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3s2: Plant biotechnology > Week 8 > Flashcards

Week 8 Flashcards

1
Q

Why is food culturally important?

A

Food is divine
Food tells us about our culture
Food connect us
Great Famine (Ireland) (1845-1852), Total death: 1 million
Great Chinese Famine (1959 and 1961), Total death: 15-55 millions
Food can create war (hunger

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2
Q

What was on the prehistoric menu?

A

Analyses of Stone Age settlements reveal that the hunters would gladly eat anything they could get their hands on
fish, meat, animal fat, wild plants
The Stone Age menu was widely different depending on the region, climate and season.

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3
Q

What is the history on human food?

A

Control of fire 1.9 mya
Major evolutionary shift to chase down food - 180,000 ya
Development of agriculture - 9,000 ya
Development of modern flour 200 ya

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4
Q

What is agriculture?

A

Agriculture is defined with varying scopes, in its broadest sense using natural resources to “produce commodities which maintain life, including food, fiber, forest products, horticultural crops, and their related services

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5
Q

What is the difference between domestication, cultivation and agriculture?

A

Domestication the morphological (and genetic) changes in plants
Cultivation the human practices (creating an ecology for plants)
Agriculture the cultivation on scales and economic change

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6
Q

How has agriculuture impacted human population?

A

Human population increased from 5-10 millions to 7 billions

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7
Q

How many centres of global crop domestication?

A

16 independant regions of domestication each region having unique crop eg middle east and wheat

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8
Q

What happened as a consequence of the domestication of wheat?

A

Changes to grain size, shape and range of phenotypic variation

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9
Q

What is an overview of climate and agriculture?

A

Temperature fluxuations before but stabalised after 9,000 BP
Wheat was domesticated due to change in middle east temperature from cool and dry to warm and dry

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10
Q

What is an overview of the work of Rachel Carson?

A

Book ‘Silent Spring’ about fertilisers and envriomental and health effects brought about from green revolution

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11
Q

What was the outcome of the work of activists like Rachel Carson?

A

The early activists of the new environmental movement had several successes attributed to Carson — from the Clean Air and Water Acts to the establishment of Earth Day to President Nixon’s founding of the Environmental Protection Agency, in 1970.

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12
Q

What is an overview of the slow food movement?

A

The Slow Food international movement officially began when delegates from 15 countries endorsed this manifesto, written by founding member Folco Portinari, on December 10, 1989.
To promote local more sustainable food

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13
Q

What is an overview of organic farming groups?

A

IFOAM - Organics International
National groups like USDA organic, Australian certified organic

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14
Q

What is the difference between conventional and organic farming?

A

Conventional : Organic
Low soil quality : Higher soil quality
Low biodiversity : Medium biodiversity
High costs medium profit : Medium costs high profit
High pesticide residues : Low pesticide residues

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15
Q

What are the quote by Norman Borlaug about organic farming?

A

There are 6.6 billion people on the planet today. With organic farming we could only feed four billion of them. Which two billion would volunteer to die?

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16
Q

What is the historical evolution of farming?

A

(a) Disciplinary basis of principles articulated within agroecology.
(b) Scales (adapted from Wezel et al. 2009).
(c) Aspects, showing the emergence of the three manifestations of agroecology (science, practice and social movement) with key topics and the nature and scope of research (adapted from Silici 2014, based on Wezel et al. 2009 and Wezel and Soldat 2009).

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17
Q

What is agroecology?

A

The application of ecological principles to agricultural systems and practices, or the branch of science concerned with this

As a scientific discipline, agroecology provides the ecological knowledge that underpins sustainable practices under the other approaches.

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18
Q

What are the subdivisions of agroecology?

A

Conservation agriculture
Regeneration agriculture
Organic agriculture
Climate-shape agricultureW

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19
Q

What are the pillars of agroecology?

A

Envrionmental stewardship
Prosperous social livelihood
Profitable farm income

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20
Q

What are the FAO 10 elements of agroecology?

