Small Molecules and Genetics - A Vision for Crop Science 2025
Small Molecules and Genetics A Vision for Crop Science 2025 Symposium „ Science for a Better Life“ 150 YEARS BAYER Leverkusen, November 4th/5th 2013 L...
Small Molecules and Genetics A Vision for Crop Science 2025 Symposium „ Science for a Better Life“ 150 YEARS BAYER Leverkusen, November 4th/5th 2013 Lothar Willmitzer Max-Planck-Institut für Molekulare Pflanzenphysiologie Potsdam-Golm
Agenda • The problem • The transformation of life sciences and genetics • Anything new in small molecules? • Genetics and Small Molecules – Any Synergy?
The Problem : Megatrends • Growing world population • Changing diets • Changing climates • New uses (bioeconomy/biofuel)
Yield has to be doubled until 2050
Genetics and agrochemicals have increased yield in the past
Hybrid breeding has revolutionized yield…
However increases are levelling off!
Biotechnology has delivered only very specific solutions
Multiresistant weeds are spreading
…leading to unusual treatments
The pressing need for new solutions in agriculture has also reached the headlines of scientific journals
The Transformation of Life Sciences and Genetics
Life Science has become quantitative • Life sciences has seen a revolution in the last 15 years which changed a largely qualitative science into a largely quantitative one • This paradigm shift was largely driven by developments in the neighbouring disciplines ( physics, chemistry, computer science) • As a result modern life sciences is a data-rich science which results in new challenges and opportunities
Transformation of Genetics • Genetics has changed from a largely indirect evidence based science ( thus heavily relying on mathematics and statistics) to a molecular features based science • Key to the transition in genetics has been the development of so-called next-generation sequencing ( NGS) technology. • NGS allows the fast, reliable and very competetive sequencing of both DNA and RNA
Nanopore sequencing allows reads of several 1000 basepairs without amplification step
Transformation of Genetics – Breeding by Design
Chromosome haplotypes of a set of maize lines for one chromosome. Identical stretches of marker scores (haplotypes) are indicated by the same colour. Box 1 indicates a region with depleted diversity whereas box 2 shows a highly variable region.
Transformation of Genetics Learning from the Past • The knowledge about the genome of thousands of breeding accessions allows the retrospective analysis of what breeders have done „unknowingly“ while developing improved varieties • This in consequence opens a new learning in breeding by extracting (novel) principles • This should result in improved molecular breeding strategies
Transformation of Genetics – Mutant Identification via Bulk Sequencing
Diagram bulked segregant sequencing. Red indicates a mutation that is causal for the mutant phenotype.
Transformation of Genetics Novel Molecular Genetics Tools • The last years have seen the development of novel high precision approaches of introducing site specific allele modifications into complex genomes ( e.g. TALEN)
Vision 2025 - Genetics • Next-Next generation sequencing will allow highly cost-effective genotyping of any organism • In consequence plant species/genotypes which for a long time were neglected in research will become important again • Realizing that genotyping becomes a commodity access to a large diversity of germplasm represents a key requirement for any crop science company
Vision 2025 - Genetics • In case of traits largely due to single genes this allows the identification of specific alleles in any plant species responsible for a wanted trait • Further diversity of alleles / genes will come from ex planta optimization approaches • Introducing alleles by precision breeding or by site-specific mutagenesis ( TALEN) will be a routine
Vision 2025 - Genetics • Complex traits such as drought tolerance, yield or hybrid compatibility are multigenic and thus will remain difficult and costly to assess • Here improved diagnostic tools are needed • First evidence suggests that these diagnostic tools might be build on molecular features (genome, transcriptome, proteome and/or metabolome) and mathematical models incorporating complex phenotypes with molecular features
General combining ability for four traits based on lipidomic data
Phenotyping is lagging behind • Genetics per se does not help but needs to be linked to excellent phenotyping • Clearly phenotyping has not kept the pace of development as compared to genetics • Thus a key request for improving crop science is the development of phenotyping
Anything New in Small Molecules?
