toolkits of genes and knowledge- ready for making improved plants richard flavell

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

40

60

80

100

120

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)



All key species

Dates

Commercial Products


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


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


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)



All key species

Dates

Commercial Products


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)



All key species

Dates

Commercial Products


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)



All key species

Dates

Commercial Products


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.

toolkits of genes and knowledge- ready for making improved plants richard flavell

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