Transcript Genomics
Nato Advanced Research Workshop Genomics for the Biosafety in Plant Biotechnology, New Challenges Klaus Ammann, Botanical Garden University of Bern, Bansko 18.10. 2003 Sustainable World System for renewable natural ressources Knowledge based Agriculture Equity: Enhance the global dialogue Innovation for the future making the best of biotech and organic farming, new technologies to process food Risk = Hazard + Chance (Risk = Hazard x Likelyhood) Proposal of the Italians to the European Union on how to label Transgenic Papaya Spitzweg, Friends of Cacti, Geologist everyone takes risks; everyone is a risk manager; Perceived directly Three types of risk. John Adams TRANSGENIC PLANTS AND THE MANAGEMENT OF VIRTUAL RISKS Perceived through science Science can reduce uncertainty by illuminating the connection between behaviour and consequence, science cannot provide “objective” measures of risk; Virtual risk Where scientists don’t know or cannot agree virtual risks are cultural constructs; they may or may not be real – Science cannot settle the issue – they have real consequences; Perceived through science Perceived directly Virtual risk (hypothesis) Monsanto: The Green Devil: A widespread View in Europe Towards a reconciliation of oldfashioned polarities pure ecology reductionistic molecular lab biology experimental causal agricultural applied ecology holistic organismic field biology observational teleonomic Sustainable World System for renewable natural ressources Knowledge based Agriculture Equity: Enhance the global dialogue Innovation: making the best of biotech and organic farming, new technologies to process food Bio-era-teleconference April 22, 2003 Prometheus Unbound: Revolutionary Advances in Biological Technologies Erucic Acid 90% Natural, Vegetable-Based Kosher Certification Available Origin: India Among other fatty acid components: Unknown 2.5 % The results of a study indicated that the low erucic acid trait in S. alba was highly heritable and controlled by a single gene and therefore, could easily be reselected following backcrossing in a breeding program. High and low Erucic Acid traits in colza http://www.who.int/fsf/Documents/Biotech_Consult_May2000/Biotech_00_10_tables.pdf Existing and Future Modifications of Canola Oil Qualities Modern Breeding Methods Cytoplasmic Male Sterile Pollen Male fertile plant of the maize hybrid Delprim on the left hand side, on the right hand side the male sterile version of the same cultivar. As can be seen from the vestigial inflorescence, the male sterile plant does not release pollen. Photograph by M. Long. Male sterile Delprim Maize Apomixis: The future: needs more genomics insight Discoveries could be greatly enhanced through genomics up to now rather conventional methods used: substantial headway in learning about the mechanisms responsible for apomixis. key structural differences between the ovaries of sexual and asexual plants that have led directly to the development of new screening tools. these, in turn, allow the identification of apomictic specimens with much greater certainty, using quicker testing procedures. The path to apomixis Steps forward: development of apomictic maize-like plants that carry a few chromosomes of Tripsacum added to the maize genome. Crossing and screening until a true apomictic maize is produced. transposons have been introduced into apomictic materials. The aim: to identify and isolate the individual genes associated with apomictic control. Candidate gene identified Molecular genetics studies have led to the identification of a very promising "candidate" gene involved in the control of apomixis. This gene (called elongate in maize) is now being cloned and experiments will soon be underway to verify its function. (why not genes ?) The candidate gene approach. Mapping shows that maize and Tripsacum exhibit a common genetic constitution. We are looking for gene(s) in maize that would be located in the same segment of the genome as apomixis is in Tripsacum (as revealed by molecular markers) and that express modifications in the mode of reproduction similar to that observed in apomicts. Elongate is the first identified candidate. Genomics could help to overcome concerns about genetic erosion with the application of apomixis A Word About Diversity A valid concern raised about