A

Diversity
Sharing knowledge
Synergies
Efficiency
Recycling
Circular and solidarity economy
Cultural food traditions
Responsible governence
Resilience
Human and social values

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21
Q

What are examples of pratical use of agroecology?

A

Diverse diet
New, Neglected and underutilized crops/plants
Crop rotations and legumes
Integrated Pest Management
Low input farming
Breeding for low input farming
Breeding for pest and diseases
Breeding for Nitrogen Use Efficiency

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22
Q

What is an overview of negelected species?

A

Neglected and underutilized species are those to which little attention is paid or which are entirely ignored by agricultural researchers, plant breeders and policymakers.
They are wild or semi-domesticated varieties and non-timber forest species that are not typically traded as commodities

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23
Q

How does agriculture reduce crops used?

A

~250,000 species of plants
~7,000 crop species throughout history
3 (Rice, maize and wheat) make up >50% of food intake
12 crops that together woth 5 animal species provide 75% of the worlds food intake

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24
Q

What is an overview of Chenopodium quinoa?

A

Was a neglected species from latin america but now is regulary consumed

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25
Q

What is crop rotation?

A

The process of gradually switching the crops that are cultivated in a field to improve soil fertility, manage pests and diseases, and increase yields.
By rotating crops, soil health and production are preserved, nutrient depletion is reduced, pests and diseases are disrupted, and soil health is increased.

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26
Q

What is legume based cropping species?

A

Legumes symbiotic bacteria fix nitrogen
When legumes decompose releases nitrogen into soil boosting fertility

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27
Q

What is integrated pest management?

A

A dynamic process that makes use of an ecological systems approach and encourages the user or producer to consider and use the full range of best pest control options available given economic, environment and social considerations

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28
Q

What is an overview of integrated pest management?

A

IPM is based on ecology, the concept of ecosystems and the goal of sustaining ecosystem functions.
It promotes the growth of a healthy crop with the least possible disruption to agro-ecosystems and encourages natural pest control mechanisms

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29
Q

What are the advantages of integrated pest management?

A

Biological control with natural enemies
Resistant varieties of crops
Greater resilience through intercropping

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30
Q

What is intercropping?

A

The push–pull system mainly consists of intercropping the crop of interest with a plant species that emits volatile organic compounds (VOCs) that repel the major pest. Planting an attractive (pull) plant around the field further enhances directional movements of the pest insect out of the field.

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31
Q

What is an example of intercropping?

A

Cabbage (maincrop) is planted with spring onion (repellent) non-host intercrop plant and with attractive B. vulgaris, Yellow rocket cress (trap plant) as a barrier plant, it reduces the infestation of cabbage by cabbage moth

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32
Q

How does intercropping benefit spring onion?

A

This occurred by repelling away the cabbage moth, that were trying to feed on the cabbage, from the push plant using stimuli that alter the host fragrance and at the same time pull away by the trap plant using highly attractive stimuli

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33
Q

What is the ultimate aim of sustainable farming?

A

Creating farming systems with less chemical inputs/no chemical inputs
How to increase crop yield in low input farming?

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34
Q

What are the pillars of climate smart agriculture?

A

Sustainably increase agriculture productivity and incomes
Adapt and build resilience of people and food system to climate change
Reduce and/or remove greenhouse gas emissions where possible

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35
Q

What is an overview of current plant immunity models?

A

Our current models of the plant immune system are single celled models.

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36
Q

What is an overview of plant immune responses?

A

Plant immune responses are triggered by extracellular recognition of microbe associated molecular patterns, and intracellular recognition of pathogen effectors.
Every plant cell is capable of perceiving a pathogen and mounting defence leading to the plant immune system is cell autonomous.

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36
Q

What is a future expansion of the single cell model?

A

Defence responses trigger dramatic changes to the cellular concentrations of many small signalling molecules and therefore we have to consider the how single cell responses impact on the connected cells.

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37
Q

What are strategies for enhancing defence with resistance genes?

