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

Tools Simple Traits (Few genes) Complex Traits (Many genes) 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

World Cereal Production and Rates of Improvement

How do we increase the slopes of the lines?

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

Tools Simple Traits (Few genes) Complex Traits (Many genes) 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

Increases in Number of Known Plant Proteins

Sequencing Cost Reductions

Tools Simple Traits (Few genes) Complex Traits (Many genes) 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-Trait Associations Identify genes Various Plant SpeciesRice Evaluate in Model Crop Energy Crops Switchgrass, Miscanthus, etc. Food Crops Corn, Soybean, etc.

Nutrient utilization Cold germination Heat tolerance Drought recovery Flowering time Increased yield Increased biomass Shade tolerance Drought tolerance Salt tolerance Stature 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 CO 2 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

Tools Simple Traits (Few genes) Complex Traits (Many genes) 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?

Tools Simple Traits (Few genes) Complex Traits (Many genes) 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.

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