11.11: Lecture 3: Snip Snip Flashcards
Domestication has created diverging branching patterns in crops
Some cereals have had a strong increase in apical dominance. This suppression of side branching concentrates seed production on a single, large terminal head. For example: Sorghum & Maize
Others like wheat and rice have been selected for multiple side branches (aka: tillers)
Here, grain production is even, with relatively simultaneous maturation
Developmental biology:
investigates how interacting processes generate an organism’s heterogeneous shape, size, and structural features.
e.g. From last week we know that we can increase radial growth in trees by over-expression of PXY
Branching and wood formation are two of many developmental traits that influence crop productivity
Brassicas are not particularly homogenous – rapa and oleracea have many forms
e.g. Kohlrabi – swollen stem
European turnip – swollen root
see: Cheng, F. et al.
‘Subgenome parallel selection is associated with morphotype diversification and convergent crop domestication in Brassica rapa and Brassica oleracea’, Nature Genetics, [online] Volume(Issue), pp. Page range. Available at: https://doi.org/10.1038/ng.3634
Plant architecture is complex but mostly determined by three parameters
(1) Height
e.g. modern wheat cultivars selected to be shorter in stem making them more efficient
(2) Branching
apical buds are not always active – activation can lead to more floral branches increasing yield
e.g. in tomato
in other species branching is undesirable e.g
trees cultivated for timber (creates knots)
maize (apical dominance produces single cob)
(3) Growth habit
For example: Chili pepper cultivars of the same species (Capsicum chinense) can have strikingly different visual appearances. (see photo in notes)
^ Their vegetative growth – formation of leaves and higher up inflorescence formation is different
A shoot is only competent to flower once it has passed from the juvenile to the adult phase
This phase transition sometimes marked by gross morphological changes
Flowering: the discovery of ‘florigen’
A small molecule acts as a chemical signal to induce flowering, It is produced in the leaves is transferred to the shoot apex via phloem
Initially named ‘florigen’
Julius von Sachs (1832-1897)
The *Father of Plant Physiology’ Proposed the existence Of a chemical produced in leaves of illuminated plants capable of inducing flowering
Conversion Of meristem vegetative to floral - occurs as a result of environmental cues triggering ‘florigen’ production
Mikhail Chailakhyan (1901-1991)
Demonstrated that it is a small molecule,
produced in leaves and transmated to the
shoot apex via the phloem; he named it
“florigen”
Growth phase dictates meristem identity:
- Vegetative meristems generate organs early
in development
Inflorescence and floral meristems generate organs
late in development
Meristems contain distinct zones:
Typically in arabidopsis the vegetative meristem is where most replication occurs at the periphery reducing risk of mutation in centre:
* Cells in the central zone are undifferentiated stem cells
* Cells in the peripheral zone proliferate and begin to differentiate into lateral organs e.g. leaves.
*Cells in the rib meristem proliferate and begin to differentiate into the stem
In the Inflorescence meristem of arabidopsis:
*Cells in the central zone are undifferentiated stem cells
*Cells in the peripheral zone proliferate and develop floral primordia.
*Cells in the rib meristem proliferate and begin to differentiate into the stem
Several physiological pathways regulate flowering
These are called ‘enabling pathways’ as they regulate floral competence of the meristem
This model corresponds to Arabidopsis but many of its modules have counterparts in other species :
florigen converts vegetative tissue to flowering:
photoperiodic pathway
autonomous pathway
vernalization
GA dependent pathway
^ Adapted from Reeves, P.H., and Coupland, G. (2001). Analysis of flowering time control in Arabidopsis by comparison of double and triple mutants. Plant Physiol. 126: 1085-1091
Florigen can be defined as:
*A graft-transmissible, phloem-mobile signal
*Synthesized in leaves and then transported to the shoot apical meristem
*Promotes the transition from vegetative growth to flowering
the 4 pathways from vegetative to inflorescence tissue: photoperiodic pathway
autonomous pathway
vernalization
GA dependent pathway
Photoperiod pathway
arabidopsis produces only leaves in short day period, then in long day periods inflorescence is triggered
Autonomous pathway:
Organisms keep time – any variation from the circadian norm can cause disreg
Photoperiod –H1 encodes a component of the circadian clock
Vernalization:
Oxford definition: the cooling of seed during germination in order to accelerate flowering when it is planted.
Fca is a mutation in summer annual arabidopsis:
See: https://doi.org/10.1016/S0092-8674(01)00573-6
^ see notes for northern blot process used to identify this mutant
GA dependent pathway:
The GA-dependent pathway in plants involves gibberellin (GA) binding to a receptor (GID1), which then interacts with DELLA proteins, leading to their degradation via the ubiquitin-proteasome pathway, ultimately relieving growth restraints and promoting various developmental processes
Sun, T.P. (2011) ‘The molecular mechanism and evolution of the GA–GID1–DELLA signaling module in plants’, Current Biology, [online] 21(9), pp. R338–R345. Available at: https://doi.org/10.1016/j.cub.2011.02.036
FLOWERING LOCUS T (FT)
*A graft-transmissible, phloem-mobile signal
*Synthesized in leaves and then transported to the shoot apical meristem
*Promotes the transition from vegetative growth to flowering
A mutation in FT leads to delayed flowering and plants with increased vegetative growth.
Constitutive expression of FT using a strong promoter leads to early flowering and plants with increased reproductive growth
Synthesised in leaves and transported to shoot apical meristems: Visible as dark patches
^ see: https://www.cell.com/fulltext/S0960-9822(07)01388-7
Is it graft transmissible?
