Plants and People MT

Describe the plant disease Rice Blast

- Pathogen: Magnaporthe oryzae (ascomycete fungus) - Host: rice (losses 10-35%) - Famous for: biggest threat to rice production, uses appressorium to punch into epidermal cells + inject into hyphae - Treatment: fungicides + resistance breeding

Describe the plant disease Black Sigatoka

- Pathogen: Mycosphaerella fijiensis (ascomycete fungus) - Host: banana (losses: 50%) - Famous for: rapid world-wide spread since 1972 - Treatment: sanitation and fungicides: 15-50% of cost price

Describe the plant disease Dutch elm disease

- Pathogen: Ophiostoma sp. (ascomycete fungi) - Host: elm trees (Ulmus minor) - Famous for: destroying nearly all elms in UK + EU in 1970s, immune response blocks exylem, but not pathogen, lives in soil, infected as soon as they become wooden - Treatment: eradicate vector (bark beetle); sanitation

Give three characteristics of the hexaploid wheat genome

- Relatively large (16,000 Mb) - Highly repetitive (~80% repeat sequence) - Relatively plastic

Where did cultivation arise?

24 independent regions, grain crops are the focus in 13 of these

Give an example of a plant disease caused by a viroid

Cadang-Cadang - Pathogen: CCCVd (Coconut Cadang-Cadang Viroid) - Host: coconut + African oilpalm, vector unknown, perhaps pollen - Famous for: killed over 30M coconut palms in Phillipines since 1927 - Treatment: no control, spreading at 0.5 km/yr

What is an apical meristem?

The tissue in most plants containing undifferentiated cells

Describe the stages in cauliflower floral induction

Vegetative meristem (makes leaves) --> Inflorescence meristem (makes floral meristems) --> Back to start + repeat (NO FLOWERS)

Give three examples of how plant pathogens can change plant behaviour

- 'Green islands' by Erysiphe graminis on wheat leaves ...to extend host life! - 'Pseudoflowers' by Puccunia monoica on Arabis ...to spread by bees! - 'Foolish seedling' by Gibberella fuijkuroi on rice produces Gibberellin ... to spread spores by wind!

What does the wheat mutant Ph1 locus contain?

- (On chromosome 5B) contains an insertion of repetitive DNA into a cdc2 gene cluster - cdc2 genes encode protein kinases that regulate cell cycle progression and affect chromosome condensation

What is ETI and how can it occur?

Second layer of induced immunity Effector recognition leads to ETI - Mostly by NLR immune receptors (NLRs: Nod-Like Receptors) - Effector-triggered Immunity (ETI) - Universal immune response, often includes hypersensitive response (HR) - Avr gene encodes recognised effector Outcome: host is resistant! 'Incompatible interaction': plant does not support life cycle of the pathogen

What do similar rates of selection for loss of shattering among crop plants suggest?

Selection pressures were similar across different taxa, places + time periods

Are traits affected by domestication or diversification controlled by few or many genes?

Several studies indicate few genes of large effect, but more recent pop genetics studies indicate selection may have affected entire genome

How has the wild mustard plant (B. oleracea) evolved through domestication?

Short internode stem surrounded by leaves in cabbage - selection for growth from apical stem 400 types of cabbage!

Describe the transformation that occurred to produce the 'naked grain' (maize)

Transformed from grains covered by hard podcase to easily-milled naked grains (tga1 gene) Crop less labour intensive to process after harvesting 'Naked grain' species-wide in maize, variety-specific in wheat + barley

What are the two types of non-host interactions?

Type-I: Pathogen lacks tools to suppress host immunity (most cases!) Type-II: Host carries fixed R genes against conserved effector(s)

Describe the stages in (normal) floral induction

Vegetative meristem (makes leaves) INDETERMINATE --> Inflorescence meristem (makes floral meristems) INDETERMINATE --> Floral meristem (makes floral organs: sepals, petals, anthers etc) DETERMINATE

Other than Nr, what is another tomato mutations used by breeders?

ripening-inhibitor (rin) --> affects transcriptional control of fruit ripening

Describe the effects of the European Corn Borer and traditional management practices

- 2-5% yield loss per larva - In 1996 cost ~$1 billion in US for crop losses and management practices - No natural resistance genes in maize/teosinte (DIMBOA - natural antibiotic, toxic for humans) - Chem methods: Insecticides (kill b4 eggs laid/burrowed in) - Bio methods: Trichogramma evanescens (predators, parasitic wasps lay eggs into caterpillars £££) + Bacillus thuringiensis (soil bacterium)

What are NLR Resistance (R) genes and where can they be found?

- >70% of the cloned R genes encode NLR (NB-LRR) proteins - Nucleotide Binding (NB) binds ADP (active) or ATP (active) + Leucine-rich Repeat (LRR): versatile protein-protein binding platform - ca. 100 NLR genes/plant - Throughout the plant kingdom - Highly polymorphic, especially in LRRs - Confer resistance against different pathogens - Often reside in (recombining) gene clusters

What is allopolyploidy and how does it arise?

- Allopolyploidy occurs when a polyploid offspring is derived from two distinct parental species - Via interspecific hybridisation followed by chromosome doubling - Polyploidy occurred in evo of ~70% o flowering plant sp

What were the origins of rice?

- From Oryza rufipogon to Oryza sativa - Origin of rice is intensely debated - Using genetics: rice has been domesticated twice (S China + SE/S Asia)

What is an alternative management strategy for the European Corn Borer and why is it advantageous?

