Generating more and better food Flashcards
1
Q
How did ancient Mesoamerican farmers transform teosinte into modern maize?
A
- 6,000-10,000 years ago, ancient Meso-American farmers changed the teosinte through selection.
2
Q
Name 3 agronomical characteristics selected for in crops.
A
- Higher yields
- Improved morphology of fruits and seeds (e.g., seedless grapes)
- Easier cultivation (e.g., easier harvest)
3
Q
Name 3 food quality/processing characteristics selected for in crops.
A
- Improved nutrients and flavor (e.g., purple tomatoes, improvement of protein and Omega-3 Fatty Acid in soybean)
- Reduced toxicity (e.g., potatoes which produce less acrylamide)
- Extended shelf life (e.g., blueberries with longer shelf life)
4
Q
Name an environmental trait selected for in crops.
A
- Adaptation to environment (e.g., drought, temperature, and resistance to pests = less pesticides = safer foods)
Has been neglected in the past, but is becoming more important.
5
Q
Natural selection
A
Historically performed by humans based on what available in nature
6
Q
Historically performed by humans based on what available in nature
A
Natural selection
7
Q
What is modern plant breeding?
A
- Based on the principles of heredity
- Darwin’s theory of evolution and natural selection (mid 1800s) and Mendel’s basic principles of heredity (mid 1800s) allow us to apply the principles of heredity and the knowledge of genetics and chromosomes to use the genetic variation (biodiversity) available in a species
- Molecular techniques for the selection of the best plants
Traditional breeding (does not include genetic modification, but may involve things like biomarkers)
8
Q
Mutation breeding
A
Induction of mutations on the genomes to generate new plants from existing plants
9
Q
Induction of mutations on the genomes to generate new plants from existing plants
A
Mutation breeding
10
Q
Transfer of genes from a species to another using lab techniques.
A
Genetic engineering
- Transfer of genes from a species to another using lab techniques. In 1970, Agrobacterium was modified to be non harmful for plants.
- In 1988 first GE crop was tested in the field (Tomato FLAVR SAVR, late ripening).
- In 1994 it was in the commercial market.
11
Q
Genetic engineering
A
Transfer of genes from a species to another using lab techniques.
- Transfer of genes from a species to another using lab techniques. In 1970, Agrobacterium was modified to be non harmful for plants.
- In 1988 first GE crop was tested in the field (Tomato FLAVR SAVR, late ripening).
- In 1994 it was in the commercial market.
12
Q
What is crucial for improving crops?
A
Genetic variation
13
Q
What does genetic variation arise from? [3]
A
- Hybridization: Recombination of alleles (variants of a gene) through sexual reproduction, introgression of genes from another species
- Mutation (changes in the DNA sequence)
- Genetic engineering.
14
Q
How is hybridization used to breed new plant varieties?
A
- Hybridisation between a donor (parent 1) and a recipient (parent 2), can be within or among species
-
Selection of the desired progeny
Eventually… - Backcross (cross of the new plant) to the recipient line (recurrent/good parent) for restoring the genome content and the phenotype of the recipient
15
Q
What does this photo show?
A
- Two siblings from the same crossing
(hybridization between a commercial
variety of grape and a variety that is
resistant to a pathogen [downy
mildew].) - One sibling is susceptible (left
picture), one sibling is resistant
(bottom)
16
Q
Name 3 common phenotyping agronomical traits in grapes.
A
- Vigour
- Yield
- Cluster architecture
17
Q
How are enological phenotype traits selected for in wine grapes?
A
- Microvinification (a winemaking technique used often for experimental batches of wine where the wine is fermented in small, specialized vats)
- HPLC & GC-MS analyses
- Wine tasting
Take home message: breeding a new grape variety requires 10-15 years of work if we are lucky!
18
Q
How can recombination of alleles through sexual reproduction create a new variety with desirable traits?
A
- Recombination of alleles (variants of a gene) through sexual reproduction within a species
19
Q
Meiosis generates […]
A
Meiosis generates new allele combinations in the gametes
20
Q
Describe the formation of gametes in the paternal line (Cabernet franc).
A
Not all the gametes (i.e., pollen genes) have the colour gene due to recombination.
21
Q
Describe the formation of gametes in the maternal line (Formation of gametes in the maternal line (Sauvignon blanc).
A
Not all gametes have the aroma gene.
22
Q
Describe the breeding of the maternal and paternal lines and selection of progeny.
