Grand Green Flashcards
(199 cards)
1
Q
Global population
A
10.4 billion in 2080?
2
Q
Famine
A
1 billion do not have enough food
3
Q
hunger and malnutrition
A
9 million people die each year (more than AIDS, malaria and tuberculosis combined); the silent pandemic; 6.3M COVID deaths ‘20-‘22
4
Q
Food cost fluctuations
A
- weather
5
Q
Non-food uses of plants
A
- feed
- biofuel
- fibre
- construction
6
Q
land use for agriculture
A
50%
7
Q
agricultural land use for meat
A
77%
8
Q
crops provide
A
- 82% calories
- 63% protein
9
Q
additional challenges
A
- less land
- less predictable water
- less fertiliser
- fewer pesticides
10
Q
8 main crops of the world
A
- maize
- wheat
- rice
- barley
- cassava
- oilseed rape
- sugarcane
- soy
11
Q
most cropland is used for
A
- cereals
- coarse grains
- oilcrops
12
Q
crop domestication
A
- no fruit abscission
- more and bigger fruits
- loss of daylength dependence
- determinate growth
- colour variation
- loss of vernalisation requirement
- increased seed number
- reduced seed shattering
- reduced height
- reduced dormancy
13
Q
conventional backcrossing
A
- visual selection of F1 plants that most closely resemble recurrent parent
14
Q
marker-assisted backcrossing
A
using background markers that allow selection of F1 plants with the most recurrent parent marker genes, and the smallest percentage of donor genome
15
Q
speed breeding
A
- providing optimal environmental conditions that enable faster growth and reproduction
- light, temperature, photoperiod, and humidity
16
Q
How to increase genetic variation?
A
- increasing germplasm (create seed stock centres)
- mutagenesis
- transformation
- genome editing
17
Q
how do you replace bases with CRISPR-Cas9
A
inefficient HR
18
Q
virus induced gene editing (VIGE)
A
CRISPR-Cas9 transgenic plant with virally transmitted sgrna
19
Q
Precision Breeding Act: 23rd March, 2023
A
genetic changes which could have arisen through traditional breeding or natural processes
20
Q
key challenges of the future
A
- drought-resistant
- flood-tolerant
- disease-resistant
- low N; nodulation
- low P; AM symbiosis
- improved photosynthesis
- flowering time
- better morphology
21
Q
additional challenges
A
- germination
- cold/frost damage
- biofortification
- morphology
- new crops
- weed control
22
Q
stress
A
Suboptimal environmental condition that adversely affects the growth and development of a plant
23
Q
abiotic stressors
A
- temperature
- water
- CO2
- light
- nutrient
- salinity
- heavy metal/xenobiotic poisoning
- mechanical
24
Q
biotic stressors
A
- pathogens
- pests
- plants
25
stress reduced crop yields by
more than 50%
26
stress responses
- tolerance
- avoidance
27
phases of stress
- alarm
- acclimation
- maintenance
- exhaustion/recovery
28
chronology of a stress response
- immediate responses
- gene expression and metabolism
- physiology
- growth and development
29
ROS
can damage proteins, lipids, DNA, causing cellular dysfunction
30
long-distance signals in plants
- ROS/calcium waves
- electric currents
- hydraulic signals
- pH
- eATP
- phytohormones
- hormone-like peptides
- miRNAs
31
water regime terminology
- water logging
- partial flooding
- complete flooding
32
flooding is a major
financial threat (US crop production 2013-2017)
33
intensity, timing and duration
of floods are changing
34
Why is submergence a threat to plants?
- water turbidity results in carbon starvation and slow diffusion of oxygen
- fermentation
- soil redox potential decreases
- reduced photosynthesis
35
one way to look at protein expression levels
relative across time/place
36
ways of studying interactions
- mass spectrometry
- biomolecular fluorescence complementation assay
37
flooding assays
- hypoxia tolerance assays in vitro
- submergence assays in vivo
38
natural strategies to withstand flooding stress
- germination
- roots
- stems
- leaves
39
Specific flooding stress adaptations
- anaerobic germination
- root repatterining
- hydraulic repatterning
- aerenchyma
- heterophylly
- LGFs
40
GWAS
- association of a specific trait with SNPs across hundreds of accessions reveals interesting regions
41
enzyme-engineering approaches
- structure-guided rational design (rational mutagenesis)
- deep mutational scanning
- synthetic biology
- de novo protein design
- random mutagenesis
- directed evolution
42
drought
ranks as the single most common cause of severe food shortages in developing countries
43
drought strategies
- desiccation
- avoidance
- tolerance
44
0.2% of the angiosperms are
dessication tolerant
45
short-distance water movement
- diffusion and osmosis
46
long-distance water movement
pressure bulk flow
47
water path
- from root to soil
- thru plant
- from leaves to atmosphere
48
factors affecting water movement
- xylem anatomy
- leaf vein pattern
- guard cell density and opening
- plasmodesmata
- aquaporins
- soil properties
- root architecture
- cell wall permeability
49
ROS formation
- Membrane damage
- Protein aggregation
- Impairment of photosynthesis
and other cellular functions
50
why is drought a stress?