- Genetic engineering: Bt maize - Don't have to spray pesticides - Huge uptake of Bt resistance genes - Seeds only slightly more expensive

Describe the potato late blight disease

- Pathogen: Phytophthora infestans (oomycete) - Host: potato, tomato, other solanaceous plants (losses: 5-78%) - Famous for: Irish potato famine 1845-1851 1.5 million people died of starvation, 1 million emigrated to USA - Treatment: hygiene; 'fungi'cides; resistance breeding

Describe the disease sudden oak/larch death

- Pathogen: Phytophthora ramorum (oomycete) - Host: rhododendron, oak, larch, beech, chestnut, ash, birch - Famous for: jumped onto larch in 2009; >10.000ha infected in 2013 - Treatment: eradicate infected trees; resistance breeding

Describe the plant disease downy mildew which appears on grapes

- Pathogen: Plasmopara viticola (oomycete) - Host: grape (Vitis vinifera) losses up to 100% without treatment - Famous for: Bordeaux mixture (copper and lime) since 1885 - Treatment: 'fungi'cides; hygiene; resistance breeding (powdery mildew is a fungus which doesn't penetrate tissue)

Describe the plant disease Wheat Stem Rust

- Pathogen: Puccinia graminis (basidiomycete fungus) - Host: wheat (losses: 10-70%) - Famous for: associated with collapse of Roman empire; Nobel Peace Price 1970 for wheat breeding by Norman Borlaug; new virulent Ug99 strain is quickly spreading to Pakistan/India - Treatment: fungicides, resistance breeding (introgressing resistance genes)

How are plants different to animals in terms of their immunity?

- Plants are sessile (can not run away from threats, they have to deal with it!) - No adaptive immunity (no somatic recombination of immunoglobulin genes) - No mobile immune cells/organs (no lymphocytes)

What is the decoy model of AvrPphB recognition?

- Real host target of AvrPphB is BIK1 - Decoy model: PBS1 only acts as co-receptor w RPS5

How can we recruit more R genes?

- Recruit from larger germplasm (cross-species/taxa) - (Synthetic) R genes for crucial 'core' effectors - Include recognition of the manipulated host target - These approaches require GM crops (to add R genes)

What is scientific breeding and what are its aims?

- Resulted from rediscovery of Mendel's laws + developing ideas of mechanisms of inheritance: chromosomes + genetic linkage - Basic aim: generate/harness genetic diversity + select plants w/ improved characteristics - Breeder seek to combine range of desirable traits (genes) in one plant

How can we improve rice resilience to flooding?

- Rice plants die within 7 days of submergence (total yield loss) - Natural submergence tolerance exists: Sub1 varieties don't increase growth/metabolism when flooded so can survive when water retreats but are low yielding - Swarna is high-yielding rice but sensitive to flooding; Sub1 is low yielding but resistant to flooding --> Swarna-Sub1 prevents total yield loss BUT 0% of rice is GM

What are target traits we want to find in wild progenitors and landraces of wheat?

- Salt tolerance - Drought tolerance/WUE - Nutrient-use efficiency

What is fw2.2 and what does it do in tomato cell division?

- fw2.2 is the protein product of the fw2.2 gene - Protein has structural similarity to mammalian Ras family GTPases (enzymes that reg cell division) - fw2.2 represses cell division in devo of tomato fruit: -ve regulator of cell division - fw2.2 encoded by transcripts that accumulate to high levels in small vs large fruit

What are the major groups of plant pathogens?

1) Viroid/virus: replicate inside host cell; 0/few proteins; viruses encode proteins, viroids don't 2) Bacteria: prokaryote, Gram(-)/(+) 3) Fungi: filamentous; a/sexual cycles, spores; ascomycetes (sac fungi) + basidiomycetes (club cell carrying spores) 4) Oomycetes: filamentous; a/sexual; NO fungi; zoospores

How do you recognise effector proteins?

1. Often secreted proteins (have SP, no TM) 2. Expressed (only) during (early stages of) infection 3. Often under positive selection (Ka/Ks>1) 4. Often no homology to annotated proteins

What is the difference between homologous and homoeologous?

Chromosomes from within a genome (e.g., 1A 1A) are homologous Between genome chromosomes (e.g., 1A 1B) are homoeologous

Describe the mechanism of NLR proteins

Conformational change occurs

How can R genes be used to protect crops?

1) R gene rotation (pathogen-dependent) 2) Polycultures 3) R gene stacking

What genes are causing the cauliflower phenotype? (Genetic studies in Arabidopsis)

- Arabidopsis APETALA1 (AP1) gene encodes MADS box transcription factor - ap1 loss-of-function mutants: flowers lack petals; occasionally form inflorescence in place of floral meristems - CAL (Cauliflower) gene encodes a protein very similar to AP1 - ap1 cal double mutant has an extreme phenotype - new meristems borne on the flanks of inflorescence meristems are themselves inflorescence meristems (rather than floral meristems) - In cauliflower (B. oleracea var. botrytis) the AP1-related gene encodes a non-functional protein (versus 'normal' B. oleracea)

Give an example of indirect recognition

- AvrPphB is T3E of Pseudomonas syringae - AvrPphB cleaves host kinase PBS1 - PBS1 cleavage activates RPS5 (=NLR) - Guard model: RPS5 guards the host target of AvrPphB

What kind of selection are R genes under?

- Balancing selection: R gene freq. responds to pathogen pressure - R genes can be ancient + are often not fixed (freq. dependent on pathogens)

How did varieties originate and what is the advantage of them?

- Began in early 19th century - Involved conscious human selection (realised like begat like w/out understanding mechanism - genetics) - Plants of variety genetically more homogeneous than landrace pops - Genetically homogeneous/homozygous - Adv: Standardisation/uniformity - Example: 'Squareheads Master' a 19th century wheat variety still used for thatching

What are some other GM rice varieties in production/use?

- Bt rice: made 2005, ready for release 2009, still not released 2019 - Ht rice: Monsanto made glyphosate resistant rice 2000, not brought to market; Bayer made glufosinate resistant rice 2002, used a little in US - Ventra Bioscience: health + medical related proteins in rice grains e.g. breast milk proteins; targeting infectious disease + malnutrition, rice grain has v little protein

What is in store for maize domestication over the next 20 years?

