Rise of Agriculture and GMO Methods

____ is deliberate management of plants that do not differ from wild populations

cultivation

____ is genetic changes in plant populations as a result of the cultivation and selection by people

domestication

_____ is selection for wanted characteristics

domestication

consistent properties of domesticated plants include:

_____ grain

seeds that _____ easily from the seed coat

_____ stalk

loss of _____

larger, separate, thick/simpler, natural seed dispersal

water, fertilize, protect from pests are examples of _____

cultivation

during maize domestication, ____ size increased

cob

the ____ around many grains were eliminated

hard casing

decrease in ____ and increase in ____ were also selected for

branching, seed size

plants became more and more dependent on _____ and vice versa

people

wild shattering grain (brittle rachis) advantage

maximizes speed dispersal

non-shattering grain (tough rachis) advantage

facilitates harvesting

for a long time, the thought was that the switch to agriculture was rapid, taking about ____ years

200

people were harvesting and eating plants long before the rise of agriculture…. at more than the opportunistic level:

_____ from 12,000 years ago

_____ from 23,000 years ago

_____ from 105,000 years show evidence of some reliance on grass seeds

sickle blades, grindstones, stone tools

hunter/gatherer society: population, mortality, offpsring

small, high, fewer

agricultural society: population, mortality, offpsring

large, lower, more

hunter/gatherer social society

little accumulation of wealth

agricultural social society

currency and politics

agriculture facilitated the population explosion of

homo sapiens

____ times increase in past 100 years (population boom)

4

people and their domesticated animals make up 97% of

vertebrate biomass

a GM crop is a plant whose _____ has been deliberately altered using genetic engineering — either to improve an _____ trait or to introduce a _____ trait that the plant wouldn’t otherwise have

genome, existing, brand new

_____ is a gene that has been inserted into an organism genome from another source

transgene

transgene is a gene that has been inserted into an organism genome from _____

another source

a plant carrying a transgene is called a

transgenic plant

transgenes can come from (5)

bacteria, viruses, fungi, unrelated plants, animals

_____ different transgenic events approved for cultivation in 32 crops worldwide

525

_____ hectares of transgenic crops grown globally in 2018, up to 1.7 million in 1996

191.7 million

change the gene → change the ____ → change the ____

protein, trait

four ways to modify a genome

transgenesis, cisgenesis, intragenesis, genome editing

_____ is inserting a gene from a different (sexually incompatible) series

transgenesis

____ is inserting a complete natural gene from the same or a compatible species

cisgenesis

____ is mix and match gene parts within the same compatible gene pool

intragenesis

_____ uses molecular “scissors” (like CRISPR) to edit existing DNA directly

genome editing

a foreign gene (the ____), often from bacteria, viruses, or unrelated plants, is inserted into a crop’s ____ using a _____ method

transgene, genome, delivery

transgenesis:

1. ____ the gene

2. _____ the gene

3. ____ into the genome

4. select and ____

identify, deliver, insert, grow

transgenesis: identify the gene

find a gene that produces a ______ (bacterial gene that makes an insectidal protein)

useful trait

transgenesis: deliver the gene

most commonly via _____, a soil bacterium that naturally inserts its _____ into plant cells

agrobacterium tumefaciens, own DNA

transgenesis: insert into genome

the transgene becomes a _____ part of the plant’s DNA, passed onto _____

permanent, offspring

transgenesis: select and grow

plants that successfully took up the transgene are (3) for the new trait

identified, grown, tested

_____ is the most widely planted GM trait in the world

herbicide-tolerant crops

herbicide-tolerant crops — the problem:

weeds compete with crops for (3). herbicides kill weeds but can also the ____

water, nutrients, sunlight

crops

herbicide-tolerant crops — the fix:

insert a gene that makes the crop _____ to a specific herbicide (like _____). now farmers can spray the ____ field (____ die, the ____ survives)

immune, glyphosate, whole, weeds, crops

herbicide-tolerant crops — how glyphosate works:

it blocks an enzyme (_____) plants need to make certain _____. the transgene codes for a version of ____ that glyphosate can’t _____

ESPS, amino acids, ESPS, block

__% of all transgenic crop area worldwide is planted with herbicide-tolerant varieties

47

38% of farmer profit gains from glyphosate-resistant soybean came from _____, not just cost savings

increased yield

bt crops (insect resistance):

bacillus thuringiensis (____) → cry protein (____) → insect pest (____)

soil bacterium with cry gene, insecticidal toxin, dies after feeding

bt crops (insect resistance):

_____ (soil bacterium with cry gene) → _____ (insecticidal toxin) → _____ (dies after feeding)

bacillus thuringiensis, cry protein, insect pest

bt crops (insect resistance) — mechanism:

the _____ gene from bacillus thuringiensis (Bt) is inserted into the crop. the plant produces the cry protein in its _____. when a susceptible insect eats the plant, the cry protein binds to receptors in the insect’s ____, creating ____ in the gut lining — leading to paralysis and ____

cry, tissues, gut, pores, death

bt crops (insect resistance) — why its considered safe for humans:

the cry protein only binds to receptors found in certain _____, not in mammals. _____ was the first commercial crop to use this technology

insects’ digestive systems, cotton

_____: a complete, natural copy of a gene — including its own ____ and ____ (its “on/off switches”) is taken from the crop species itself or a sexual compatible relative, and inserted back in

cisgenesis, promoter, terminator

unlike transgenesis, _____ crops contain ONLY genetic material that could have theoretically have arrived there through ______ (just done more ____ and ____). no ____ DNA

cisgenic, traditional breeding, fast, precise, foreign-species

cisgenesis real examples:

_____ resistance in potato

_____ resistance in apple

high ____ activity in barely (improces nutrient availability)

late blight, scab, phytase

no cisgenic crop has been _____ yet, but regulators in the ____ consider cisgenic plants’ risk similar to ____ plants

commercialized, EU, traditionally bred

____ is when genetic elements (gene, promoter, terminator) all come from the same species or compatible relatives but they’re ______ in new ways. a gene’s “on/off switch” might come from a completely _____ gene than the one it’s attached to now

intragenesis, recombined, different

innate potato uses ____ to silence (turn off) four of its own genes

intragenesis

innate potato:

asn1: less ___ → less ____ (potential carcinogen) forms when fried

asapragine, acrylamide

innate potato:

ppo5: less _____ → less _____

polyphenol oxidase, black-spot bruising

innate potato:

PhL and R1: less ____ → further reduces _____ formation

reducing oxidase, acrylamide

innate potato results in a potato with improved ____ and a ____ cooked product, using only the potato’s _____

shelf life, healthier, own genes rearranged

sexually INCOMPATIBLE species (bacteria, virus, unrelated plant)

transgenesis

gene, promoter, terminator can all be from the foreign source

transgenesis

same species OR sexually compatible relative

cisgenesis and intragenesis

complete natural gene WITH its own original promoter and terminator

cisgenesis

gene, promoter, terminator can be MIXED from different genes within the gene pool

intragenesis

genome editing is precisely cutting and editing a plant’s existing ____, often without adding any ____ at all

DNA, foreign genes

a genome editing tool finds a specific, exact spot in the DNA and makes a cut (called a _____). the cell’s own ____ process then fixes the cut, often introducing the desired ____

double-strand break (DSB), repair, change

ZFNs stands for

zinc finger nucleases

ZFNs is ___ based, ____ generation, expensive and hard to ____

protein, first, customize

TALENs is ____ based, more ____ than ZFNs but still ____ to engineer

protein, precise, complex

CRISPR/CAS9 uses a short guide ____ + ____ protein

RNA, Cas9

____ is cheap, fast, and easy to redesign for new targets

CRISPR/Cas9

CRISPR/Cas:

1. ____ finds the target

2. ____ makes the cut

3. ____ repairs the cut

guide RNA, Cas9, cell

CRISPR/Cas9 — guide RNA finds the target:

a short single guide RNA (sgRNA), about ___ nucleotides, is designed to ____ a specific DNA sequence in the genome

20, match

CRISPR/Cas 9 — Cas9 makes the cut

the Cas9 protein, guided by _____, binds to the matching DNA and cuts both strands, creating a ______

sgRNA, double-strand break

CRISPR/Cas 9 — cell repairs the break

the plant’s own repair machinery fixes the cut and in doing so, can knock out a ____, fix a ____, or insert a ____

gene, mutation, new sequence

why CRSIPR took over: cheap, simple to design, and easy to retarget for new genes (no ____ needed)

protein re-engineering

NHEJ stands for

non-homologous end joining

____ is the cell’s quick fix (error prone, no template needed)

NHEJ

____ is the cell’s precise fix (uses a template to repair the cut)

HDR

HDR stands for

homology-directed repair

NHEJ often causes ____ at the cut site

small insertions or deletions

____ can shift the gene’s reading frame, effectively knock the gene OUT (turning it off)

NHEJ

use ____ when silencing a gene you don’t want active (browning enzyme in potatoes)

NHEJ

____ can produce exact point mutations (correcting or introducing a specific change)

HDR

HDR can insert a whole new ___ or ____ at the cut sit

gene, genetic element

use ___ in swapping a disease-susceptible gene version for a resistant one

HDR

if the final plant (____ product) contains no _____, it may be treated like a conventionally-bred plant

end, foreign DNA

point mutation via HDR:

a 1-3 base change is made (similar to natural mutations or chemical mutagenesis). often

non regulated

gene knockout via NHEJ:

a gene is ____ using the plant’s own repair process; no foreign DNA remains in the final plant. often

non regulated

new gene inserted via HDR:

a foreign or new gene/genetic element is inserted at the cut site. the result resembles a ___ plant. treated like

transgensis

transgenesis foreign DNA

yes

transgenesis source of genetic material

sexually incompatible species

transgenesis example

Bt cotton (insect resistance)

cisgenesis foreign DNA

no

cisgenesis source of genetic material

same species/compatible relative, intact gene

cisgenesis example

late blight resistance potato

intragenesis foreign DNA

no

intragenesis source of genetic material

same species/compatible relative, mixed parts

intragenesis example

innate low-acrylamide potato

genome editing foreign DNA

depends