GFP in the root via phloem transport (phloem movement is bidirectional)
FLOWERING LOCUS T (FT) meets the “florigen” criteria
Florigen is defined as :
*A graft-transmissible, phloem-mobile signal
*Synthesized in leaves and then transported to the shoot apical meristem
*Promotes the transition from vegetative growth to flowering
FT binds to FLOWERING LOCUS D: a bZlP
family receptor protein in the meristem
converting Vegetative tissue to Inflorescence tissue
FT is part of the conserved family of floral inducers and repressors
see: Benlloch, R., Berbel, A., Ali L., Gohari, G., Millán, T., and Madueño, F. (2015). Genetic control of inflorescence architecture in legumes. Front. Plant Sci. 6: 543; ; Wickland, D.P., and Hanzawa, Y. (2015). The FLOWERING LOCUS T/TERMINAL FLOWER 1 gene family: Functional evolution and molecular mechanisms. Mol. Plant 8: 983-997. Matsoukas, I.G. (2015). Florigens and antiflorigens: a molecular genetic understanding. Essays In Biochemistry 58: 133-149
FT and TFL1 compete for the same binding site
Therefore manipulating FT and TFL levels allows us to control inflorescence architecture
When FT binds to FD, the switch from vegetative to reproductive growth is triggered at the apical meristem. TFL1 competes with FT for binding to FD thus repressing flowering.
Which genes does TFL repress?
TFL and FD occupancy of genomic regions
LFY and API are transcription factors
that regulate meristem identity
Zhu, Y., Klasfeld, S., Jeong, C.W. et al. TERMINAL FLOWER 1-FD complex target genes and competition with FLOWERING LOCUS T. Nat Commun 11, 5118 (2020). https://doi.org/10.1038/s41467-020-18782-1
LFY regulates meristem identity
lfy (mutant of LFY) fails to make the transition from inflorescence to floral meristem
https://doi.org/10.1016/j.tplants.2010.03.007
AP1 regulates meristem identity
https://doi.org/10.1242/dev.119.3.721
Inflorescence -> floral
Indeterminate -> determined no. Of organs
leading to:
*Partial failure of inflorescence to floral meristem transition
*Remain partially indeterminate
*Secondary flowers (like a tomato)
In brassicas:
Selection for flower clusters lead to cauliflower
Selection for flower clusters and stems lead to brocolli
FT and TFL1 compete for the same binding site
Therefore manipulating FT and TFL levels allows us to control inflorescence architecture
Modern agriculture is underpinned by changes to inflorescence architecture
e.g. soybean see: Revolutions in agriculture chart a course for targeted breeding of old and new crops - Eshed et al
e.g. for tomato: see the self-pruning gene family in tomato Carmel-Goren et al.
Cutting and pasting DNA with CRISPR/Cas9
Basis of the CRISPR/Cas9 system in genome editing
* DNA damage causes mutations
* DNA repair enzymes can be GFP tagged and observed
DNA repair mechanisms:
* HR – Homologous recombination
The problem is that whilst accurate this process is slow and inefficient
Comparitively non-homologous repair is error prone
- NHEJ – non-homologous end joining
deletions are easier to control than insertions - insertions can be added inaccurately
So, pasting DNA uses endogenous repair mechanisms - What about the cutting mechanism?
See next: Discovery of CRISPR
Discovery of CRISPR
see ???
CRISPR/Cas9 for genome engineering
Jennifer Doudna recognised the lack of ethical regulation in relation to plant biology means that this tech will soon provide huge benefits in plant and agriculture development
see agrobacterium process used in prev lecture for the introduction of mutation into poplar tree to increase cambium cell expression
CRISPR/Cas9-induced sp5g muation results in early flowering in long days in tomato plants
Double-determinant sp CR-sp5g show yield increases in tomatoes when grown at high density
CR-sp5g is a qualitative. The deletions
cause loss of SP5G
QUANTITATIVE
Qualitative 5-CIS-reguIatory elements
Qualitative Changes
QUALITATIVE
Quantitative LJTRs/exons/introns
QUANTITATIVE
Qualitative
3-cis-regulatory elements
Qualitative Changes
*New loss-of-function alleles into old and new crops
*Generating identical alleles in elite backgrounds
*Introduction of species-specific gene modifications
e.g., Male sterility for hybrid seed production,
disease resistance, allergen or toxin removal, etc.
Quantitative Changes
*Generating allelic series for phenotypic selection
*Base edits or in-frame deletions in coding regions
*Interfering with RNA or protein stability
*Modifying cis-regulatory elements (activators/repressors)
see Eshed et al 2019
in summary:
Qualitative
the same outcome could technically be achieved through random mutagenesis
However – closely located genes can be hard to edit in this way
Quantitative trait changes
Modifying activators and repressors for more extensive impact
Increasing no. of stem cells can increase no. of organs
Arabidopsis clv mutants – machinery restricting no. Of stem cells is deregulated – resulting in higher sepal count
arabidopsis floral morphology, clv mutant has greater no. Of floral organs
Clv3 binds Clv1 to regulate cell division
in corn cob morphology, cle7 mutant has a greater no. Of kernels – resulting in a larger cob diameter – however the cob is stunted in length and therefore this mutation is not commercially beneficial
^i.e. a disregulation of plant architecture occurs as a result
however edited ZmCLE7 promoter results in increased yield