- low energy stress
- low oxygen stress
- osmotic stress
51
short-term water responses
- balance
- protection
52
water balance
- stomata
- osmolyte
- aquaporin
53
protection
- LEA
- chaperones
- AOs
54
long term flood responses
- source and sink relations
- drought escape
55
source and sink relations
- roots
- hydraulics
- epidermal wax
- leaf abscission
- reduced stomata
- reduced shoot growth
56
drought escape
reproductive phase transition
57
monitor drought
- soil monitoring
- plant monitoring
58
soil monitoring
- humidity
- drip irrigation
- partial root zone drying
59
plant monitoring
- thermal imaging
60
biological innovations for drought
Osmotic adjustment
Regulation of stomata conductance Improved water use efficiency Improved photosynthetic rate Delayed senescence
Root architecture
Regulation of reproductive phase transition
61
ways of improving drought
- chemicals
- memory
- drought-tolerance
62
drought chemicals
- osmoprotectants
- growth effectors
63
drought memory
seed priming
64
forward genetics
- phenotype to gene
1) mutagenesis
2) screen
3) map [GWAS]
4) complementation testing
5) KOs
6) expression
65
backwards genetic
- gene to phenotype
66
manipulating relevant genes
- transgenic approaches
- breeding (MAS)
- gene editing
67
conventional breeding
Search for progeny combining both parental traits
VERY LONG AND TEDIOUS PROCESS (8-12 selection generations)
BASED ONLY ON PHENOTYPE
68
GENOTYPE-BASED selection of progeny
- Progeny with “tolerance” trait identified
- Progeny with highest % of high-yield parent identified
69
Gene editing
IF YOU KNOW WHAT IS THE CAUSAL GENE/MUTATION
HIGHLY PRECISE, FLEXIBLE, AND FAST GENOME MANIPULATION
70
3400 calories
per person per day
71
Average increase
~15 extra daily calories
per year; (0.6% increase per year)
72
78 million additional loaves of bread every day next year
= 15 million additional tons of wheat next year
= 51,000 additional km2 of wheat next year
Or
= 2,340,000 additional km2 of cows next year
73
Average 1.1% yield improvement
per year since 1960
74
Average 0.3% increase in land use
per year
75
Cut down ~15 billion trees
a year
76
~ 30% of humanities
CO2 emissions
77
you can measure the evolution of a
protein site
78
India crashed into mainland Asia
- Himalayas began to erode
- Weathering of Himalayas caused to CO2 to plummet
79
What are the consequences of photorespiration?
No carbon gain
No growth
Risk loosing both N and C
30-50% of all plant energy spent undoing this reaction at current atmospheric CO2.
80
If evolution cant change rubisco perhaps it can change its environment!
Ratio O2 : CO2
Atmosphere 500 : 1
Solution 10 : 1
81
Most plants
Photosynthesis in one cell
82
C4 plants
Photosynthesis distributed across two cells
83
C4 photosynthetic partitioning evolved independently
>70 times
84
Independent origins plus different ages
- = huge diversity in anatomy
- huge diversity in biochemistry
85
light
- not equally absorbed by the earth
- scattered by the atmosphere
- only a fraction is used for photosynthesis
- light environment is constantly fluctuating
- position in canopy has large effect on light levels
- chlorophyll light interception responses
86
Three ways people have tried to improve responses to light availability
Speed up rubisco reaction time.
Speed up NPQ reaction time.
Change light absorption in canopy.
87
if you have improved a characteristic what should you ultimately measure?
