Toolkits of Genes and Knowledge- Ready for Making Improved Plants

1. Toolkits of Genes and Knowledge- Ready for Making Improved Plants Richard Flavell

2. 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 Outline

3. 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 Twenty Seven Years On Since the First Transgenic Plants

4. Future of Transgenic Biology- Let’s Imagine, Predict, Expect Commercial Products New Synthetic Species Complex Traits (Many genes) Knowledge driven transgenic solutions to problems All key species Simple Traits (Few genes) Tools 1970 2000 2030 2060 2090 2120 2150 Dates

5. 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

6. What is Needed Versus What can be Done

7. 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? What is needed v What can be done

8. Corn. Wheat and Soybean Yields Over the Century - USA

9. World Cereal Production and Rates of Improvement

10. How do we increase the slopes of the lines?

11. 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” Company Pledges and Quotes

12. 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 Basis for Predicting Yield Increases

13. Future of Transgenic Biology- Let’s Imagine, Predict, Expect Commercial Products New Synthetic Species Complex Traits (Many genes) Knowledge driven transgenic solutions to problems All key species Simple Traits (Few genes) Tools 1970 2000 2030 2060 2090 2120 2150 Dates

14. 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

15. 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

16. Molecular Biologist’s Tool Kits provide almost unlimited means of creating variation (but today are focused on a few genes at a time) Evolution and Plant Breeding Need Genetic Variation and Selection

17. Tools, Methods etc

18. Increases of Numbers of Known Plant Genes 2003-2008

19. Increases in Number of Known Plant Proteins

20. Sequencing Cost Reductions

21. Future of Transgenic Biology- Let’s Imagine, Predict, Expect Commercial Products New Synthetic Species Complex Traits (Many genes) Knowledge driven transgenic solutions to problems All key species Simple Traits (Few genes) Tools 1970 2000 2030 2060 2090 2120 2150 Dates

22. 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 Tools, Methods

23. Mutation mapping QTLs mapping Association Mapping-random populations Pedigree analysis with markers Expression Analysis Transgene insertion All need phenotype analysis What do Genes do In Planta? To Find Gene-trait Associations

24. Gene-TraitAssociations Identify genes Transform into Model Plant Evaluate in Model Crop Various Plant Species Arabidopsis Rice Energy Crops Food Crops Switchgrass, Miscanthus, etc. Corn, Soybean, etc. High-Throughput Trait Pipeline Hundreds of candidate trait genes identified  Biomass yield Plant architecture Tolerance to environmental stresses Nitrogen use efficiency Disease resistance

25. Gene-Trait Associations Heat tolerance Drought tolerance Increased yield Nutrient utilization Cold germination Increased biomass Root growth Drought recovery Shade tolerance Flowering time Salt tolerance Stature control

26. 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 Conclusions from Gene-Trait Studies Using Transgenes

27. 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

28. 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

29. 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 Systems Biology of Traits

30. Activation of Flowering-Signal Perception and Transduction to Apical Meristem

31. Future of Transgenic Biology- Let’s Imagine, Predict, Expect Commercial Products New Synthetic Species Complex Traits (Many genes) Knowledge driven transgenic solutions to problems All key species Simple Traits (Few genes) Tools 1970 2000 2030 2060 2090 2120 2150 Dates

32. 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? What is needed v What can be done

33. How do we increase the slopes of the lines?

34. Future of Transgenic Biology- Let’s Imagine, Predict, Expect Commercial Products New Synthetic Species Complex Traits (Many genes) Knowledge driven transgenic solutions to problems All key species Simple Traits (Few genes) Tools 1970 2000 2030 2060 2090 2120 2150 Dates

35. 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. Summary

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