A

Understanding the genes a plant needs to fight off a pathogen
Exploiting these genes by, Introducing them in to susceptible varieties or enhancing or blocking their activity

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38
Q

What are strategy for enhancing defence with other immune responses?

A

Understanding the immune responses a plant triggers to fight off a pathogen eg Systemic acquired resistance/defence priming
Manipulating these responses in other ways triggering gene expression in response to other cues enhancing or blocking the response

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39
Q

What are different genes of Maize with different susceptibility to the same nothern leaf blight?

A

Oh7B - very susceptible
Ki3 - slightly susceptible
M162W - immune

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40
Q

What is an overview of finding resistance genes by QTL analysis?

A

Analysis of the distribution of different molecular markers and the trait of interest in a large segregating population
F2 generation shows variation trait so is used as base as F1 is heterozygous

41
Q

What does recombination frequency show about gene location?

A

When you find low recombination frequency between the trait you’re looking for and the molecular marker then you know the marker is close to the gene that causes the trait

42
Q

What is an overview of LOD score?

A

The LOD score is the logarithm of the odds that the loci are linked by recombination.
Plotting LOD score against the location of known markers allows the location of the gene of interest to be narrowed down

43
Q

When narrow down location, how do you find the gene?

A

If you are working with an organism with a sequenced genome have a look at what is in the vicinity of the most closely linked markers and make an educated guess!
If working with an organism without a sequenced genome you may have to find the gene of interest by genome walking using a series of PCR primers

44
Q

What is genome wide association mapping?

A

A genome-wide association study is an approach that involves rapidly scanning markers across the complete sets of DNA, or genomes, of many organisms to find genetic variations associated with a particular disease

45
Q

What is an overview of GWAS for disease resistance?

A

A novel QTL for powdery mildew resistance in Nordic Spring Barley
Most cultivars showed weak infection (90 score 1, lowest) only 5 that scored 8, highest.

46
Q

What is an overview of SNP array?

A

An array (or chip) is an array of short DNA sequences that encode known SNPs
Genomic DNA is amplified and tagged with fluorescent tag
SNPs that the genomic DNA binds to are marked by fluorescence and read out +/- presence of the SNP in the genomic DNA sample

47
Q

How do you read SNP arrays?

A

The association/correlation between each SNP and the phenotype is calculated and generates a probability of association (p) and used to generate a Manhattan plot
SNPs associated with resistance can be examined alone or in combination

48
Q

How can you find an R gene by forward genetic screens?

A

Mutagenise seed stock using irradiation or chemicals
Screen for increased susceptibility to pathogen
The mutant gene must be required for pathogen resistance and identify gene by QTL mapping or NGS

49
Q

What is the difference between mutagenesis and genetic variation?

A

The identification of the genetic variation is technically the same, the source of the variation is different

50
Q

What can you find with mutagenesis?

A

R genes, PRRs and other genes that have unknown immune function

51
Q

What is an overview of receptor-ligand model for race-specific resistance?

A

One Avr gene gets into cell
Specific R gene binds to Avr gene and triggers immunity

52
Q

What are examples of PRRs?

A

Cf2 contains LRR and TM
Xa21 contains LRR, TM and S/T kinase

53
Q

What are examples of NLRs?

A

RPP5 contains TIR (Toll-interleukin receptor), NBS (nucleotide binding sites) and LRR
RRS1 contains TIR (Toll-interleukin receptor), NBS (nucleotide binding sites) and LRR with WRKY attached

54
Q

What are examples of miscellaneous immune proteins?

A

Pto which is S/T Kinase
RPW8 which is TM and CC domains

55
Q

How can you find NLR proteins using Renseq?

A

Targeted with short oligos which only bind to NLRs after mutagenising them
Done in wheat

56
Q

How can you do after finding NLR proteins with Renseq?

A

Genome mapping and find those which are resisitant which are susceptible
To do this pulled down all seqences and sequences them to corralte presence or presence of SNP to phenotype

57
Q

What is the advantage of using Renseq?

