Toolkits of Genes and Knowledge- Ready for Making Improved Plants
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Toolkits of Genes and Knowledge- Ready for Making Improved Plants Richard Flavell
description
Toolkits of Genes and Knowledge- Ready for Making Improved Plants Richard Flavell. 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 - PowerPoint PPT Presentation
Transcript of Toolkits of Genes and Knowledge- Ready for Making Improved Plants
Toolkits of Genes and Knowledge- Ready 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
1970 2000 2030 2060 2090 2120 2150
Tool
s
Simple T
raits
(Few g
enes)
Complex Traits
(Many g
enes)
New Synthetic Species
Knowledge driven transgenic solutions to problems
All key species
Dates
Commercial Products
Future of Transgenic Biology- Let’s Imagine, Predict, Expect
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
b = 0.02
b = -0.00
b = 0.45
b = 0.33
b = 1.14
b = 1.71
0
20
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60
80
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140
1860 1880 1900 1920 1940 1960 1980 2000
Year
Bu
sh
els
per
Acre
Corn Soybeans Wheat
World Cereal Production and Rates of Improvement
How do we increase the slopes of the lines?
b = 0.02
b = -0.00
b = 0.45
b = 0.33
b = 1.14
b = 1.71
0
20
40
60
80
100
120
140
1860 1880 1900 1920 1940 1960 1980 2000
Year
Bu
sh
els
per
Acre
Corn Soybeans Wheat
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
1970 2000 2030 2060 2090 2120 2150
Tool
s
Simple T
raits
(Few g
enes)
Complex Traits
(Many g
enes)
New Synthetic Species
Knowledge driven transgenic solutions to problems
All key species
Dates
Commercial Products
Future of Transgenic Biology- Let’s Imagine, Predict, Expect
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
1970 2000 2030 2060 2090 2120 2150
Tool
s
Simple T
raits
(Few g
enes)
Complex Traits
(Many g
enes)
New Synthetic Species
Knowledge driven transgenic solutions to problems
All key species
Dates
Commercial Products
Future of Transgenic Biology- Let’s Imagine, Predict, Expect
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
Mutation mapping QTLs mapping Association Mapping-random populations Pedigree analysis with markers Expression Analysis Transgene insertion
All need phenotype analysis
High-Throughput Trait Pipeline
Transform into Model Plant
Arabidopsis
Hundreds of candidate trait genes identified Biomass yield Plant architecture Tolerance to environmental stresses
Nitrogen use efficiency Disease resistance
Gene-TraitAssociations
Identify genes
Various Plant Species Rice
Evaluate in Model Crop
Energy CropsSwitchgrass,
Miscanthus, etc.
Food CropsCorn, Soybean, etc.
Nutrient utilization Cold germination
Heat tolerance
Drought recovery
Flowering time
Increased yield
Increased biomass
Shade tolerance
Drought tolerance
Salt toleranceStature control
Root growth
Gene-Trait Associations
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-but- one 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
1970 2000 2030 2060 2090 2120 2150
Tool
s
Simple T
raits
(Few g
enes)
Complex Traits
(Many g
enes)
New Synthetic Species
Knowledge driven transgenic solutions to problems
All key species
Dates
Commercial Products
Future of Transgenic Biology- Let’s Imagine, Predict, Expect
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?
b = 0.02
b = -0.00
b = 0.45
b = 0.33
b = 1.14
b = 1.71
0
20
40
60
80
100
120
140
1860 1880 1900 1920 1940 1960 1980 2000
Year
Bu
sh
els
per
Acre
Corn Soybeans Wheat
1970 2000 2030 2060 2090 2120 2150
Tool
s
Simple T
raits
(Few g
enes)
Complex Traits
(Many g
enes)
New Synthetic Species
Knowledge driven transgenic solutions to problems
All key species
Dates
Commercial Products
Future of Transgenic Biology- Let’s Imagine, Predict, Expect
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
