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Biotech and innovative breeding for the new Agri-Food System CGIAR Research Programs (CRPs)
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10th Asia-Pacific Biotech Congress, Bangkok Thailand By P. Ellul, Senior Officer, CGIAR System Organization 25-27 July 2016
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Biotech and innovative breeding for the new Agri-Food System CGIAR Research Programs (CRPs)
- Biotech and innovative breeding for the new Agri- Food System CGIAR Research Programs (CRPs) 10th Asia-Pacific Biotech Congress, Bangkok Thailand P. Ellul, Senior Officer CGIAR System Organization 25-27 July 2016
- www.cgiar.org Yield increase and the Green Revolution • Pilot program (1940s-50s) for developing semi-dwarf, high- yield and disease-resistant varieties • Mexico self-sufficient in wheat in the 1950s • Varieties imported by India and Pakistan => Green Revolution 1 • CIMMYT created in 1966 (Rockefeller and Ford Foundations, and the Mexican Government) Norman Borlaug 1970 Nobel Peace Price
- www.cgiar.org CGIAR from 1971 to 2011 2
- www.cgiar.org CIMMYT Mexico City Mexico IFPRI Wash. DC USA CIP Lima Peru CIAT Cali Colombia Bioversity International Rome Italy AfricaRice Bouaké Côte d’Ivoire IITA Ibadan Nigeria ILRI Nairobi Kenya World Agroforestry Nairobi Kenya ICARDA Beirut Lebanon ICRISAT Patancheru India IWMI Colombo Sri Lanka IRRI Los Banos Phillippines World Fish Penang Malaysia CIFOR Bogor Indonesia 3
- www.cgiar.org 1st Strategic Research Framework (2008) 4 • Donors united in CGIAR Fund • 15 Centers collaborating in transversal cross-cutting CGIAR Research Programs (CRPs) • 1st Portfolio of 16 CRPs • 80% part of CGIAR’s work, through CRPs • Focused on delivering + development outcomes • CGIAR funding average growth ... from $0.7B USD (2011) to $1B USD in 2014
- www.cgiar.org 16 CGIAR Research Programs (CRPs) 5
- www.cgiar.org 16 CGIAR Research Programs (CRPs) 6 • MAIZE • WHEAT • GRiSP (Global Rice Science Partnership) • Roots, Tubers & Bananas • Dryland Cereals • Grain Legumes • Livestock & Fish • Humid Tropics • Aquatic Agricultural Systems • Dryland Systems • Climate Change, Agriculture and Food Security (CCAFS) • Forests, Trees and Agroforestry (FTA) • Water, Land and Ecosystems (WLE) • CRP for Managing & Sustaining Crop Collections • Policies, Institutions & Market • Agriculture for Nutrition & Health
- www.cgiar.org CGIAR Strategy 2017–2030 2nd CGIAR’s Strategy and Results Framework (SRF) 2017–2030 is ambitious. It defines our aspirations and strategic actions to deliver on our mission. Our vision: A world free of poverty, hunger and environmental degradation. Our Mission: To advance agri-food science and innovation to enable poor people, especially poor women, to increase agricultural productivity and resilience, share in economic growth, feed themselves and their families better, and conserve natural resources in the face of climate change and other threats.