A
- Lots of variation
- The ‘problem’ of hybridization - what you obtain might be very different from the original plant.
- But when we find a plant we like we can clone it infinitely (i.e., take a branch and put it in dirt and it will grow; much easier than cloning an animal)
23
Q
Describe the effect of crossing over on two genes located in the same chromosome
A
Not all gametes have the alleles we are looking for; gametes produced will have new combinations of alleles.
24
Q
Describe why not all the gametes have the alleles we are looking for.
A
Crossing over and recombination (i.e., independent assortment)
25
How do crossing over and recombination affect the chances of obtaining the desired combination of alleles?
Shuffling of alleles due to **crossing over and recombination**, imply lower chances to obtain the “wanted” combination of alleles.
26
What are the problems of traditional breeding?
* We have thousands of genes that recombine in a random fashion
* Wide hybridization introduces many potentially negative genes combinations in order to obtain one desirable gene trait
* We have to eliminate undesired traits introduced by recombination
* Backcrossing of the new selection with the recurrent (good) parent
27
What is traditional breeding?
Crossing individuals with desirable characteristics and selecting
among the progeny
## Footnote
Concerns with how long traditional breeding takes, and how much space & resources are required.
28
What challenges arise when recombining alleles through sexual reproduction between interfertile species?
* Lots of unwanted traits may be inherited along with desired traits.
* Wide hybridization introduces many potentially negative gene combinations to obtain one desirable gene trait.
29
Why is backcrossing of the new selection with the recurrent (good) parent necessary?
* We have to eliminate undesired traits introduced by recombination
* Back-crossing of the new selection with the recurrent (good) parent
30
What are the pros of hybridization (traditional breeding)? [2]
* It applies to **all traits**, provided that the source of improved trait and the recipient are interfertile
* **No knowledge** is required on the genetic control of the trait.
31
What are the cons of hybridization (traditional breeding)?
* Meiosis and **crossing over** cause a **random assortment** of parental chromosomes and alleles, the parental genotype (and phenotype) cannot be recovered in filial generations
* The donor transmits **half of its genome** to the progeny (in addition to the gene/s that control the trait under improvement)
* Backcrossing may be required for recovering most of the recipient genome, if long seed to seed cycle, the **backcrossing process is long**
32
What is a molecular marker? [2]
* A molecular marker is a molecule (normally a specific DNA sequence/feature) of an organism that can be used to reveal certain characteristics about the organism.
* A fragment of DNA that is **associated with a certain location within the genome**.
33
What are the advantages of molecular breeding using Marker Assisted Selection (MAS)? [4]
* Using molecular biology (the genotype) to help select the progeny
* Improve efficiency and speed up screening methods
* Simultaneous selection for multiple traits
* Screening not based on the phenotype and hence not affected by environmental factors
## Footnote
Requires knowledge on the control of traits.
34
What is a nontransgenic approach to increase genetic variation?
Mutagenesis - creation of genetic variants by introducing mutations
## Footnote
Mutation is the permanent alteration of the nucleotide sequence of the genome of an organism.
35
Define: mutation.
The permanent alteration of the nucleotide sequence of the genome of an organism.
| A change in the genome sequence of an organism.
36
# Describe the approach.
Mutagenesis - creation of genetic variants by introducing mutations
## Footnote
Mutation is the permanent alteration of the nucleotide sequence of the genome of an organism.
A **nontransgenic approach** to increase genetic variation
37
The permanent alteration of the nucleotide sequence of the genome of an organism.
Define: mutation.
38
What is a transgenic approach to increase genetic variation?
Genetic engineering - introduction of one (or a few) foreign 'good' genes into the best accepted cultivar using **horizontal gene transfer**
| Agrobacterium transformation; biolistic
## Footnote
1970s to present day
39
Genetic engineering - introduction of one (or a few) foreign 'good' genes into the best accepted cultivar using **horizontal gene transfer**
Transgenic approach to increase genetic variation
## Footnote
1970s to present day
40
Define: horizontal gene transfer
Movement of genetic material between unicellular and/or multicellular organisms rather than transmission of DNA from parent to offspring (Vertical Gene transfer).
41
Movement of genetic material between unicellular and/or multicellular organisms rather than transmission of DNA from parent to offspring (Vertical Gene transfer).
Define: horizontal gene transfer
42
Define: spontaneous mutation
Occurs without treatment of the organism with an exogenous mutagen.