- CRISPR-Cas9!!!! (2020 - DuPont Pioneer, increased amylopectin) - Commercial: herbicide tolerance - new herbicides required as weeds becoming resistant; insect resistance - new insecticides required as pests becoming resistant; specialty production - vaccines (hepatitis B), pharmaceuticals - International development: yield - 50% increase in on farm yield needed by 2050; nutritional quality - vitamin A, iron, zinc; reduced inputs - nitrogen fixation (reduce fertilizer), drought tolerance (reduce water)

What are plant diseases caused by (and what are they not)?

- Caused by microbial pathogens e.g. viruses/viroids/bacteria/fungi/oomycetes - NOT by herbivores/insects - NOT by malnutrition /abiotic stress

What does the wheat Q gene confer and what does it encode?

- Confers the 'free-threshing' character - Encodes an AP2-type transcription factor - Q differs from q both by an AA substitution in the AP2-like protein it encodes + by being more highly expressed (in domesticated than wild form)

What controls tomato fruit ripening?

- Controlled by the plant hormone ethylene - Ethylene is responsible for the changes in texture, softening, colour + other processes involved in ripening - Other ethylene effects are loss of chlorophyll, stem shortening + abscission of plant parts - Ethylene gas used commercially postharvest to ripen tomatoes, bananas + pears - Domestication: Tomato breeders have used genetic changes in ethylene responsiveness to delay ripening, thus reducing spoilage of fruit during transport e.g. the Neverripe(Nr) mutation

Describe the genetics of oilseed rape

- Crop (B. napus - AACC) resulted from an allopolyploidisation event between two diploid Brassica species: B. rapa (AA, 2n = 20) + B. oleracea (CC, 2n = 18) - Is a recent amphitetraploid (2n = 38)

How can we explain the differences between teosinte and maize genetically?

- Cross maize w/ its wild ancestor - QTL analysis to link trait to locus on chromosome - Only 5 loci needed to explain difference: Chr 1 Shattering, growth habit, branching pattern, ear and spikelet architecture Chr 2S Number of rows of cupules Chr 3L Growth habit, ear architecture Chr 4S Glume hardness Chr 5 Ear architecture

What toxins are present in Bacillus thuringiensis?

- Cytolysins (Cyt): only kill Coleoptera + Diptera - Crystal delta-endotoxins (Cry): only kill Lepidoptera, only folds in alkaline environment, sits in membranes of stomachs + haemorrhages, raise pH has no effect so fine for humans (acidic stomach environment)

Describe the properties of the altered function mutant DELLA protein gai

- Dwarf stature - Growth cannot be restored by exogenous GA - Elevated GA levels - GA promotes an interaction between DELLA and the GID1 GA receptor - GID1-DELLA interactions target DELLA for destruction in the proteasome - Disturbed feedback regulation of GA biosynth - gai mutant is semi-dominant

Discuss integrated decoys

- E.g. PopP2 is T3E (effector) of Ralstonia solanacearum - Different integrated domains - Common in angiosperms - Independent integrations (act to do same thing in different positions)

Describe how variation at the Chr1 locus can explain differences between teosinte and maize

- Encodes a 'TCP' protein (growth regulator) - Expressed in axillary meristems of maize but not teosinte - tb1 gene suppresses growth of axillary branches in maize - Presence of maize tb1 gene in teosinte suppresses branches - Domestication selected for mutations that permitted tb1 gene expression in axillary meristems - Big difference in promoter region: less nucleotide diversity in maize than teosinte - selective sweep: all cultivated maize have same variant of promoter that activates expression at meristem - tb1 variant with Hopscotch insertion swept to high freq in modern maize = few branches

What are the challenges for wheat production?

- Environmentally sustainable increase in wheat productivity - Wheat that is highly productive in salt-high, water-low, nutrient-low soils

What is the Fasciated gene?

- Fasciated gene cloned by positional cloning - The gene encodes a YABBY-like transcription factor (FASCIATED) - YABBY transcription factors first implicated in determining leaf adaxial/abaxial polarity (identity of each side) - FASCIATED controls carpel number in flower/fruit development - Extremely large fruited tomatoes contain a DNA insertion in the FASCIATED gene --> lower levels of FASCIATED transcripts and increased locule number

Give some key facts/statistics about wheat

- Feeds more people than any other crop - Current production: ~ 600 million tons per yr - Future needs (by 2050) require 2% annual production increase - Wheat prices (US$) are up nearly 200 percent

What is golden rice, how is it produced and why do we need it?

- Golden rice V1 (2000): Phytoene synthase (Psy) from daffodil Narcissus psuedonarcissus + Carotene desaturase (CrtI) from the soil bacterium Erwinia uredovora XXXX - Golden rice V2 (2005): Phytoene synthase from maize+ Carotene desaturase (CrtI) from the soil bacterium Erwinia uredovora - precursor to vitamin A YES! - 250 Million children <5 years old suffer from Vitamin A deficiency, 1% of those children die (2.5 million every year) - WT: no vit A, GRV1: RDA in 3kg rice, GRV2: RDA in 150g rice

What is Ht maize?

- Herbicide tolerant maize - Resistant to glyphosate herbicides e.g. Roundup - Herbicide inhibits ESPS so organisms can no longer make aromatic AAs --> death - Use less herbicide - only kill when it's a problem

In wheat, homologues pair at meiosis, whilst homoeologues do not. Why?

- Hexaploid wheat contains a mutant Ph1 locus that prevents homoeologous pairing or recombination - Ensures 'diploid' inheritance, but also inhibits breeders from 'introgressing' potentially useful genes from wild relatives in cultivated wheat - But how this particular mutation affects cdc2 activity and thus homoeologous pairing at meiosis remains a mystery

What are the short-term consequences of allopolyploidy?

- Immediate genome instability - Substantial DNA sequence loss - Substantial epigenetic change (e.g., change in cytosine methylation) - These changes happen in both F1 and subsequent allopolyploid generations

What are the long term consequences of allopolyploidy?

- Inbuilt heterozygosity promotes fitness - Gene 'loss' through natural mutation + relaxed selection

What was the wheat 'green revolution'?