- www.cgiar.org New SRF and the second generation of CRPs New SRF guides the development and implementation of an ambitious portfolio of “second-generation” CGIAR Research Programs (CRPs) Focuses on selected grand challenges, and is articulated in 3 strategic goals, or System Level Outcomes (SLOs), which by 2030 will contribute significantly to the achievement of key Sustainable Development Goals (SDGs)
- www.cgiar.org System Level Outcome (SLO) 1 Reduced Poverty • 350 million more farm households should have adopted improved varieties, breeds or trees, and/or improved management practices • 100 million people, of which 50% are women, assisted to exit poverty Targets for 2030
- www.cgiar.org System level Outcome (SLO) 2 Improved Food & Nutrition Security for Health • Yield increase rate of major food staples from current <2.0 to 2.5%/yr. • 150 million more people, of which 50% are women, meeting minimum dietary energy requirements • 500 million more people, of which 50% are women, without deficiencies of one or more of the essential micronutrients • 33% reduction of women in reproductive age who are consuming less than the adequate number of food groups Targets for 2030
- www.cgiar.org System level Outcome (SLO) 3 Improved Natural Resource Systems & Ecosystem Services • 20% increase in water and nutrient (inorganic, biological) use efficiency in agro-ecosystems, including through recycling and reuse • Reduce agriculturally-related greenhouse gas emissions by 0.8 Gt CO2-e yr–1 (15%) compared with a business as usual scenario in 2030 • 190 million hectares (ha) degraded land restored • 7.5 million ha of forest saved from deforestation Targets for 2030
- www.cgiar.org The 2nd generation of CRPs (2017-22)
- www.cgiar.org CGIAR Genebanks (CRP / Platform) 25 food crops and 740,000 accessions Accessions AfricaRice Rice 20,000 Bioversity Banana, Plantain 1,298 CIAT Beans, Cassava, Tropical forages 65,635 CIMMYT Maize, Wheat 155,129 CIP Potato, Sweet potato, Andean Roots & Tubers 16,495 ICARDA Grain legumes, Wheat, Barley, Forage & range crops 135,406 ICRAF Trees 5,144 ICRISAT Dryland cereals, Grain cereals 156,313 IITA Banana, Plantain, Maize, Cowpea, Cassava, Yam 28,286 ILRI Tropical forages 18,291 IRRI Rice 116,817 Total 712,568
- www.cgiar.org Agri-Food System’ s workflow & biotech PGR managers Researchers (Pre-breeders) Seed multiplication Seed Quality Control Seed storage Seed dissemination SNP validation Gene pyramiding MAS Genomic Selection Genome editing Genetic engineering Multi-location field trials Pre-breeders Researchers Breeders Genetic Diversity Seed Systems Variety Improvement Trait Discovery Genebanks & passport data Genotyping/genomic data (GbS, Reseq.) Phenotypic data Geo-location data • Mapping lines • QTL discovery • Gene discovery • SNP discovery • Doubled Haploids • Mutagenesis • Genetic engineering • Reverse breeding • Trait performance Value chain, systems’ analysis, etc… Breeders Implementers/ technicians Seed Researchers Implementers, developers Multidisc. Res. (ecology, social sciences,…) Foresight Cropping systems Value chain Scaling out Post harvesting technologies Capacity building Other SAI approaches
- www.cgiar.org Agri-Food System’ s workflow & biotech SNP validation Gene pyramiding MAS Genomic Selection Genome editing Genetic engineering Multi-location field trials Pre-breeders Researchers Breeders Genetic Diversity Seed Systems Variety Improvement Trait Discovery • Mapping lines • QTL discovery • Gene discovery • SNP discovery • Doubled Haploids • Mutagenesis • Genetic engineering • Reverse breeding • Trait performance Value chain, systems’ analysis, etc… Breeders Implementers/ technicians