the clone-like nature of apomixis is its possible effect on genetic diversity. Diversity in the agricultural systems of indstrialized countries is already fairly restricted. By contrast, in the world's developing regions, landraces, wild relatives, and farmers' cultivars may be found in close proximity. This project's focus has been on "facultative" apomixis, in which sexual reproduction occurs in approximately 3% of a population, thus allowing gene flow and diversity to continue. In Tripsacum, for example, more than 1,500 genotypes have been identified, clearly indicating that apomixis does not preclude diversity (the wide diversity between two Tripsacum genotypes is demonstrated in the photo). Nevertheless, as with any new technology, CIMMYT and its partners will exhaustively test and later assess the potential impact of apomictic maize prior to its release. Figure A shows a maize-Tripsacum F1 hybrid produced early in the project and its genetic makeup. The 36 light blue chromosomes are from Tripsacum; the 10 dark blue chromosomes are from maize. Figure B shows a more recent maizeTripsacum hybrid (BC5) resulting from extensive backcrossing and screening. The single bright yellow chromosome is from Tripsacum and the 20 faint yellow chromosomes are from maize. How success will be measured? Illustration- Real dates to be defined after crops meetings H. Iron Bean Kenya Vit A -QPM Maize S. Africa Vit A -QPM Maize NigeriaZimbabwe Vit A Cassava Ghana H. Iron Bean Nicaragua Iron Rice H. Iron Rice S.Potato Bangladesh Philippines Vit A Rwanda Thailand S.Potato Golden Rice Uganda, Vietnam-India Vit A Cassava Kenya Brazil Mozambique 2005 Years H. Iron Barley Syria H. Iron Wheat Pakistan Golden Rice Hi Iron S.Asia 2010 Example of transgenic timeline depends on crop- traits Activities Year 1 Year 2 Year 3 Gene isolation, charac. Bioinformatics Construct preparation Transformation Check for clean event Trait stability Year 6 Transgene efficacy Food safety, bioavailabitiy Biosafety trials Engage Civil Society Year 5 Transgene expression Regulatory permit Backcrossing (MAS) Exp. testing Yield Testing Seed prod..-Release Year 4 Env safety Biofortification Project Coverage Potential regional areas of impact of first tier crops Community-based efficacy studies in selected target sites. Beans Maize Cassava Maize Beans Cassava Maize Rice Wheat Beans Cassava Maize S.Potato Mapping of Ferritin Genes in Bean Amplification of a Ferritin SCAR with primers For1 and Rev2 in two parents G21242 (A) and G21078 (B) and their progenies. AB Segregating fragment . Progeny Chromosome 5 FeZn MW Std. BMd20 M1202A L0205B E0403A H1902B H1901A FERRIT2 P0903B A0102B M1201B P0904A P0902A H1802A BMd28 V1001A R0402A P0901A L0401A P0102B L0301B BM175 CLON070 P <0.0010 <0.0050 <0.0100 <0.0500 Above Increased effect from B Relative Costs of Biofortification Worldwide • 500 million vitamin A pills distributed annually – minimum cost: $125 million • $200 million public investments in iodine fortification leveraged $1.5 billion in private industry contributions Relative Costs of Biofortification Costs of Plant Breeding • $15 million over ten years: develop & test (say) high-iron, high-zinc rice and varieties adopted in limited number of countries • Fixed, one-time investment at a central location – research that can be leveraged across time and space Calcium Deficiency in Bangladesh Calcium Deficiency in Bangladesh Novel Gene Discovery is Critical Molecular Biology Clone Single Gene Study Expression of Single RNA DNA RNA Study Expression of Single Protein Protein Study Activity of Single Protein Function Genomics Sequence Entire Genome of Organism(s ) Analyze 1000’s of mRNAs (ESTs, Microarrays) Analyze 100’s of Proteins (Proteomics ) Quantify 100’s of metabolites (Metabolite Profiling) Figure 1. A diagrammatic indication of the relationship between economic development and environmental concern. The three primary economic systems of agrarian-, industrial-, and knowledge-based service are indicated with arbitrary indications of wealth and development. SO2 emission is used merely as an indicator of industrial development and the subsequent environmental concern generated The Population/Biodiversity Paradox. Agricultural Efficiency to Save Wilderness Anthony J. Trewavas Plant Physiology Jan. 2001 Future Schemen Trevavas