- Increased production of high yield varieties of wheat: dwarf mutants - Taller wheat plants put more of their resources into stem than grains therefore fewer grains produced than in dwarfs - Yield increases seen in Mexico, India and Pakistan

What is the plant immune system like?

- Innate immunity (inherited, no somatic recombination) - Pre-existing barriers (passive) - Two layered immune system (active responses: PTI and ETI) - Cell autonomous (present in every plant cell!)

What makes up the structure of a kernel of wheat?

- Kernel is seed from which wheat grows - Endosperm is source of white flour, contains proteins, carbs, iron, vitamins + fibre - Bran is in whole wheat flour, small amount of protein, large quantities of vits + minerals + fibre - Germ is embryo or sprouting section of seed, contains fat

Describe how variation at the Chr4 locus can explain differences between teosinte and maize

- Locus on Chr4 responsible for all variation in glume hardness - Encodes SBP domain transcription factor - Expressed in inflorescences - Single AA difference in coding region of maize + teosinte - knocks out function of gene

What is the wheat domestication syndrome?

- Loss of spike shattering - Loss of tough, adherent glumes - Loss of seed dormancy

Give an overview of crop domestication

- Many different crops have undergone systematic human cultivation - Maximise yield - decrease in natural seed and fruit dispersal mechanisms to reduce yield loss - shifts in cultivation area often require changes in day length dependence or vernalisation - synchronous germination - Determinate growth often selected because they are more robust and have a better yield and are better suited to mechanical harvesting methods - Aesthetic preferences often drives convergent adaptations e.g. colour

Give an overview of tomato domestication

- Morphological variation in tomato size is conferred by fw2.2 + fasciated - The difference is a consequence of the level of expression of a gene encoding a regulatory protein (rather than a difference in the function of the encoded protein)

What does the Never-ripe (Nr) mutation do?

- Never-ripe (Nr) encodes a variant ethylene receptor - Nr mutants have a non-ripening phenotype (reduced amounts of ethylene) - It is the result of reduced ethylene responsiveness in fruit tissues - It has a mutation in the ethylene-binding domain of the NR receptor - (Does eventually ripen)

What are new solutions to increase rice yield?

- No increase in rice yield since 2000 - Convert rice into a C4 plant: predicts 50% yield increase, fertiliser reduction + more drought-tolerance - Commercial: herbicide tolerance - paddy fields good at supressing weeds but problem species include wild rice; insect resistance - some insect pests and Bt rice already on market in China; rice blast resistance - major yield loss disease - International development: yield - 50% increase in on farm yield needed by 2050; nutritional quality - vitamin B1, iron; reduced inputs - nitrogen fixation (reduce fertilizer), drought tolerance (reduce water); rice blast resistance - major yield loss disease

How durable are single R genes?

- Not usually durable - boom + bust cycles - Arms-race: R genes are young + fixed by selective sweeps

Describe the impact of Bt maize on the environment

- Of 168 datasets comparing yields of GM + conventional crops (not just maize), 124 showed increased yields, 32 indicated no difference + 13 were negative - Bt crops (not just maize) have reduced the impacts of agriculture on biodiversity, through enhanced adoption of conservation tillage practices + reduction of insecticide use - General consensus is that Bt maize has been positive for yield and biodiversity - But... how long will it last?

What are effectors?

- Pathogen-derived molecules that manipulate the host cell - Incl. pathogen-derived phytohormones, phytotoxins, + small RNAs - 4->1000 per pathogen - Some are recognized by R genes + were studied first (Avr genes) - Often interfere with immune signalling (biased view!) - Includes prokaryote molecules that act inside Eukaryote hosts(!) - Darwin: 'Gene with extended phenotype'! (effect on pathogen + host)

Describe the plant disease Fusarium wilt

- Pathogen: Fusarium oxysporum (ascomycete fungus) - Host: many crops, incl. tomato, melon, banana, palm etc. - Famous for: soil-borne, enters through root and grows in xylem; jumps host by horizontal chromosome exchange - Treatment: fungicides, resistance breeding

Describe the plant disease ash dieback

- Pathogen: Hymenoscyphus fraxineus (ascomycete fungus) - Host: Ash trees (Fraxinus ornus) - Famous for: appeared in 1992 in Poland, since 2012 in UK; evolved from saprophyte; sexual stage still on leaf debris - Treatment: none: lethal to young trees, old trees will slowly die but: 10-15% of Ash trees are completely resistant

How do you make purple tomatoes and what is the benefit of doing so?

- Scientists expressed two genes from snapdragons that induce the production of anthocyanins in snapdragon flowers - Anthocyanins accumulated in tomatoes at higher levels - fruits are an intense purple colour - Anthocyanins are naturally occurring pigments found at high levels in berries e.g. blackberry + cranberry - Anthocyanins offer protection against certain cancers, cardiovascular disease + age-related degenerative diseases - Scientists are investigating ways to increase the levels of health-promoting compounds in more commonly eaten fruit and veg - Lifespan of cancer-susceptible mice (Trp53-/- mice) was significantly extended when their diet was supplemented with the purple tomatoes compared to supplementation with normal red tomatoes --> first example of a GM plant with a trait that really offers a potential benefit for all consumers

Describe R gene distribution in nature

- Some R genes are millions of yrs old - Not fixed in natural pops - Robust immunity in plants acts at pop level

Describe the origins of bread wheat

- Successive cross-hybridisations involving diploid grass wheat progenitor species in a region of the world known as the 'fertile crescent - Maize + rice from single diploid progenitor - Three different diploid genomes, 'A', 'B' and 'D', contributed to the hexaploid (ABD) bread wheat genome: A genome donor - Triticum uratu; B - unknown; D - Triticum tauschii - AA x BB --> AABB (durum wheat) x DD --> AABBDD (bread wheat) - Domesticated ~8-10,000 years ago

How does breeding vary in practice?