- www.cgiar.org Leading international sequencing consortia ICRISAT / Grain Legumes & Dryland Cereals CRPs Chickpea (Nature Biotechnology- 2013) Pigeonpea (Nature Biotechnology- 2012) Pearl millet- 2016 Kindly provided by Dr Rajeev Varshney (ICRISAT/ Grain Legumes and Dryland Cereals)
- www.cgiar.org Co-leading international sequencing consortia ICRISAT / Grain Legumes & Dryland Cereals CRPs Sesame (Genome Biology 2014) Kindly provided by Dr Rajeev Varshney (ICRISAT/ Grain Legumes and Dryland Cereals) Mungbean (Nature Communication- 2014) Pearl millet- 2016 (in revision)
- www.cgiar.org From re-sequencing 300 chickpea accessions… to the 3K genome initiative 4.9 Million SNPs 596,000 indels 512,000 CNVs Kindly provided by Dr Rajeev Varshney (ICRISAT/ Grain Legumes and Dryland Cereals)
- www.cgiar.org Sequencing 3,000 rice accessions indica aus temperate tropical japonica aromatic admixed GRiSP CAAS Kindly provided by Dr. Ken Mc Nally (IRRI/GRiSP) From Alexandrov, et al. SNP-Seek database of SNPs derived from 3000 rice genomes. Nucl. Acids Res. 2015;43(D1):D1023-D1027
- www.cgiar.org Rice SNP-Seek database / 20 Million SNPs From Alexandrov, et al. SNP-Seek database of SNPs derived from 3000 rice genomes. Nucl. Acids Res. 2015;43(D1):D1023-D1027
- www.cgiar.org High density genotyping: Seed of Discovery http://seedsofdiscovery.org
- www.cgiar.org High density genotyping: Seed of Discovery ● Maize: ~27,000 accessions in CIMMYT’s genebank o Developed new GbS method for composite DNA samples (30 plants per accession); the method simultaneously Quantifies allele frequencies within accessions (SNP), and Estimates genetic distances among accessions o Completed the sequencing of 20,000 accessions diversity analysis in progress ● Wheat: ~140,000 accessions in CIMMYT’s genebank o Completed sequencing of 42,000 accessions o Data being used to assemble AM panels Kindly provided by Dr. Peter Wenzl, ex-SeeD Project leader at CIMMYT; currently Genebank Manager at CIAT
- www.cgiar.org High density genotyping: Seed of Discovery
- www.cgiar.org Translational genomics for agriculture From Varshney et al., PLOS Biology 2014 http://journals.plos.org/plosbiology/article?id=info:doi/10.1371/journal.pbio.1001883
- www.cgiar.org Engineering biofortified rice varieties
- www.cgiar.org Engineering biofortified rice varieties OsNAS2 = rice nicotianamine synthase SferH-1 = soybean ferritin gene
- www.cgiar.org Engineering biofortified rice varieties Fe concentration (μ g g−1 DW) of polished seeds harvested from T1 homozygous plants of representative NAS, Fer, and NASFer events, null segregant, and non-transformed rice under greenhouse conditions.
- www.cgiar.org Engineering biofortified rice varieties Proof of concept = attaining Fe/Zn nutritional targets under flooded field conditions to fulfil 30% of EAR (Estimated Average Requirement) in the human diet
- www.cgiar.org Impacting research for development => multi-institutional + multi-disciplinary 1. Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute (IRRI), Manila, Philippines. 2. Centro Internacional de Agricultura Tropical (CIAT), Cali, Colombia. 3. Social Sciences Division, IRRI, Manila, Philippines 4. Faculty of Geo-Information and Earth Observation (ITC), University of Twente, The Netherlands. 5. Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan. 6. Centre for Environmental Risk Assessment and Remediation, University of South Australia, Australia. 7. United States Department of Agriculture-Agricultural Research Service, Cornell University, USA. 8. School of Biological Sciences, Flinders University of South Australia, Adelaide, Australia. 9. School of Botany, The University of Melbourne, Victoria 3010, Australia. 10. Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development, Bogor, Indonesia. 11. Research Center for Biotechnology, Indonesian Institute of Sciences, Cibinong, Indonesia.
