Transcript Toolkits of Genes and Knowledge- Ready for Making Improved Plants

Toolkits of Genes and KnowledgeReady for Making Improved Plants
Richard Flavell
Outline
 Strategic view of tools and knowledge
development-what do we have and what will we
have
 What is needed versus what can be done
 Sources of genetic variation past and future
 Brief review of tools, methods
 Brief review of transgenes for trait improvement
 Summary and perspective
Twenty Seven Years On Since the First
Transgenic Plants
 Today’s transgenes are just the tip of the iceberg
 Beneath the surface is an enormous knowledge
base and storehouse of tools that is growing
daily for tomorrow’s successes
 Very few plant transgenes have reached the
market place yet. Thus the potential still has to
be imagined
 Let’s do that
Future of Transgenic BiologyLet’s Imagine, Predict, Expect
Commercial Products
Knowledge
driven
transgenic
solutions to
problems
All key
species
1970
2000
2030
2060
Dates
2090
2120
2150
It was only 66 years from when the
Wright Brothers first got an aeroplane
off the ground to when the US put a
man on the moon
What is Needed Versus What can be Done
What is needed v What can be done
 What plant improvements are needed to achieve
enough food, feed, fibre and energy from sustainable
systems and to sustain the planet based on acceptable
criteria?
 Has anyone modeled what number, scale and diversity
of plant breeding programs (not yields) are needed to
make acceptable yield potentials for all the loved crops,
growing in appropriate places on less land than used
today
Can needs be satisfied using the timescales of plant
breeding and existing genetic variation?
Corn. Wheat and Soybean Yields Over the
Century - USA
140
120
b = 1.71
Bushels per Acre
100
80
60
b = 1.14
b = 0.45
40
b = -0.00
b = 0.33
20
b = 0.02
0
1860
1880
1900
1920
1940
Year
Corn
Soybeans
Wheat
1960
1980
2000
World Cereal Production
and Rates of Improvement
How do we increase the slopes of the
lines?
140
120
b = 1.71
Bushels per Acre
100
80
60
b = 1.14
b = 0.45
40
b = -0.00
b = 0.33
20
b = 0.02
0
1860
1880
1900
1920
1940
Year
Corn
Soybeans
Wheat
1960
1980
2000
Company Pledges and Quotes
 Monsanto:
– Pledged “to produce seeds that would double
yields of corn, soybean and cotton by 2030 and
that would require 30% less water,land and
energy per unit of yield to grow”
 Dow:
– “In 20 years we will look back and see that we
were simply playing with genes in 2008”
Basis for Predicting Yield Increases
For doubling of rate of yield gain from using markers etc
 Will know:
– Roles of all chromosome segments and variants in the
germplasm
– Effects of recombining “ every segment” in all combinations
– How to select any combination-markers for all genes
– Molecular basis of variation and key traits
 Will have a huge collections of transgenes to protect
yield
 Will be able to target transgenes into
minichromosomes/preferred positions using optimal
promoters
Future of Transgenic BiologyLet’s Imagine, Predict, Expect
Commercial Products
Knowledge
driven
transgenic
solutions to
problems
All key
species
1970
2000
2030
2060
Dates
2090
2120
2150
Evolution and Plant Breeding Need Genetic
Variation and Selection
 Natural evolution’s toolkit is based on
mistakes that survive in individuals:
–
–
–
–
–
–
–
–
Chromosome duplications
Gene loss
Sexual recombination
Mutations in coding sequences
Changes in gene activity in space and time
Changes in activity reducing systems-RNAi
Transposable elements
Interspecies hybridization
Evolution and Plant Breeding Need Genetic
Variation and Selection
 Breeders Toolkits Confined to:
– Sexual recombination between variants
– Very Rarely: Interspecies Sexual Recombination-intra-specific,
inter-specific and inter-generic
– Mutagens
 Breeders work with complete genomes of genes
– This makes improving plants in specific ways very hard and
time-consuming
There surely have to be more efficient ways otherwise
life on the planet will remain miserable for many
Evolution and Plant Breeding Need Genetic
Variation and Selection
Molecular Biologist’s Tool Kits provide almost
unlimited means of creating variation (but today
are focused on a few genes at a time)