- Techniques vary between crop species - There are aspects which are common across most crops due to universality of laws of inheritance

Give an example of the phenotypic consequences of genomic plasticity

- The Hardness (Ha) locus controls grain hardness - Ha is located on chromosome 5D - The 5A and 5B orthologous genes are non-functional because of DNA elimination in the tetraploid ancestor of bread wheat - Elimination thought to be due to 'illegitimate recombination' between repetitive DNA - Wheat genetic buffering enables flexibility in chromosome engineering: e.g., nullisomic-tetrasomic lines: can tolerate loss of entire chromosome e.g. lacking 2x 1A, balanced by 4x 1D

Describe the emergence of resistance in Ht and Bt crops

- The more widespread the use of Bt crops the more species that evolve resistance - >281 documented examples of evo of glyphosate resistance in 36 different plant species - Have to go back to old management practices

Compare PTI and ETI

- The same in composition; ETI is a stronger response (associated w cell death) - HR (PCD) only with ETI, but not always; not essential - Combination of diverse weaponry (responses) - Irrespective of type of inducer (any pathogen) - Acting against all pathogens (universal)

How can plant pathogens enter host tissue?

- Through stomata - Through lenticells (functionally analogous to stomata, found in periderm of organs + bark) - Through hydathode (pore that secretes water through pores in epidermis) - Through wounds - Through lateral roots (breaking through cortex) - Through nectarthode (opening at base of flower from which nectar exudes) - Using haustoria - Using appressoria - Killing host cells

Describe the tomato family, its origin and domestication

- Tomato belongs to Solanaceae family, containing >3000 species inc. many plants of economic importance inc. potatoes, aubergines, petunias, tobacco, peppers + physalis - Botanically tomato is a fruit berry not a vegetable - Originated from Andean region - Domestication probably occurred in coastal Peru, starting w/ wild, small-fruited species like Solanum pimpinellifolium that might have been weed in early maize crops - Exact date of domestication unknown, already cultivated for food in Mexico by 500 BC - Early versions were small + most likely yellow - Tomato semi-advanced in domestication b4 Spanish brought tomato to Europe in 15th/16th C - Further domestication on more intense scale occurred throughout Europe in 18th/19th C

Give an example where PRRs have been transferred

- Tomato can not sense bacterial PAMP EF-Tu - Tomato + Arabidopsis EFR -> broad range bacterial resistance! - Tomato pathogen prevents recognition of flagellin, not EF-Tu

How has tomato size changed through domestication?

- Tomato is a fruit: domesticated fruits usually larger + more palatable to human than wild progenitors - Cultivated tomato plants produce fruit as much as 1000 times larger than wild progenitors - Quantitative trait loci (QTL) analysis enabled identification of a single gene, fw2.2 (fresh weight), that plays a major role in determining fruit size (inhibits cell division so less in bigger fruit)

Why are tomatoes important?

- Tomato ranks 1st in the world for veg + accounts for 14% of world veg production - Source of important nutrients such as lycopene, β-carotene + vitamin C - Modern commercial varieties have poor taste + lack sugar --> resulted from breeding tomatoes to ripen uniformly red in the 20th C - A model organism for scientists with a small genome of ~900 Mb

What is Bt cotton/maize?

- Transgenic expression of Bt (Bacillus thuringiensis) protein in cotton + maize which kills insect gut cells - Bt gene inserted into crop

Describe the structure of the cauliflower

- Typically, only the head (the white curd) is eaten - Curd is composed of white inflorescence meristems - Development arrests following the formation of inflorescence meristems - Cauliflower and broccoli curds are composed of inflorescence meristems and flower buds, respectively

What are non-enzymatic apoplastic effectors?

- Unrelated, small, stable, secreted proteins - Acting as inhibitors + preventing degradation + recognition

What was discovered from QTL analysis of rice?

- Used to work out which locus responsible for trait - Chr7 - Brown pericarp (Rc): encodes bHLH transcription factor, regulates production of proanthocyanidin, 14bp deletion destroys DNA binding domain of gene causing loss of function - Chr7 - Prostrate growth 1 prog1: encodes zinc finger protein (like tb1 in maize), expressed in axillary meristems (like tb1 in maize), protein promotes outgrowth of tillers - gain of function (opposite to tb1 in maize)

How has variation changed as a result of domestication of wheat?

- Wheat domestication has reduced genetic variation: gen bottlenecks from original hybridisation events; subsequent breeding strategies - There is substantial gen variation in wild progenitor + landraces: recent projects aim to capture this variation

What does the tomato mutation jointless do?

- jointless has been used by tomato breeders to reduce the problem of crop loss due to premature fruit drop - Normal gene (Jointless) encodes a MADS-box transcription factor that controls genes involved in the development of abscission zones - During abscission, the plant hormone ethylene stimulates cells to produce enzymes that degrade the middle lamella between cells in the abscission zones - Tomato plants with the jointless mutation (bp deletion) fail to develop AZs on their pedicels and so abscission of flowers or fruit does not occur normally.

What does the ripening-inhibitor (rin) mutation do?

- rin reduces ethylene output + hence delays ripening - Normal Ripening-Inhibitor gene encodes MADS-box transcription factor that regulates ethylene production - Mutated rin allele has deletion at the 3′-end - rin cannot transmit the ethylene signal downstream to ripening genes due to the mutation - Mutation often used in the heterozygous form (RIN/rin) to create long shelf life fruits - rin has been used widely in the breeding of commercial tomato lines in which ripening is retarded - However, the mutation decreases lycopene content but the genes encoding possible allergenic proteins were expressed at a lower level in the rin hybrid fruit than in the wild-type fruit

What are the two groups of effector proteins?