- www.cgiar.org Sweet potato : a naturally transgenic crop ? Root, Tubers and Bananas CRP
- www.cgiar.org Blue sky biotech research: the C4 rice project www.c4rice.irri.org
- www.cgiar.org Challenge: Kranz (C4) anatomy into C3 plants
- www.cgiar.org Roadmap of the C4 rice project www.c4rice.irri.org
- www.cgiar.org C4 rice principal investigators
- www.cgiar.org Disruptive technology: Genome Editing (GE) GE is the process of precise genome modification using engineered endonucleases Nucleotides can be • added • deleted • replaced
- www.cgiar.org Disruptive technologies: Genome Editing
- www.cgiar.org Pigs edited to protect them against African Swine Fever (Roselyn Institute, University Edinburgh)
- www.cgiar.org GE => Interspecies allele introgression in one generation • RELA (transcription factor) is one of the pig genes associated with ASFV infection. • RELA gene causes the immune system to overreact with devastating effects • Warthogs and bush pigs – both more resilient to ASFV - carry a different allelic version of the RELA gene => by changing ‘only’ 5 nucleotides in the pig RELA gene, it is converted into the resistant-gene that is found in the warthog. From Science Daily, 23 February 2016. www.sciencedaily.com/releases/2016/02/160223132535.htm
- www.cgiar.org Genetic engineering or Genome editing ? From “ Root, Tubers and Bananas” CRP full proposal
- www.cgiar.org Genetic engineering or Genome editing ? From “ Root, Tubers and Bananas” CRP full proposal http://www.cgiar.org/our-strategy/second-call-for-cgiar-research-programs/cgiar- research-programs-platforms-full-proposals-for-review/
- www.cgiar.org Genome Editing (GE) & Freedom To Operate? www.pipra.org Public Intellectual Property Resource for Agriculture
- www.cgiar.org Conclusions CGIAR Portfolio 2017-22 addresses the [3 SLOs s + n SDGs] 8 Agri-Food System (AFS), 4 Global Integrating CRPs and 3 platforms (Excellence in breeding, Genebank, Big data) Genomic characterization (sequencing and re-sequencing) High throughput genotyping and phenotyping Translational genomics and pre-breeding: Molecular Assisted Selection (MAS), Genomic Selection (GS), Genome Wide Association Studies (GWAS), etc… Genetic engineering for specific traits Genome editing for specific traits
- www.cgiar.org Our main donors Australia Austria Bangladesh Belgium Bill & Melinda Gates Foundation Canada China Denmark European Commission Finland France India International Fund for Agricultural Development Iran Ireland Japan Korea Luxembourg Mexico Morocco Netherlands New Zealand Norway Portugal Russia South Africa Sudan Sweden Switzerland Thailand Turkey United Kingdom United States of America World Bank
- www.cgiar.org Thank you
Editor's Notes
- CIMMYT grew out of a pilot program sponsored by the Mexican government and the Rockefeller Foundation in the 1940s and 1950s aimed at raising farm productivity in Mexico. The wheat specialist in that program, Norman Borlaug, worked with Mexican researchers and farmers to develop hardier, short-stemmed wheat varieties that resisted devastating rust diseases and yielded much more grain than traditional varieties. The new wheat lines were bred and selected at various Mexican locations in a range of climate conditions, which meant they were adaptable to a range of farm settings. The higher yielding varieties helped Mexico attain self-sufficiency in wheat production in the 1950s. Additionally, the varieties were imported by India and Pakistan in the 1960s to stave off famine, soon bringing those countries record harvests. This led to the widespread adoption of improved varieties and farming practices, which became known as the “Green Revolution.” CIMMYT was formally launched as an international organization in 1966. Borlaug, who worked at CIMMYT as a wheat scientist and research leader until 1979, received the 1970 Nobel Peace Prize
- ICRISAT (Rajeev Varshney) led international sequencing consortium to sequence genomes of pigeonpea, chickpea and pearl millet.
- Rajeev co-led genome seqencing groundnut, mungbean, sesame, and Adzuki bean.