## Footnote
These mutations are rare.
43
Define: induced mutation
Occurs due to the treatment of a plant or plant parts such as seed, stem, cuttings, pollen, and ovules with the mutagens.
| This treatment increases the frequency of mutations.
## Footnote
Induced mutation or mutagenesis is the sudden heritable change in the genome of an organism (not caused by genetic recombination or segregation) but induced by physical, chemical, or biological agents.
44
Occurs without treatment of the organism with an exogenous mutagen.
## Footnote
These mutations are rare.
Define: spontaneous mutation
45
Occurs due to the treatment of a plant or plant parts such as seed, stem, cuttings, pollen, and ovules with the mutagens.
## Footnote
This treatment increases the frequency of mutations.
Define: induced mutation
## Footnote
Induced mutation or mutagenesis is the sudden heritable change in the genome of an organism (not caused by genetic recombination or segregation) but induced by physical, chemical, or biological agents.
46
Define: mutagen.
A chemical or physical agent that causes mutations.
## Footnote
Frequency of mutations generated is higher than spontaneous level.
47
What is ethylmethane sulfonate?
A common chemical agent that alters the base-pairing properties of the modified nucleotide and so leads to **point mutations**
48
What are the 4 types of point mutations?
* Synonymous (a.k.a. silent)
* Nonsynonymous (a.k.a. missense)
* Nonsense
* Readthrough
49
What is a synonymous mutation?
a.k.a. silent mutation
* Nucleotide change results in no change of the amino acid or amino acid functionality
50
Synonymous mutation
a.k.a. silent
51
Nonsynonymous mutation
a.k.a. missense
52
What is a nonsynonymous mutation?
a.k.a. missense mutation
* Nucleotide change results in a codon that codes for a different amino acid
53
Nonsense mutation
54
What is a nonsense mutation?
A sense codon is changed to a termination codon
55
Readthrough mutation
56
What is a readthrough mutation?
A termination codon is changed to a sense codon
57
What is a radiation induced mutagenesis?
* Radiation can generate base modifications and single or double strand DNA breaks.
58
What are some different types of mutagens?
59
What are the pros of mutation breeding? [3]
* Accelerates the process of developing traits for selection (is generally quicker than hybridization)
* Maintain the general genetic background of a genotype
* Can generate new alleles that are not present in nature for that plant
60
What are the cons of mutation breeding? [2]
* It is a random/non targeted process
* Large libraries of mutants are required
61
Describe how mutation breeding is used in plant breeding. [2]
1. Seeds, cuttings or the shredded leaf of a plant tissue are irradiated (e.g., gamma rays); alternatively treated with chemicals
2. The irradiated material is cultivated or planted and individual plants are picked and examined.
| 1930s to present day
62
Mutagenesis has been [...]
widely used to generate new plant varieties/cultivars
63
Describe mutagenesis in agriculture.
There are more than 3,000 mutant varieties officially released for commercial use in more than 210 plant species from more than 70 countries.
64
Define: transgenesis
Insertion of recombinant genetic elements in which one or more components (gene, promoter, and terminator) are taken from sexually incompatible gene pool.
65
Define: cisgenesis.
Insertion of an identical copy of a complete genetic element, including gene, promoter, and terminator from the same gene, within the sexually compatible gene pool.
66
Define: intragenesis
Insertion of recombinant genetic elements in which one or more components (gene, promoter, and terminator) are isolated from **different genes within the sexually compatible gene pool**.
67
Define: genome editing.
Introduction of targeted mutation at specific loci in the genome.
68
Insertion of recombinant genetic elements in which one or more components (gene, promoter, and terminator) are taken from sexually incompatible gene pool.
Define: transgenesis
69
Insertion of an identical copy of a complete genetic element, including gene, promoter, and terminator from the same gene, within the sexually compatible gene pool.
Define: cisgenesis.
70
Insertion of recombinant genetic elements in which one or more components (gene, promoter, and terminator) are isolated from different genes within the sexually compatible gene pool.
Define: intragenesis
71
Introduction of targeted mutation at specific loci in the genome.
Define: genome editing.
72
What are the four basic steps for making a genetically modified plant?
1. Identify a gene of interest (whatever organism)
2. Place gene of interest into a vector (e.g., plasmid)
3. Transfer plasmid into plant cells using agrobacterium-mediated transformation or gene gun (biolistic)
4. Generate a new plant from transformed cells.
73
What is *Agrobacterium tumefaciens*?