1) Apoplastic effectors - inhibitors, enzymes + others 2) Cytonuclear effectors - (entry!) T3Es, TFs, enzymes

Give eight pre-existing barriers found in plant immune systems (plant doesn't induce anything)

1) Bark 2) Cuticle + cell wall 3) Elevated stomata (more difficult to enter) 4) Chemical barriers e.g. tomatine in tomato 5) Plant is insensitive for phytotoxin 6) Key host target is missing 7) Pathogen does not recognise the host plant 8) Plant does not provide essential nutrients for pathogen

Give 5 examples of the lifestyles of plant pathogens

1) Biotroph: colonise + feed from living host tissues e.g. viruses, rusts + mildews, resistance often based on recognition + induced responses 2) Obligate biotroph: can only grow on its living host e.g. all viruses, rusts + mildews, auxotrophic = incomplete metabolism 3) Necrotroph: kills host + feasts on dead tissue, often produce death-inducing toxins, resistance often based on detoxification/absence of toxin target 4) Hemibiotroph: biotroph only initially then necrotroph 5) Saprotroph: lives on decaying tissues (does not kill), many pathogens can be facultative saprophytes (switches to pathogenic to infect living tissues)

Give the first 7 key facts about Brassicas

1) Brassica is a genus of plants in the mustard family (Brassicaceae) 2) Also known as cruciferous (flower has 4 petals in cross shape) vegetables, cabbages or mustard plants 3) Cruciferous vegetables are one of the dominant food crops worldwide 4) Genus contains more important agricultural + horticultural crops than any other genus 5) Most are annuals or biennials 6) Native in the wild in western Europe, the Med + temperate regions of Asia 7) Cultivated for at least 2500 yrs in SE Europe

Give three examples of phytotoxins (small molecules that act inside the host) used by plant pathogens for host manipulation

1) Coronatine - Pseudomonas syringae pv. tomato (bacterial hemibiotroph, speck disease on tomato) - Produces Coronatine (COR), which re-opens stomata (because stomata close upon flagellin recognition) 2) Syringolin A - Pseudomonas syringae pv. syringae (bacterial hemibiotroph, speck disease on bean/pear) - Produces Syringolin A (SylA), facilitates wound entry, SylA diffuses, blocks host proteasome + signalling by stress hormones, creating susceptible host tissue 3) Rhizoxin - Rhizopus microsporus (fungal necrotroph, sunflower rot) - Produces Rhizoxin: targets β-tubulin, blocks microtubule formation Fungus has rhizoxin-insensitive mutant β-tubulin - NB: Produced by endosymbiont Burkholderia rhizoxinica

Describe the common breeding practice (8 steps)

1) Female parent emasculated + pollen transferred from male parent with paint brush to cross 2) Pollinated plants bagged to ensure female parent receives only pollen from male parent 3) Seed collected from pollinated plants + sown out to produce F1 pop in which all plants are uniform 4) Seed from F1 plants collected + sown to produce F2 pop in which plants are genetically v diverse 5) Plant breeder selects plants w/ best characteristics from which seed will be saved for sowing next gen 6) Process of selection + resowing continues + moves from glasshouse into small plots in field 7) At each stage breeder is measuring yield + quality characteristics + looking for disease resistance 8) Selection from yield plots grown in field at diverse locations around the country b4 variety entered into registration trials

Give three examples of phytohormones used by plant pathogens for host manipulation (changing growth/block immunity)

1) Gibberellin: Gibberella fujikoroj - Fungus causing 'bakanae'/'foolish seedling' disease in rice - Produces plant elongation hormone gibberellin (GA) (leading to isolation of GA in 1935) - stimulates internode growth 2) Ustilago maydis (biotrophic basidiomycete, corn smut on maize) - Produces auxin to induce plant tumor growth 3) Agrobacterium tumefaciens - Transforms host plant with T-DNA (Transfer-DNA) Via Type-IV Secretion System (T4SS) - Induces auxin and cytokinin to produce tumors

Give three strategies to increase crop resistance

1) Induce one immune response: is usually unsuccessful; acting collectively 2) Constitutive immune response: usually reduces growth! High SA levels 3) Chemically induced immunity e.g. Actigard/BION (Syngenta) (-ve effect of yield)

Give 6 general features of landraces

1) Often visually distinct/identifiable 2) Genetically adapted to local environment 3) Often have specific historical origin (local names), often associated w/ particular geog region 4) Populations are genetically dynamic over time (affected by year to year changes in selection pressure) 5) Pops are genetically more homogeneous than wild pops but less homogeneous than modern varieties (bottleneck) 6) Display high yield stability (varies little yr to yr) but low yield (compared to modern)

Give three examples of cytonuclear effectors

1) T3 effectors targeting immune kinases e.g. Pseudomonas syringae - Many effectors act redundantly on same immune pathway 2) SWEET TALE transcription factors e.g. Xanthomonas campestris - TALE: Transcription Activator-Like Effector) - Activate host genes in nucleus - Switch on gene expression of SWEET transporters 3) Metabolic effectors: Opines e.g. Agrobacterium tumefaciens - Transfer-DNA expresses enzymes to generate opines - Opines are N-rich + cannot be metabolised by plants (can be by pathogen)

What are CWDEs?

Cell Wall Degrading Enzymes - Produced by plant pathogens (not released by biotrophic organisms)

How have breeders increased the pace of breeding? (7)

1) Parallel selection programmes - in N + S hemispheres allows two generations per yr 2) Single seed descent - single seed is selected randomly from each selected plant to make bulk = rapid screening in artificial growth rooms, 2 or more gens per yr 3) Doubled haploids - haploid plants generated + then made diploid, 100% homozygous in 1 gen 4) Mini-tuber breeding in potatoes - plantlets regenerated in aseptic conditions from explants, many from single mother plant, plantlets transported from lab to greenhouse, 10-12 wks plants produce mini tubers which are pathogen free + allow propagation of new lines 5) Embryo rescue - expands range of available characters by making crosses between plants which would not normally produce viable offspring 6) Genome science - transformed breeders' understanding of function/location of individual genes + increased speed w/ which gen variation can be analysed e.g. marker assisted selection 7) Transformation - allows desired traits to be added, modified or deleted in plant variety w/out reshuffling entire genomes, GM