- Now, ICRISAT is leading The 3000 Chickpea Genome Sequencing Initiative funded mainly by Ministry of Agriculture, Government of India and also from Australia and Canada. In addition to ICRISAT, IIPR, Junagadh Agricultural Uni, Rajasthan Agricultural Research Institute, Regional Agricultural Research Station-Sehore, ICARDA, Uni of Western Australia and Uni of Saskatchewan are the partners in this project. They are sequencing 3000 chickpea lines and also phenotyping this collection at six different locations. CNV = large segments of DNA, ranging in size from thousands to millions of DNA bases, varying in copy-number (more than two in diploid); they are copy number variations or CNVs
- That allows GWAS in Maize and GS in Wheat Association Mapping in W & M Interest of private partners (big 6), ARIs (Cornell); contractual and IP issues on “in silico” or “dematerialized” germplam information
- Excellence in science and research/ published in Nature in feb 2016
- Construct include NASFer-274 containing rice nicotianamine synthase (OsNAS2) or soybean ferritin (SferH-1) genes and both of them in the same construct Rigorous selection was applied to 1,689 IR64 transgenic events for insert cleanliness and, trait and agronomic performances. Single locus insertion without a yield penalty or altered grain quality were selected
- 10 research centers and 6 countries (North / South)
- C3 carbon fixation is one of three metabolic pathways for carbon fixation in photosynthesis, along with C4 and CAM. This process converts carbon dioxide and ribulose bisphosphate (RuBP, a 5-carbon sugar) into 3-phosphoglycerate through the following reaction In the majority of plants, including rice, CO2 is first fixed into a compound with three carbons (C3) by the photosynthetic enzyme ribulose bisphosphate carboxylase oxygenase (Rubisco) The fundamentals of C4 photosynthesis are shown in a simplified form in the figure on the right. The photosynthesis processes of C4 plants are divided between mesophyll and bundle sheath cells. Two steps of C4 photosynthesis that occur in the mesophyll cells are the light-dependent reactions and a preliminary fixation of CO2 into a molecule called malate (C4). Rubisco is inherently inefficient because it can also catalyze a reaction with oxygen from the air, in a wasteful process known as photorespiration (rather than photosynthesis). At temperatures above 20°C, there is increasing competition by oxygen (O2), with a dramatic reduction in CO2 fixation and photosynthetic efficiency. While all this is happening, water is escaping from the leaves while the CO2 is diffusing in. Thus, in the hot tropics where most rice is grown, photosynthesis becomes very inefficient.
- C4 plants are more efficient in carbon dioxide concentration that results in increased efficiency in water and nitrogen use and improved adaptation to hotter and dryer environments. In nature, this has occurred more than 50 times in a wide range of flowering plants, indicating that, despite being complex, it is a relatively easy pathway to evolve. Kranz (C4) anatomy arose before the C4 biochemistry within the bundle sheath cell, in response to photorespiration. Therefore, strategies to engineer C4 photosynthesis should first address the introduction of Kranz anatomy (= wreath bundle sheath cells) into C3 plants.
- Long term project Funded by BMGF for IRRI
- A U.S. National Science Foundation (NSF)–funded collaborative project between Yale and Cornell universities is using laser micro-dissection technologies to capture specific cell types in sorghum, maize, and rice leaves for further analysis of proteins and gene transcripts. A quantitative inventory of these molecules in each cell type will provide information regarding the regulation of gene expression and will explain how sorghum, maize, and rice plants differ in photosynthesis and in other cellular functions. We intend to integrate information from the NSF and this project using bioinformatics and systems modeling. At Washington State University and the University of Toronto, extensive research is being conducted on the structural and biochemical diversity among the 19 families of plants found to have C4 species, and on the progressive evolution from C3 to C3-C4 intermediates, and to C4 photosynthesis. Julian Hibberd (Cambridge) and Peter Westhoff (Dusseldorf) have been developing molecular tools to enable cell-specific genes to be introduced into rice via transformation.
- Warthog = Phacochoerus africanus (closed to wild boar)
- PIPRA was created in 2004 with support from the Rockefeller and McKnight Foundations. The initial members of the PIPRA network included the University of California (Oakland, Davis and Irvine); the Donald Danforth Plant Science Center; North Carolina State University; Ohio State University; Boyce Thompson Institute for Plant Research; Rutgers, The State University of New Jersey; Michigan State University; Cornell University; University of Wisconsin-Madison; and University of Florida
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