Tools, Methods etc
Increases of Numbers of Known
Plant Genes 2003-2008
Increases in Number of Known Plant
Proteins
Sequencing Cost Reductions
Future of Transgenic BiologyLet’s Imagine, Predict, Expect
Commercial Products
Knowledge
driven
transgenic
solutions to
problems
All key
species
1970
2000
2030
2060
Dates
2090
2120
2150
Tools, Methods
 Gene silencing
– RNAi; Virus induced gene silencing
 Transformation stimulation; Rep A, Lec1
 Chemical induced switching
 Promoters, natural and synthetic, for controlling when
and where genes are active
 Site specific insertion- Homologous recombination
– Zinc finger nucleases; meganucleases; Cri/lox; FLp/frt
 Artificial chromosomes
What do Genes do In Planta?
To Find Gene-trait Associations

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
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

Mutation mapping
QTLs mapping
Association Mapping-random populations
Pedigree analysis with markers
Expression Analysis
Transgene insertion
All need phenotype analysis
High-Throughput Trait Pipeline
Energy Crops
Identify
genes
Transform into
Model Plant
Various Plant Species
Arabidopsis
Gene-Trait
Associations
Evaluate in
Model Crop
Switchgrass,
Miscanthus, etc.
Rice
Food Crops
Corn, Soybean, etc.
Hundreds of candidate trait genes identified
 Biomass yield  Plant architecture
 Tolerance to environmental stresses
 Nitrogen use efficiency
 Disease resistance
Gene-Trait Associations
Heat tolerance
Drought tolerance
Increased yield
Nutrient utilization
Drought recovery
Root growth
Cold germination
Increased biomass
Shade tolerance
Flowering time
Stature control
Salt tolerance
Conclusions from Gene-Trait Studies
Using Transgenes
 Single genes can be made that enhance every trait
examined
 Several tens of genes found for most traits that will
improve trait in a species-thus there must be many ways
to improve a trait
 Some genes function across dicot--monocot divide
 Fewer improvements are found the further the test
species is away from the species where the gene was
selected
Screens for High Priority Traits
• Drought (including surrogates)
• Low Nitrogen (including surrogates)
• Cold and Freezing
• Heat (all stages)
• Light (e.g., shade tolerance)
• UV tolerance
• Photosynthetic efficiency
• Low pH and aluminum
• High pH
• Growth rate
• Flowering time
• Stay green and maturity
• Plant architecture
• Fertility
• Organ size
• Stature
• Stalk thickness
• Ozone
• High CO2
• High Nitrogen
• Carbon/Nitrogen
• Seed morphology
• Biotic, fungal
• Composition
• seed oil
• seed protein
• lignin
• sterols
• and others
Systems biology of Traits
 Discover all genes involved by “saturation
genetics”
 Understand wiring diagrams at cell, tissue,
organ and whole plant levels
 Understand control systems
Build new traits through “Synthetic Biology”
and package into heritable units for next-butone generation plant breeding
Systems Biology of Traits
 Flowering: over 70 genes known with principal
regulators
 Stresses, including disease, heat, cold,
drought: 100+ genes known and pathways
being assembled. Major controlling genes
known
 Growth on limiting nitrogen: Many genes
being identified
Activation of Flowering-Signal Perception and
Transduction to Apical Meristem
Future of Transgenic BiologyLet’s Imagine, Predict, Expect
Commercial Products
Knowledge
driven
transgenic
solutions to
problems
All key
species
1970
2000
2030
2060
Dates
2090
2120
2150
What is needed v What can be done
 Has anyone modeled what number, scale and
diversity of plant breeding programs (not yields)
are needed to make acceptable yield potentials
for the all loved crops, growing in appropriate
places on less land than used today
Can needs be satisfied using the timescales of
plant breeding and existing genetic
variation?
How do we increase the slopes of the
lines?
140
120
b = 1.71
Bushels per Acre
100
80
60
b = 1.14
b = 0.45
40
b = -0.00
b = 0.33
20
b = 0.02
0
1860
1880
1900
1920
1940
Year
Corn
Soybeans
Wheat
1960
1980
2000
Future of Transgenic BiologyLet’s Imagine, Predict, Expect
Commercial Products
Knowledge
driven
transgenic
solutions to
problems
All key
species
1970
2000
2030
2060
Dates
2090
2120
2150
Summary
 We may not have enough genetic variation in the relevant species to
enable the required improvements
 The genetic basis of traits is too complex to perform improvements
in all the species de novo rapidly enough by ordinary breeding
 Key crop species do not have the traits required-transgenes have to
be used
 Comparative trait biology coupled with transgenes looks the most
cost-effective way to make improvements in all species in the future
 Products drive innovation, familiarity and acceptance
 Unless we maintain momentum now, then when the more
extensive opportunities should arrive they will not—we will
have wasted the opportunity and the planet will be much
poorer.
 END