Soil bacterium that infects plants through wounds and openings; induces tumour-like growth or gall on the infected plant using horizontal gene transfer.
| Our good friend!
74
Why is *Agrobacterium tumefaciens* considered 'Nature's Genetic Engineer'?
75
How does *Agrobacterium* introduce a foreign gene into a plant?
Tumor inducing plasmid (Ti)
76
What are the components of the Tumor Inducing plasmid? [4]
* **Acetosyringone receptors** – Leads bacteria towards the plant wound
* **Virulence** - Excise the T-DNA region of the plasmid and promote its transfer and integration into the plant genome
* **Plant growth hormones** - Stimulates undifferentiated growth
* **Genes for opine biosynthesis** - Provide Energy
## Footnote
*Agrobacterium tumefaciens* is 'Nature's Genetic Engineer'.
77
How do we use *Agrobacterium* to introduce a foreign gene into a plant?
* We replace the tumor producing genes with other genes.
* New foreign genes can be carried as passengers when the T-DNA integrates into the plant genome.
* No tumors are formed (**disarmed Ti Plasmid**)
78
What kind of genes can be added to T-DNA to use *Agrobacterium* to introduce a foreign gene into a plant? [3]
* Selectable markers (Kanamycin / Hygromycin)
* Genes for crop improvement (nutritional value and insect resistance)
* Any other DNA sequence
79
Describe the making of a GM plant in the lab using *Agrobacterium*.
* Discs removed from leaf
* Leaf discs incubated with genetically engineered *Agrobacteria* for 24 hours
* Selection medium only allows plant cells that have acquired DNA from the bacteria to proliferate (e.g., grown on media with kanamycin - genetically engineered DNA will contain kanamycin resistance)
* Shoot-inducing medium (i.e., contains specific hormones)
* Transfer shoot to root-inducing medium
* Grow up rooted seedling
* Adult plant carrying transgene that was originally present in the bacteria
80
What is Kanamycin resistance?
An example of **selectable marker** used to understand if the
transformation is successful.
81
What is an example of selectable marker used to understand if the transformation is successful?
Kanamycin resistance
82
What is an alternative to *Agrobacterium*?
The gene gun
## Footnote
The term **biolistic** refers to a method of gene transfer in which DNA is physically delivered into cells using high-velocity particles, typically metal (like gold or tungsten) coated with the genetic material. The technique is commonly known as **gene gun** or particle bombardment. It is used in genetic engineering to introduce new genes into plants, animals, and even microorganisms. This method is especially useful for organisms that are difficult to genetically modify using other techniques like viral vectors or chemical treatments.
83
Why are alternatives to *Agrobacterium* necessary?
Monocot plants are not very susceptible to bacterial infection, in that case we use the gene gun.
## Footnote
The term **biolistic** refers to a method of gene transfer in which DNA is physically delivered into cells using high-velocity particles, typically metal (like gold or tungsten) coated with the genetic material. The technique is commonly known as **gene gun** or particle bombardment. It is used in genetic engineering to introduce new genes into plants, animals, and even microorganisms. This method is especially useful for organisms that are difficult to genetically modify using other techniques like viral vectors or chemical treatments.
84
Describe biolistics in action.
* Helium chamber
* Rupture disc
* Macrocarrier
* DNA coated gold particle
* Stopping screen
* Focusing device
* Target tissue
85
What is European Corn Borer *Ostrinia nubilalis*?
* Feeds on over 250 different kinds of plants
* In corn, causes the plant and the kernels to fall
* Big toxin issues
* In U.S., control and yield loss combined exceed $1 billion annually
86
What is *Bt* corn?
* *Bt* stands for *Bacillus thuringiensis*, which is a soil-dwelling microorganism that contains the *Bt* toxin
* *Bt* corn is genetically engineered to produce the CRY protein (crystal protein), precursor to the *Bt* toxin.
87
How does *Bt* corn work?
* *Bt* Corn is accomplished through inserting the CRY gene from *Bt*.
* This allows the plant to produce CRY proteins all by itself.
* When ingested by an insect, insect digestive enzymes activate the toxic form of the crystal protein.
* The digestive system of the insect crystallizes and the insect starves to death.
88
What are the benefits of *Bt* corn? [2]
* Protection by *Bt* corn is as good, if not better, than that provided typical commercial insecticides.
