1.3 New tools for engineering future crop traits Flashcards
What are the benefits of modern gene editing & reprogramming the expression of master regulators?
- Crop improvement, eg rapid, targeted modification of plant morphology
- Rapid domestication of new species (whereas before it took centuries!). Important to help crops adapt to climate change, soil aridity, etc
List 13 common domestication syndrome traits.
- Determinate growth habit (flowering occurs at top of plant, halting further growth)
- Reduced height
- Reduced dormancy
- Increased seed number
- Reduced pod/seed shattering (where seed pods undergo dehiscence / splitting up – leads to seed loss, reduced yield, next season’s crop being more likely to shatter. So you want retention of mature seed on plant)
- Elimination of seeds
- Improved harvest index (proportion of plant which can be used), yielding larger & more abundant fruit
- No fruit abscission
- Synchronous ripening, shorter maturity
- Reduced content of bitter & harmful compounds
- Colour variation (seeds, fruit)
- Loss of vernalisation requirement (don’t need a cold period for fertility)
- Loss of daylength dependence (photoperiodism, reliance on circadian rhythms)
how can we domesticate new crops, quicker?
1) Modern transgenics: reconfiguring pre-existing biochemical/metabolic & regulatory pathways
2) Exploiting the large reservoir of plant diversity that remains untapped
1) Many of the traits above are multigenic, resulting from alterations to complex developmental and metabolic pathways. So we need to understand how 1D DNA is translated to 4D output.
- What is the benefit of engineering plastid biochemical pathways, as opposed to genomic ones (whether endogenous or not?)
- Give an example of engineering a non-endogenous pathway into a plant.
- Chloroplasts conduct most energy production & biosynthesis in plant cells – small genomes but capable of high levels of gene expression. So engineering plastids could manipulate crop productivity & metabolic properties especially effectively
- Transfer of the algae pathway for astaxanthin (what makes salmon/flamingoes pink) into Nicotiana tabacum via chloroplast transformation
Reprogramming plant biochemical pathways can be used to speed up the domestication process. Name another benefit of the technique.
Scaled production of secondary metabolites
* Many plant pathways are unique, producing secondary metabolites which are hard/expensive to produce synthetically
* Plants can be grown for bioproduction at higher scale and cheaper than microbes
* So we’re researching how to
* Transfer plant pathways to bacteria & yeast
* Can reprogram pathways in plants for higher yields / different products
Crop domestication can be accelerated via reconfiguring endogenous regulatory pathways, in order to recreate well-understood domestication traits in other plants.
Give 4 examples of the latter (ie how we can reprogram endogenous regulatory networks).
- Loss-of-function approach
- Knockout approach
- CRISPR-mediated, targeted genome editing
- Introducing ectopic (abnormal) positive feedback regulatory loops for hyper-expression of endogenous pathways (selective pathway amplification)
Give an example of reprogramming an endogenous regulatory network using the loss-of-function approach.
loss-of-function mutant seed shattering At screen
engineering for reduced pod shatter
How does pod shattering usually occur in an Arabidopsis silique (fruit)?
loss-of-function mutant seed shattering At screen
- At maturity, silique & seeds dessicate, causing tissue shrinkage & tension within walls of fruit
- Dehiscence zone (junction between valves & replum) is weak, so tension causes valves to tear away from the replum at the valve margins → seed pod shatters
- Process made efficient by specialised cells:
- Strong, lignified cells within each value are connected to a strengthened layer at the valve margin — so the tension is transmitted to the margins
Describe how seed shattering is regulated in Arabidopsis.
loss-of-function mutant seed shattering At screen
- Two MADS box factors called Shatterproof 1 (SHP1) and Shatterproof 2 (SHP2) specify the lignified cells at valve margins
- Mutation of both genes results in loss of the lignified layer and the separation layer within the dehiscence zone, producing shatterproof siliques
- Shatterproof (SHP) expression is limited to the valve margin (C) through the action of two regulatory genes:
- Fruitful (Ful) is a gene which encodes a MADS box protein, which is expressed in the valve. Loss of Ful function causes expansion of SHP expression into the valve (G)
- Replumless (Rpl) is a gene which encodes a homeodomain protein, which is expressed in the replum
- ^I.e. Rpl and Ful are expressed either side of valve margin, in order to limit SHP expression to the valve margin
-
SHP1 & SHP2 then regulate downstream factors which are required for specification/formation of the lignified layer (made of lignified valve margin cells) & the separation zone/later in the valve margin
- eg bHLH-class transcription factors, Indehiscent (IND) and Alcatraz
Two MADS box factors called Shatterproof 1 (SHP1) and Shatterproof 2 (SHP2) in Arabidopsis specify the lignified cells at valve margins. What does mutation / loss of function of the genes cause?
loss-of-function mutant seed shattering At screen
loss of the lignified layer and the separation layer within the dehiscence zone, producing shatterproof siliques
Fruitful (Ful) is a gene which encodes a MADS box protein, which is expressed in the valve. What does loss of Ful function cause?
loss-of-function mutant seed shattering At screen
expansion of SHP expression into the valve (G)
Replumless (Rpl) is a gene which encodes a homeodomain protein, which is expressed in the replum. What does loss of Rpl function cause?
loss-of-function mutant seed shattering At screen
expansion of SHP expression into the replum (F)
Indehiscent (IND) is a factor which is required for specification/formation of the lignified layer separation layer in the valve margin. What does mutation of IND cause?
loss-of-function mutant seed shattering At screen
disrupted valve margin & loss of lignified cells
- Mapping genetic interactions involved in establishing dehiscence zone has allowed development of engineering to reduce pod shatter in what plant?
- What is the goal?
- How is this done?
loss-of-function mutant seed shattering At screen
- Rapeseed (canola)
- Goal is to balance reduced pod shatter with ease of seed separation during harvest
- Rapeseed lines have been selected with defects in the IND gene → causes disrupted value margin & loss of lignified cells
Knockout approach
TBC when i understand