Give three examples of cultural selection for food preference

1) Popcorn: selection of toughened pericarp led to evo of popcorn maize varieties 2) Fragrant rice: fragrance due to increased levels of 2-acetyl-1-pyrroline conferred by mutation causing loss of betaine aldehyde dehydrogenase 3) Sticky rice: stickiness due to reduction in amylose levels in grain starch, results from intron 1 splice-donor mutation in the waxy gene, causing loss of starch granule bound starch synthase

List 10 important things to know about rice

1) Products: Almost entirely human food (not animals) + fireworks 2) Producers + importers: main producers are China + India, main importers are China (not enough to meet demand) 3) Pests + diseases: Xanthomonas campestris pv. Oryzae is a bacterial leaf blight which can reduce yields by 40% (flooded areas), Magnoporthe grisea is a rice blast fungus which can reduce yields by 50% (everywhere) 4) Physiology: C3 photosynth, monecious w/ hermaphrodite flowers, require high temp. (20-40*C), sensitive to day length, semi-aquatic so requires more water to produce than other crops, grain accumulates few compounds compared to maize (almost entirely starch) 5) Deficiencies: 100% nutrients in unprocessed paddy rice to <30% nutrients in white rice (poor in vits, mins + AAs, only cals) (rice hulls used for fireworks) 6) Ancestor: Oryza rufipogon - branches grow out not up 7) Genetics: 12 chromosomes (small), diploid genome, genome size 430 million bp, >3000 different rice varieties sequenced 8) Natural diversity: 21 wild Oryza species and 2 cultivated species, >120,000 different named cultivars, Oryza sativa (Asian) - indica (non-sticky long grain) - & japonica (sticky short grain, with temperate, tropical and aromatic varieties), Oryza glaberrima (African), majority of cultivars grown are inbreds 9) Global development: most important food crop in SE Asia, 90% of rice consumed by those who grow it (subsistence farming), major calorie provider for 3.5 bil, 50% yield increases needed in dev world by 2050, need to improve yield, nutritional quality + reduce fertiliser 10) Changing global diet: Maize is now the major output of maize, used for animal feed

List the first five important things to know about maize

1) Products: food to alcohol to medicines to biofuels, majority fed to animals 2) Producers + importers: main producers are America, Brazil, China, main importers are Europe + China 3) Pests + diseases: >100 diseases (viral, bacterial, fungal), insects + nematodes cause crop losses e.g. Ostrinia nubilalis European corn borer - 2-6% yield loss per borer per plant 4) Physiology: C4 Photosynth, monoecious (separate M + F flowers), grow in v diverse climates, diff compounds accumulate in kernels in diff varieties, kernels accumulate lipid transfer protein (allergies) 5) Deficiencies in lysin, niacin --> pellagra, tryptophan

Give 11 key facts about oilseed rape

1) Rapeseed "rape"- cultivated over most of the world for >4000 y 2) 13th century in Europe: cultivated on a commercial scale - primary use was lamp oil 3) Known as a "break crop" - one that helps improve yield of following cereal crops, in particular wheat 4) If grown continuously yields decrease because of build-up of soil borne pathogens: fungi + nematodes 5) Rape flowers in May, in July it desiccates (treated with glyphosate), and late July is harvested 6) Until 1970's oilseed rape crop was barely grown in the UK when there was a dramatic increase in commodity prices 7) Not v high yielding crop versus cereals (3 t/h vs 8 t/h for wheat) 8) W/ higher commodity price + use as break crop means remains important crop in arable rotation (UK 90-100% self-sufficient) 9) Now bred for use as cooking oils 10) Increasingly processed for use as biodiesel 11) UK exports to many countries e.g. Germany, China + India (yield increase kept up with increase in production)

Give six examples of cellular induced responses

1) Release of reactive oxygen species (ROS)/Oxidative Burst - Crosslinks cell wall - (In/)activates proteins - Damages pathogen - Signals locally 2) Hypersensitive Response (HR) - Rapid death of plant cells associated w restriction of pathogen growth - Programmed cell death (PCD) 3) Extracellular traps - Secreted DNA is used as trap for microbes (some escape using nucleases) - Induced release by border cells at root tip 4) Callose deposition - Extracellular deposition of β-1,3-glucose (β-glucan) - Local, focal strengthening of cell wall at infection site + prevent invasion - Papillae under penetration peg of appressorium - Relatively late response 5) PR (pathogenesis-related) protein accumulation - Accumulate in apoplast and vacuole to high levels - Upon infection; induced via stress hormone SA; digest part of pathogen 6) Phytoalexin accumulation (host-sp immune response) - Synthesized locally, the novo - Antimicrobial compounds - Often anti-oxidative - Broad spectrum activities - Chemically diverse, e.g. terpenoids, glycosteroids + alkaloids

What are the four consequences of indirect perception?

1) Some R genes have dual recognition e.g. RRS1 recognises both fungus + bacteria 2) Plants have less R genes than existing pathogens - 100 R genes/plant vs 10,000 pathogens 3) Indirect perception can be more durable - evasion of indirect recognition -> virulence penalty 4) Limits to transfer of R genes: Restricted Taxonomic Functionality (RTF)

Give four examples of induced responses which are organ-specific

1) Stomatal closure - Pre-invasive immunity - Stomatal cells can sense pathogens + close the gate 2) Tylose formation in Xylem - Outgrowths of xylem parenchyma cells into the lumens of adjoined vessels via vessel-parenchyma pits (dam up) - Induced by wounding + pathogen infection 3) Leaf abscission - Abscission of infected area from leaf/whole leaf 4) Cork formation - Cork: mostly suberin (waxy, hydrophobic polyaromatic/polyaliphatic) - Seals off infection site

What are the two main categories of grain crop domestication traits?