* Normal spray-on *Bt* insecticide is subject to inconsistency due to degradation from UV radiation, desiccation sensitivity, incomplete coverage of fields, and a diminished effect on older larva.
89
What are the drawbacks of *Bt* corn? [3]
* *Bt* corn is more expensive
* Does not have an effect on aphids, spider mites, black cutworm, western bean cutworm, rootworms, wireworms, white grubs, seedcorn maggots, and seedcorn beetles.
* In 1998, StarLink *Bt* Corn (resistance to glufosinate, and a variant of the *Bt* protein called Cry9C) was prohibited for human consumption and allowed only for animal feed by the US government because of the possibility of allergic reactions for humans. In 2000, StarLink corn were detected in taco shells, recall
of Taco Bell-branded taco shells.
90
What are the pros of genetic engineering? [4]
* The donor genotype can be a taxonomically distantly related organism
* Rapid, no backcrossing required
* The background genome of the recipient genotype remains intact
* Multiple traits can be introduced without altering the genetic background
91
What are the cons of genetic engineering? [4]
* It applies to monogenic traits
* Knowledge of the causal gene is necessary
* Ecological impact: e.g. gene flow via pollen from GM crops to wild relatives
* Not always accepted by the society!
92
Domestication and breeding of crops [...]
started thousands of years ago and continue with more advanced technologies
93
Multiple traits of interest some of them have/will have [...]
a direct impact on food science
94
Major strategies for improving crops are: [3]
* hybridization
* mutagenesis
* genetic engineering (cis-genesis is a new tool)
| They are all currently adopted.
95
Genetic engineering strategy adoption depends on multiple factors including: [3]
* type of trait
* type of plant
* market acceptance
96
Describe the traits of commercialized genetically modified crops. [5]
* Insect resistance
* Abiotic stress tolerance
* Disease resistance
* Herbicide tolerance
* Nutritional improvement
97
What percentage of the world's arable land was used for GM crops in 2015, and which countries were the leading producers?
* In 2015, GM crops were grown in 28 countries and on 179.7 million hectares – that is over 10% of the world’s arable land and equivalent to seven times the land area of the UK.
* The USA, Brazil and Argentina are the leading producers.
98
Discuss the controversy on genetically modified plants.
* Scientists generally agree - GMOs are great.
* Consumers generally agree - GMOs are bad.
99
Define: phenotype
Consequence of the interaction between the plant genetic background (i.e., genotype) and the biotic and abiotic conditions experienced by the plant in its growing environment.
100
Define: phenotyping
The process of characterizing plant traits in detail.
101
Consequence of the interaction between the plant genetic background (i.e., genotype) and the biotic and abiotic conditions experienced by the plant in its growing environment.
Define: phenotype
102
The process of characterizing plant traits in detail.
Define: phenotyping
103
Define: genotype
The plant genetic background; also used to refer to individuals with distinct genetic background
104
Define: genotyping
The analysis of **variations** in genomes between individual organisms.
105
The plant genetic background; also used to refer to individuals with distinct genetic background
Define: genotype
106
The analysis of **variations** in genomes between individual organisms.
Define: genotyping
107
Give an example of a hybridization based marker.
Restriction Fragment Length Polymorphisms
| 1980s
## Footnote
Based on restriction enzymes for DNA; nobody is using this technology anymore.
108
Give examples of PCR-based markers. [3]
* Random amplified polymorphic DNA (1990s)
* Amplified fragment Length polymorphism (mid 1990s)
* Simple-sequence repeat (1990s, 2000s) - microsatellites!
| 1990s
109
Give an example of a sequence targeted marker.
Single nucleotide polymorphism
| 2000s onward
110
What is a SNP marker? [2]
* A single nucleotide polymorphism, or SNP ('snip'), is a variation at a single position in a DNA sequence among individuals
* Occurs in more than one percent of the general population
111
Define: genetic mapping
* Statistical methods that link certain complex phenotypes to specific regions of chromosomes
* Genome-wide association mapping is one such method (usually abbreviated as GWAS; genome-wide association study)
| (each dot in graph represents a SNP; numbers are chromosome #)
## Footnote
The threshold line shows which SNPs are associated with the trait of interest.
112
What is the pH differential method?
* Widely used method for the deterination of total anthocyanins
* Leverages the absorbance of different anthocyanins at different pHs