- yield
88
Chloroplast descended from photosynthetic bacteria that lived in
upper levels
89
Photosynthesis using infra red light emitted from
deep sea hydrothermal vents
90
Functional reconstitution
in vitro
91
Rhizosphere zone
immediately around roots
92
Endosphere inside roots but extracellular
(nb phyllosphere (leaf), spermosphere (seed))
93
5-20% of plant photosynthate is
exuded by roots
94
Microbiome detection
Metagenomics (DNA), metatranscriptomics (RNA), metaproteomics
95
Microbiome structure
Operational taxonomic Unit (OTU) i.e. bin sequences to >= 97% identity, now amplicon sequence variants (ASV) most common
96
Bray Curtis dissimilarity
- difference or dissimilarity between two samples based on their species composition or abundance in ecological studies, particularly when analyzing community structure
- value between 0 and 1, where 0 indicates identical communities and 1 indicates completely different communities
97
Microbiome mapping
- Fluorescently labelled bacteria can be counted by flow cytometry
- Bacteria can be tracked in microfluidic devices
- Global mutagenesis (TnSeq, BarSeq) used to determine effects of mutation
98
All nodulating plants are in
Eurosid 1 clade
99
Fabales,
95% in Legume Family = Fabaceae (or Leguminosae)
100
3rd largest family of plants
19,400 species
101
Three subfamilies of Fabacea
1:Mimosoideae
2:Caesalpinioideae 3:Faboideae (Papilionoideae)
102
Not all nodulate,
rare in Caesalpinioideae
103
Parasponia
only non-legume host (Rosales)
104
Soybeans
twice as much protein per acre as any other major vegetable or grain crop, 5 to 10 times more protein per acre than land for grazing animals to make milk, and up to 15 times more protein per acre than land set aside for meat production.
105
Medicago truncatula
model indeterminate plant (375 Mb)
106
Lotus japonicus
model determinate plant (470 Mb)
107
Both M. truncatula and L. japonicus have
small diploid genomes, easy to transform
108
Glycine max (soybean)
1.1.Gb polyploid genome
109
Synteny mapping
analysis and comparison of the relative order of genes or genetic markers between different species or within different regions of the same genome. It helps identify regions of conserved gene order across different species, which can provide insights into evolutionary relationships and functional genomics.
110
Most rhizobia are Five main groups of alpha-proteobacteria
i) Rhizobium; ii) Bradyrhizobium; iii) Azorhizobium; iv) Sinorhizobium; (renamed Ensifer) v)
Mesorhizobium
111
Beta proteobacteria
(e.g. Burkholderia and Cupriavidus)
112
Phosphorus (P)
The 11th most abundant element in the earth’s crust
The 5th most abundant element in a plant
The 2nd most common limiting macronutrient for plant growth
113
Phosphorus uses
- Energy donors ATP, ADP, AMP
* Phospholipids
* Nucleic acids - DNA, RNA
* Starch/sucrose synthesis
* Protein modification, regulation of metabolic pathways such as energy transfer, and amino acid synthesis
114
Phosphate Depletion
* Stunted growth, chlorosis, increased levels of anthocyanins
* Increased root-to-shoot ratio
* Low metabolism & reduction in
photosynthesis
* Sulpholipids/glycolipids replace phospholipids in membranes
* Delayed flowering and poor seed quality/low crop yields
* Reduced Nitrogen uptake
* Leaf drop
* Poor frost resistance
115
P is essential for
growth, functioning and reproduction of all life on earth
116
Pi fertilisers
boost plant growth and crop yields
117
Approaching a
period of “peak
phosphorus” as
depleted
deposits
118
Phosphate rock is a
non-renewable resource
119
90% of the world’s Pi rock reserves are in only
5 countries
120
~80% soil-applied phosphate remains
unavailable to the plant (Hinsinger et al., 2011)
121
P deficits cover
29% of the global cropland area impacting crop yields
122
71% of the cropland area had overall Phosphorus
surpluses
123
High P fertilizer application relative to crop P use (Low Phosphate Use Efficiency) resulted in a greater
proportion of the intense P surpluses
(>13 kg of P·ha−1·y−1) globally
124
PSR in shoots (systemic signals delivered through xylem and phloem translocation system):
* Increased Pi recycling and mobilization
* Reduced rate of photosynthesis
* Increase in sugar concentration
* Increase in anthocyanin accumulate
* Lipid remodelling
* Shoot growth retardation
125
PSR in roots (local):
* Increase in Pi uptake, transport and translocation
* Changes in Root System Architecture (RSA)
* Increased secretion of Organic Acids and Acid Phosphatases * Changes in metabolic pathways
* Lipid remodelling
* Exudation of flavonoids and strigolactone (SL)
* Interaction with Arbuscular Mycorrhizal Fungi
126
necessary?
attenuated
127
RT-PCR
showing homolog transcript levels
128
Spatial expression pattern
- are different cells doing the same thing?