Small Molecules – Some Basics • Small molecules are key in modern agriculture • At present herbicides, insecticides and fungicides represent the major plant protection classes • Plant growth modulators (and biologicals) represent new opportunities in small molecules
Small Molecules – Identification • Identification of active ingredients/ lead compounds for active ingredients is limited by two parameters • - diversity of the compounds screened • - recognition of the wanted event (readout)
Small Molecules and Readout • Readout is key to recognition of the small molecule • High through put methods require miniaturized and cost-efficient solutions • Transgenic plants allow the construction of efficient and sensitive (surrogate) readouts based on gene function
Transgenic indicator plants : Endomembrane motility in mutants and after inhibitors
Doering et al. (unpublished)
Small Molecules Diversity and Biologicals • Biologicals presently see a revival as a partly novel concept in agriculture • Biologicals means the application of biological systems ( bacteria, fungi and the like) to crop plants • However it is a reasonable assumption that biologicals exert their function also via (several/a multitude) of small molecules • Thus they by definition represent a rich resource of small molecules which should be exploited
Small Molecules Diversity and MetaMetabolomics • The majority of bioactive molecules is derived from natural compounds • Exploration of natural compounds is essentially limited to systems which can be cultivated or are accessible in large amounts in nature • The vast majority of microorganisms however can not be cultivated in the laboratory • Meta-Metabolomics may allow access to a largely unexplored area
Metametabolomics : Novel chemical diversity Metabolite Fingerprinting of BACs 6e+06 Total
Vision 2025 - Small Molecules • Faster and more precise readout systems will be available driven by the improved understanding of the molecular network of (crop) plants • Sensitive non-invasive readout systems (probably resulting from optical approaches) will be in place allowing more specific analysis of the action of small molecules screened • More diverse biological systems will be used as resources for small bioactive molecules (metametabolomics, biologicals) • Small RNA´s might be added to the tool-box of small molecules
Vision 2025 - Small Molecules • High through put biochemical methods will be established allowing the identification of (proteinaceous) targets for small molecules (mass spectrometry) • Reverse docking methods will be improved allowing the identification of candidate targets for small molecules
Genetics and Small Molecules Any Synergy ?
Systems Biology integrates Small Molecules and Genetics • Systems Biology aims at reconstructing complete regulatory networks integrating information on various molecular levels • This means that (endogenous) small molecules as integral parts of any biological systems are included in the network • In parallel functional genomics and genetics has/will allow(ed) to assign a function to many/all genes
I. Environmental Changes
Time resolved transcriptomic and metabolomic Dynamic environmental response networks analysis of A. thaliana exposed to different light or temperature regimes Experimental design
400 µE
150 µE 75 µE 0 µE
Linear: 0, 20... 360 min = 19 times Log: 0, 5,10min... 21.3h = 10 times
ATMYB75 INTERACTI ON 21°C-DARK -1 4°C-DARK -1 32°C-DARK -1
ATMYB75
RRRCFFFCRRRFFCFFF
CRRRRFFFFCRRRFFFF
Alignment RRRC-FFFC-RRRFFCFFF CRRRRFFFFCRRRFF--FF
Scoring 8.98
INTERACTIO N 21°C-DARK 1 4°C-DARK 1 32°C-DARK 1
WRKY26
SCORE 10.12 9.88 9.13
WRKY26
SCORE 4.31 8.88 1.11
High scoring subnetworks are subjected to experimental validation HEAT
COLD
TF non-TF gene metabolite
DARK
Systems Biology Integrates Small Molecules and Genetics • As a result genes can be linked to a phenotype and to a small molecule • This should allow the identification of genes for breeding ( genetic fixation) • AND the small molecule resp. a lead structure for (conditional) modulation of the phenotype
Conclusions • Genetics driven by NGS will broaden accessible genotypes and species • Phenotyping needs massive development • Small molecules diversity will be broadened by novel resources • Novel readouts/assays will facilitate and specify identification of lead compounds • Understanding of integrated regulatory networks ( systems biology) will create maximal synergies between genetics and small molecules