1) Successful germination (affected by increased soil disturbance/depth of seed burial) 2) Increased ease of harvesting

List the second six important things to know about maize

6) Ancestor: Zea mays ssp. parviglumis (teosinte) - ears look nothing like corn, not soft, wooden cases, fewer kernels 7) Origins: Balsas valley in Mexico, Coxcatlan cave (layers of sediment) 8) Genetics: 10 chromosomes, ancestor was polyploid, maize now diploid, genome size same as human, B chromosome (not essential for life), ring chromosomes, multiple transposable element families 9) Genetic engineering: first commercial GM maize released in 1996, today GM maize ~90% all maize in USA , acreage increasing worldwide, 1st commercial CRISPR/cas9 maize release 2020 10) Global development: most important food crop in Sub-Saharan Africa + S. America, major calorie provider for 900 million people worldwide, 30% annual food aid shipments are maize, 50% yield increases needed in devo world by 2050, major need to improve yield, nutritional quality + reduce fertiliser 11) WORLD'S MOST PRODUCED CROP

Give the second five key facts about Brassicas

8) Cultivated sp grown worldwide but many of wild sp grow as weeds (N + S America + Australia) 9) Extensive selective breeding has produced large variety of Brassica cultivars 10) Almost all Brassica plant parts have been developed for food 11) Contain high amounts of sulphur containing compounds called glucosinolates - linked to anticancer 12) Most Brassicas can stand some frost + some can stand actual freezing depending upon condition of crop + freeze duration

What is cultivation?

A change in human behavioural ecology that selected for crop domestication traits (began to replace foraging 3,000 to 11,000 years ago)

How can effectors suppress PTI?

Adaptation by specialised pathogens: dozens of effectors manipulate the host - e.g. inhibitors, E3 ligases, proteases - intrinsic activities inside the host cell - often block PTI signalling - effector-triggered susceptibility (ETS) Outcome: host is susceptible! 'Compatible interaction': plant supports life cycle of the pathogen

What is the possible discrepancy between archaeological + molecular data?

Archaeological data suggests multistage process with traits evolving sequentially over thousands of years Molecular data tends to suggest rapid process involving just a few genes

Give an example of a small RNA which targets and degrades plant mRNA

Botrytis cinerea (grey mould) Small, fungal RNA's enter host cells, probably via exosomes to block/degrade specific host transcripts

How else can we edit plant genomes?

CRISPR/cas9

Do domestication genes differ from diversification genes?

Domestication genes (8 of 9): encode transcriptional regulators Diversification genes: more than half (of those of known function) encode enzymes

How can PTI and ETI responses be considered universal?

ETI: Avr gene in one pathogen would trigger effective resistance when expressed by another pathogen (!) PTI: (Likewise, bacterial PAMP triggers effective resistance against fungal/oomycete pathogens)

Describe the foraging lifestyle

Eating wild cereals, seeds, nuts and fruits Gathered from local environment Precarious, seasonal, labour-intensive, only able to support a low density population

What is hybrid breeding?

Exploiting 'hybrid vigour' or 'heterosis' in the first cross (F1) generation Widely used in field vegetables, sugar beet, maize and oilseed rape (not maize/rice) Little understanding of process even now

Give an example of a plant disease caused by bacteria

Fireblight - Pathogen: Erwinia amylovora (Gram(-) bacterium) - Host: apple, pear + other Rosaceae - Famous for: entry of wounds + flowers by rain + bees - Treatment: removal + burning of infected branches/trees

Explain the evolution of crop diversity

Following domestication, selection for culturally desirable traits (often locality specific) expanded diversity e.g. 'naked grain', preferred cooking/processing qualities, desirable visual or gustatory features

What is plant domestication?

Human selection alters the genetic architecture of wild species populations resulting in new forms of plant altered to meet human needs

How much do we know about the genetic nature of the changes from the wild Brassica to the cultivated forms?

In most cases (e.g. cabbage, turnip, Brussel sprout etc) we do not know However, we do know something of the molecular changes that resulted in cauliflower

How can fruit size also be increased (not through less fw2.2)

Increased organ (locule) number A locule is a cavity or compartment within an organ or part of an organism (animal, plant, or fungus)

What are cultivated crops the product of?

Initial domestication and subsequent diversification driven by human selection

How was more successful germination achieved?

Larger grains; larger seeds perform better than smaller seeds following deeper burial in the soil; deeper seed burial is common in soils disturbed by human tillage

Over what spatial scale can induced responses operate?

Local responses -HR Systemic responses - Systemic Acquired Resistance (SAR): induced, broad range, costly, 'adaptive'

What are landraces?

Locally adapted genotypes

How was increased ease of harvesting achieved?

Loss of seed-shattering: the hallmark of domestication in grain crops Loss of seed-shattering renders crop dependent upon humans for propagation and survival Attributed to use of sickle for harvesting (selects for plant seed retention) Mutant alleles favouring loss of shattering identified in rice (sh4 + qSH1) + wheat (Q)

Over what temporal scale are different induced responses used?

Minutes/hours: - Protein phosphorylation cascades - ROS burst - Ion fluxes (pumps Ca across) Hours/days: - Transcriptional reprogramming - Hypersensitive Response (HR, PCD) - SA/Ethylene biosynthesis Days: - Callose deposition - PR proteins -Phytoalexin production

Did domestication happen once: a single time in a single geographic area?

Most studies of neutral DNA variation suggest yes e.g. using DNA fingerprinting However, recent modelling studies suggest that genetic bottlenecks might mask the occurrence of multiple domestication events

What are PAMPs and how are they recognised?

PAMP: Pathogen-associated Molecular Patterns First layer of induced immunity = PAMP perception on cell surface: - By Pattern Recognition Receptors (PRRs) - Activates PAMP-triggered Immunity (PTI) - Universal immune response Outcome: no disease (plant is not a host) No further growth of non-specialised microbes

Give an example of a plant disease caused by a virus

Papaya Ring Spot - Pathogen: Papaya Ring Spot Virus PRSV - Host: papaya + cucurbits - Famous for: Hawaiian papaya production dropped 94% in 1950s - Treatment: transgenic RNAi plants (1998)

What are selective sweeps?

Reductions in nucleotide variation that have resulted from strong selective pressures on particular loci