A

Only identify those which are NLRs

58
Q

What are the limitations of using Renseq?

A

Assumptions that oligos are binding to NLR resistance
Genes are tissue and condition dependant, so use RNA instead to give higher resolution

59
Q

How can you find novel resistance to pathogens in Aegiliops tauschii?

A

Find wild populations of Aegilops tauschii and break into accessions
Create an interaction matrix for resistance that each plant has against different races/ species of pathogens

60
Q

How can you translate resistance to pathogens in Aegiliops tauschii to genetics?

A

Perform RenSeq
Correlate the resistance phenotypes with the NLR sequences (k-mers)
Identify which K-mers are assciated with which phenotype

61
Q

What are the pros and cons of using Aegiliops tauschii to NLR proteins?

A

It offers a new source of genes due to it not being involved in crop wheat genotype
Cant be bred it so must use genetic tools eg GM crop

62
Q

What is a problem immune genes in responding to pathogens?

A

Single genes can be relative easily overcome as pathogens which have a fast rate of evolution
Wheat stem rust strain Ug99 broke Sr31 in 1999 deployed in late 70s, only resistance gene

63
Q

How can you reduce rate of pathogens overcoming immune genes?

A

‘gene stacking’
The combining multiple resistances genes in single varieties, increase the evolutionary barrier to overcome
Easier to use by new methods such as golden gate cloning

64
Q

In the five-transgene casette in wheat to fungal rust pathogen what genes were their?

A

Sr55 - hexose sugar transport
Sr22 - NLR
Sr35 - NLR (coiled-coil)
Sr45 - NLR
Sr50 - NLR

65
Q

What was the generation of the five-transgene cassette?

A

Stacked by modular cloning, within left and right border region
So they are added to a single stack

66
Q

Why do all the genes in the five-transgene need to be on a single construct?

A

For ease of cloning/generation
To ensure they are on a single locus
Closer together the lower the recombination frequency

67
Q

What is an overview of the effect of gene stack?

A

The gene stack worked, but we need to wait to see how pathogen evolution responds

68
Q

What is an alternative NLR enfineering?

A

Pathogen effectors can bind integrated domains of NLRs (e.g. HMA domain)
If we can engineer these integrated domains to recognize other pathogen molecules we can generate novel resistance. therefore GMA removed Pik-2 Helper NLR

69
Q

What happens to FLS2 in absence of flagellin?

A

FLS2 and BAK1 interact BIK1, and BAK1 interatcs with and phsophorylates BIR2

70
Q

What happens to FLS2 in presence of flagellin?

A

Flg22 binds to FLS2, the BAK1-BIR2, complex dissociates and FLS2
Flg22 and BAK1 form a heterodimeric complex
BAK1 phosphorylates BIK1 and BIK1 phosphorylates both FLS2 and BAK1

71
Q

How doe elf18 trigger immunity?

A

EFR recognises elf18 (Elongation factor)
EFR binding to elf18 triggers rapid burst of ROS production

72
Q

What is an overview of EFR biotech in tomato?

A

Tomato lacks EFR, so put in arabidopsis EFR
When elf18 was put in mutant ROS burst occcured but not in wildtype
Gave tomatoes resisance to Ralstonia solanacarum

73
Q

What happens downstream of PRRs?

A

Cytoplasmic kinase promote downstream signalling eg promote callose deposition

74
Q

What is systemic acquired resistance?

A

Systemic acquired resistance (SAR) is a mechanism of induced defense that confers long-lasting protection against a broad spectrum of microorganisms

75
Q

What primes systemtic acquired resistance?

A

Harmless microorganisms
Chemicals eg SA and SA analogous such as Beta-aminobutyric acid
Peptides sich as flg22 a flagellin derivative

76
Q

What is biocontrol?

A

THe use of other organisms to ward off pathogenic microorganisms and disease

77
Q

How can plants and microbes promote immunity?