129
Concanamycin A:
Potent inhibitor of V-ATPase resulting in vacuolar alkalinisation and fragmentation
130
iTRAQ analysis
quantitative proteomics technique used to measure the relative abundance of proteins across multiple samples in a single experiment. It allows researchers to compare protein expression levels between different conditions (e.g., different tissues, time points, or experimental treatments) in a highly efficient and reproducible manner
131
if you're testing a protein you could test its
homology
132
if you're doing a mutant analysis you could do
- mutant combos
- OX lines
133
Reciprocal micrografting
- By swapping the root and shoot tissues between two plants, researchers can determine whether certain traits or characteristics are regulated by the root or the shoot.
-
134
When would you use YFP?
- enhanced photo stability for live cell imaging
- efficient at folding v fast
135
When would you use mCherry?
- better penetration
- higher photo stability
136
plant symbiosis
Plants can derive up to 100% of their phosphorus needs and around 40% of their nitrogen needs from AM fungi
137
what percentage of plants are non-mycorrhizal?
~7%
138
what percentage of plants have AMS?
72%
139
AMF
570MYA
140
AMS enhances overall maize grain yield by
~30%
141
Top-5 crop diseases are all filamentous!
- Stem rust
- Rice blast
- Late blight
- Soybean rust
- Corn smut
142
Top-5 tree diseases are all filamentous
- Dutch elm disease
- Chestnut blight
- Sudden larch death
- Ash Dieback
- Blue stain disease
143
Three main crop protection strategies
- Resistance breeding
- Agrochemicals (fungicides)
- Good sanitation
144
Wheat rust
- 7,500 BC
- Aristotle's time (384-322 BC)
- ‘Robigalia’ festival in Rome on April 25: Sacrifice puppy to Robigus to avoid rust
- Problematic in 17th century Europe
145
Norman Borlaug
Developed semi-dwarf, high-yield, disease-resistant wheat varieties.
146
Uganda, 1999
Devastating rust epidemic
New stain broke through existing R genes
Spreads by wind.
147
strain UK-01
- 2013: first rust in UK in 58 years
- 20% of UK wheat varieties are resistant to UK-01
148
Cladosporium fulvum
- serious losses in greenhouse-grown tomato
- new outbreaks in UK every year since 2000
149
Edman sequencing
150
PCR with degenerate primers
- uses primers containing mixed or ambiguous bases to amplify DNA sequences with some variability
- useful when the exact target sequence is unknown
- Gene discovery – Amplifying homologous genes from different species.
- Metagenomics – Detecting diverse microbial genes in environmental samples.
- Evolutionary studies – Identifying conserved gene regions across species.
- Pathogen detection – Detecting viral or bacterial genes with some sequence variation
151
Map-Based Cloning
- Genetic Mapping with Molecular Markers
- Fine Mapping
- Physical Mapping & Candidate Gene Identification
- Gene Validation
152
Gene-for-gene transient assays
- Selection of Genes
- Cloning & Expression (CaMV 35S)
- Agrobacterium-mediated transient expression (Agroinfiltration) or viral vectors to deliver genes into plant cells
- Co-Infiltration into Host Plant (Control treatments include empty vector or non-interacting genes)
- Observation of Hypersensitive Response (HR); visually assessed within 24–72 hours as necrosis or electrolyte leakage (measured with conductivity assays).
153
Tomato brown rugose fruit virus
- First identified in Israel (2014) – now spreading worldwide
- Outbreaks in the UK (one in 2019, four in 2020)
154
Eupatorium yellow- vein virus (EpYVV)
autumnal appearance of eupatorium plants in summer
155
Tobacco mosaic virus
- Work in the 1880s demonstrated that the tobacco mosaic disease was caused by an infectious agent (Mayer, 1886) that could pass through porcelain filters (Iwanowski, 1892)
- Beijerinck (1898) realized the agent was unlike any previously identified pathogen and coined the term VIRUS
- 1930s Stanley crystalized TMV.... Viruses are a very distinct form of life
156
Virus-infected plants show greater resistance to
drought
157
2020
Approx. 2000+ viruses and satellites
158
virus couples
Some viral diseases are now recognised as being caused by two or more viruses – with a single virus not causing disease symptoms...
