacterial microbes) analysis of soils from defence elicited Arabidopsis, looked at unplanted soil, soil with healthy Arabidopsis plant and then soil with plants with different treatments for eg downy mildew
- found that stress treatments resulted in different community structures in soil, the downy mildew treatment had the largest effect, the microbial species that were acquired eg xanthomonas sp, bacteria were found to have been acquired through the treated plants
- the last experiment used infected soil for a second planting. found that spore production was decreased when soil was already exposed to downy mildew (hpa), innoculation of hpa condition soil to disease suppresion so second planted plants became more resistant.
step by step soil microbe recruitment
Step by step soil microbe recruiting
- step 1-attack by pathogen or herbivore, trigger local and systemic signals that activate root immunity
- step 2-change in root exudation profiles of primary and secondary metabolites
- step 3-selection and/or recruitment of beneficial root microbes, resulting in altered root microbiome activities
- step 4- the altered micro-biome antagonises pathogens and herbivores via ISR, direct antagonism, parasitism, or nutrient competition.
why is symbiosis between plants and rhizobia benefical
Nitrogen fixation
- rhizobia form symbiotic relationship, they fix atmospheric nitrogen (N2) into form plants can use (NH3)
soil health
presence of rhizobia enhance soil structure and fertility through formation of organic matter and nitrogen compounds, this indirectly benefits other plants and organisms, contributing to more balanced and resilient ecosystem
agriculture
symbiosis with rhizobia often show increased growth and yield compared to non-leguminous plants or those without rhizobial partners. incorp legumes into crop rotation enhances fertility for subsequent crops, without needing harmful nitrogen fertiliser that causes eutrophication and greenhouse gas)
nitrogen fixation process between rhizobia and plants
○ Flavonoid Release: Leguminous plants release flavonoids into the soil, which attract rhizobia.
○ Nod Factor Production: In response to flavonoids, rhizobia produce Nod factors, signaling molecules that initiate root hair curling and infection thread formation in the plant. Nonspecific= nodABC, specific LPS= liposaccharides and EPS=extra cellular saccharides 1. Infection Thread Formation: ○ Rhizobia enter the root hairs and form an infection thread, a tubular structure through which they travel into the root cortex. MAMPs could trigger basal defence response, the ROS scavengers in rhizobia detoxify this , T3/T4 effectors limit basal defence but trigger ETI, but the rhizobial EPS (extrapolysaccharides) detected by NB-LRR limit defence responses 2. Nodule Formation: ○ Rhizobia stimulate the plant cells to divide, forming a nodule. Within the nodule, rhizobia differentiate into bacteroids, the form capable of nitrogen fixation. 3. Nitrogenase Activity: ○ Enzyme Complex: The nitrogenase enzyme complex, catalyzes the reduction of atmospheric nitrogen (N₂) to ammonia (NH₃).(if o2 levels are satisfied) ○ Energy Requirement: This process requires a significant amount of ATP, supplied by the plant through photosynthates.
plant nodulation genes
Early Nodulation Genes
Function
Early nodulation genes are involved in the initial recognition and signaling between plants and rhizobia, leading to root nodule formation.
Key Genes
* Nod Factor Receptor Genes (NFR1, NFR5): Recognize Nod factors from rhizobia.
* PsENDO11- that encodes a protein associated with the early stages of nodule formation
Mechanism
1. Nod Factor Recognition: NFR1 and NFR5 receptors detect Nod factors.
2. Calcium Spiking: NOD factors induce CA2+ spiking as a secondary messenger.
- calcium spiking correlates with gene expression of ENDO11
4. Gene Expression: Leads to root hair curling, infection thread formation, and cortical cell division for nodule initiation.
Late nodulation genes are involved in meeting the requirements of nitrogen fixation
- leghaemoglobin
binds o2 very tightly and releases it only at low O2 levels
- once the plant late nodulation genes have been swtiched on, bacterial nif genes are switched on (nifA gene o2 sensor, only switches on expression of gene that incode nitrogenase once o2 level falls enough)
bacterial gene expression
bacterial gene
nif- nitrogen fixation
fix- genes found in nodulating strains
include the structural gene for the nitrogenase enzyme
- regulated by nifA, which is O2 sensitive, gene for N2 fixation only switched on when the O2 level drops late in nodule development need both nif and fix gene for fixation of N2
mutations in cytokinin in nodulation
mutations in cytokinin receptor lead to spontaneous nodule formation in absence of rhizobia, energetically costly
(R.facians also increase cytokinin to form leafy galls)
epigenetic memory in plants
Epigenetics
- heritable trait passed down via cell division, meiosis or mitosis that cannot be explained by variation in DNA sequence
- Plants have sort of shown this, progeny of infected plant (pst DC3000) would show individuals with higher resistance, it was found they were more resistant to other biotrophic pathogens too not just specific pathogen, progeny showed SA-pathway priming
auxin and cytokinin roles in N fixation
auxin
hormone that regulates plant growth, inc cell elongation, division and differentiation, auxin is key to root architecture and nodule formation
- high level of auxin inhibit nodule formation, during rhizobia infection auxin is reduced to allow for nodule formation instead of root elongation, important for root curling which traps rhizobia
cytokinin
promotes cell division and differentiation, crucial for initiating nodule organogenesis, rhizobia can stimulate cytokinin production, this cause cortical cells to turn into meristematic region for new nodule
understanding these are crucial for enhancing nitrogen fixation through breeding, engineering or through hormone treatments
how to increase Nitrogen use efficiency
- Breeding and Genetic Engineering
- Selective Breeding: Develop crop varieties with high NUE.
- Genetic Engineering: Enhance nitrogen transporters and assimilation pathways using techniques like CRISPR/Cas9.
- Enhanced Root Systems
- Improved Root Architecture: Select for deeper and more extensive root systems.
- Mycorrhizal Associations: Promote symbiosis with mycorrhizal fungi to enhance nitrogen uptake.
- Soil Management Practices
- Precision Fertilization: Apply nitrogen fertilizers optimally using precision farming techniques.
- Organic Amendments: Use compost, manure, and cover crops to improve soil nitrogen.
- Integrated Soil and Water Management
- Optimized Irrigation: Ensure adequate water supply to aid nitrogen uptake.
- Soil Health: Maintain optimal soil pH and promote beneficial microbial activity.
- Advanced Agricultural Technologies
- Remote Sensing: Use drones and satellites to monitor crop nitrogen status.
- Soil Sensors: Deploy sensors for real-time soil nitrogen data.
how many carbon atoms go to nodules for nitrogen fixation
1/3 of carbon atoms fixed in leaves
leaf structure and water use
water light and co2 effect open v closed
stomata on leaf responsible for opening and closing stomata- for CO2 for photosynthesis and H2O for transpiration
gaurd cells repsonsible for opening and closing, when flaccid stomata are closed, to open H+ forced out of gaurd cell, K+ is uptaken via activation of K+ channels, this lowers water potential drawing water in, opening it
low light and low CO2 promote opening
low water promotes closure
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L1- intro9
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L2- rhizobia25
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L3- grand challenges - photosynthesis20
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L4- Grand challenges water use6
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L5- Grand challenges nitrogen use10
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L6- Pathogens and immunity7
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L7- Crop breeding17
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L8- Plant innate immunity19
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L9- Acquired immunity13
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L10- Onset of acquired immunity9
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L11- maintenance of acquired immunity8
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L12- indirect ecological defence8
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