A

Biocontrol PGPR are recruited via plant exidates
These bacteria then trigger Induced systemic resistance

78
Q

How do biocontrol PGPR reduce infection?

A

Produce antibiotics that kill pathogens (though pathogens do the same)
Compete with pathogen

79
Q

What is banangeddon?

A

Plant disease (Fusarium) threatening banana supply, famous in Australia
Made worse by banana being made by clonal expansion so no genetic diversity

80
Q

Why are bananas infertile?

A

They are triploid
Also makes inheritance for potential genetics hard

81
Q

What genes were put into cavendish to make them Fusarium oxysporum death?

A

RGA2 is an NLR
Ced9 (anti-apoptosis gene from nematodes)
Inserted with traditional agrobaterium method

82
Q

What are the phenotypes of cavendish grown with Fusarium oxysporum?

A

Wildtype - wilt
RAG2 - no wilt
Ced9 - no wilt

83
Q

What is an overview of Fusarium disease?

A

A vascular colonising disease
Causes wilt because fungus block xylem preventing leaves from getting water

84
Q

What is an overview of RAG2 lines and Fusarium oxysporum resistance?

A

RAG2-4 - consistant high infection like wildtype eg 2015 60% infected
RAG2-5 - consitant level of low infection with 2012 to 2015 15% infected

85
Q

What is an overview of Ced9 lines and Fusarium oxysporum resistance?

A

Ced9-17 - match wiltype with 90% infected in 2015
Ced9-21 0% infected throughout 2012 to 2015 study

86
Q

How does Ced9 promote immunity?

A

Overcoming tissue necrosis is the most ideal method to avoid Fusarium multiplication and spread in banana.
Oxidative stress-induced cell necrosis is prevented by the activation of antiapoptotic pathways by Ced-9

87
Q

Why do same lines of Ced9 and RAG2 have different effect?

A

Location and expression of gene is random luck so multiple is needed to account for this

88
Q

What is an overview of magainin?

A

Antimicrobial peptide, from skin secretion of african clawed frog

89
Q

What was the transformation of magainin?

A

The convential structure with NPTII antibiotic resistance and UBQ3 promtor, high level plant promoter
Made two variation internal cell production and produced in cell but expelled through secretion by secretory signal

90
Q

What did they test magainin induced resistance in tobacco?

A

Necrotrophic pathogens Sclerotinia and Alternaria which both showed resistance with the secretory signal

91
Q

What is an overview of secreted vs non secreted magainin in banana?

A

Plant 168, secreted, and showed less colonisation
Plant 164, not secreted, and showed less colonisation
Both exposed to Fusarium oxysporum

92
Q

What is are important banana rhizosphere bacteria?

A

Pseudomonas fluorescens strain Pf1
Bacillus subtilis strains 10 and 56

93
Q

How did control vs symbiotic bacteria impact number of leaves?

A

Control - 5
Symbiotic bacteria 1 min - 9
Symbiotic bacteria 5 mins - 11

94
Q

How did control vs symbiotic bacteria impact plant height?

A

Control - 4.3 cm
Symbiotic bacteria 1 min - 6.8 cm
Symbiotic bacteria 5 mins - 7.3 cm

95
Q

How did control vs symbiotic bacteria impact photosynthetic rate?

A

Control - 15.1 umol CO2 m^2 s^-1
Symbiotic bacteria - 26.1 umol CO2 m^2 s^-1

96
Q

How did control vs symbiotic bacteria impact on chitanase production?

A

Control - 35.4
Symbiotic bacteria - 96.3

97
Q

How did control vs symbiotic bacteria impact on Beta-1,4 glucanase production?

A

Control - 103
Symbiotic bacteria - 218

98
Q

How did control vs symbiotic bacteria impact % disease index?

A

Control - 18.5%
Symbiotic bacteria - 79.2%

99
Q

How did control vs symbiotic bacteria impact banana bunch weight?

A

Control - 10.7 kg
Symbiotic bacteria - 20.8 kg

3s2: Plant biotechnology (9 decks)

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