159
Papaya “sticky” disease
PMeV infects with a second virus such as PMeV
160
Most vectoring of plant viruses is via
invertebrates, especially aphids (66%)
161
The “number 1” model plant pathogen
Pseudomonas syringae*
162
Phytoplasmas are
obligate parasites with small genomes (<1Mb) and depend on host cells for some biosynthetic processes
163
Plant-feeding insects damage plants and
act as vectors for plant diseases
164
psammophory
Over 200 species of plants coat themselves in sand, which makes them less appealing to herbivores
165
biological communication
“Information transmission that is fashioned and/or maintained by natural selection”
166
Signals are
traits whose value to the signaler is that they convey information to receivers
167
Communication
if signaling plant derives a fitness benefit from conveying information to others
168
semiochemical
a generic term used for a chemical substance or mixture that carries a message
169
Hormone
semiochemical produced in one part of an organism that exerts an effect in another part of an organism
170
Allomone
semiochemical produced and released by a living organism that benefits the donor (signal producer)
171
Kairomone
semiochemical produced and released by a living organism that benefits the receiver
172
Synomone
semiochemical that is adaptively advantageous to both the emitting and the receiving organism
173
Volatile organic compounds (VOCs)
- key agents of chemical communication for plants
- compounds that have a high vapor pressure and low water solubility
- Up to 36% of assimilated carbon may be released by plants as complex bouquets of VOCs
174
VOCs act in conjunction with other signals such as flowers or temperature to
communicate messages to pollinators
175
odour can be particularly important for
nocturnal animals
176
Could enhancing scent production in commercially bred flowers enhance both
appeal and pest/disease resistance?
177
Kin recognition in
competitive root interactions
178
Antagonistic root growth
- competition
- inhibition (allelopathy)
179
Studying VOCS
Plants producing essential oils are distilled and the extracted oils analyzed by gas chromatography, often coupled to mass spectrometry
180
Plant headspace is sampled using sorbents
- sampling of airborne organic pollutants
- Tenax TA, Chromosorb 106, Porapak N, and Carbopack F
-
181
Ways to measure volatiles
- sorbents
- Solid phase microextraction
- eNose
- Insect electroantennogram
182
Electronic nose (eNose)
Metal Oxide Sensors: when volatile compounds are adsorbed onto the surface of the semiconductors this generates a change in the electrical resistance which varies with the type of volatile compound and its concentration.
183
Challenge of testing hypotheses about volatile (airborne) signaling...
- Use of realistic (natural) volatile concentrations
- Use of single compounds rather than mixtures
- Enclosed plants – altered gas exchange (CO2, H2O, O2)
- Use of detached leaves (more sensitive to VOCs)
- Well-controlled, biologically meaningful stimuli (e.g. chewing damage involves mechanical and chemical stimuli such as saliva)
184
Scent production by snapdragons decreases after
fertilisation
185
Traps based on
plant volatiles and sex pheromones
186
Vernalisation is
the process by which prolonged exposure to cold temperatures promotes flowering.
187
Ageing enhances
flowering competence
188
Reproductive phase transitions are regulated by
microRNAs
189
Flowering time is a
domestication trait
190
P. syringae
- bacterial speck disease
- many strains
- also infects model plants
190
Plant domestication traits
* increased seed retention (non-shattering)
* increased size
* changes in shoot branching and stature
* loss of seed dormancy
* synchronous germination
* taste change: loss of bitterness, enhanced sweetness
* fruit colour polymorphisms
* change of flowering time
191
Bacterial growth assay (colony counts)
1) syringe infiltration by hand
2) make leaf extract; dilution series
3) count colony-forming units (CFU)
192
Phytophthora infestans
- single most important disease facing the potato industry
- €6 billion losses globally: control and damage
- also infects tomato
193
The history of potato blight
- Potato domesticated 7-10 kya in Peru/Bolivia, driving (pre-)Inca empire
- late blight until 1840s (co-evolved in Mexico with wild potato)
- Great Famine in Ireland was caused by strain HERB-1
- ~ 1M people died, ~1-2M emigrated
194
Virus-induced Gene Silencing (VIGS)
- RNAi technique to transiently deplete mRNA levels of specific genes in plants
- Tobacco Rattle Virus (TRV) RNA2 is transcribed from T-DNA of binary agroinfiltration vector
195
Cloned by association genetics
identifying and isolating a gene based on its statistical association with a particular trait in a genetically diverse population. This approach is often used in natural populations or breeding lines rather than controlled genetic crosses.
196
2009 milestone:
genome of P. infestans sequenced by large consortium
197
effectoromics
1) Sequence your pathogen
2) Select core effector candidates
3) Clone into binary PVX vector
4) Agroinfect wild relatives
5) Identify NLRs responsible for recognition by co-expressing wild-relative NLR candidates in N. benthamiana (by agroinfiltration)
6) Transform NLR into potato to introduce resistance against P. infestans
7) Stack NLRs into potato for durable resistance
198
GMO landscape remains challenging
BASF’s Fortuna (GM potato containing Rpi-blb1 & Rpi- blb2 from S. bulbocastanum) stopped in 2013 because of ‘uncertainty in the regulatory environment and threats of field destructions’.
