Biotech and innovative breeding for the new Agri-Food System CGIAR Research Programs (CRPs)
1. 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
2. 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
5. 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
7. 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
8. 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.
9. 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)
10. 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
11. 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
12. 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
17. 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)
18. 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)
19. 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)
20. 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
21. 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
23. 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
25. 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
28. 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.
29. 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
30. 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.
36. 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
39. 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
41. 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/
43. 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
44. 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
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