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3.1 session by hershey
Genetic tools and knowledge for cassava
productivity and special uses
1. What is the status of cassava production and how did
we get here?
2. Lessons learned along the way
3. Where do we want to go from here?
4. What are the tools, knowledge and systems that we
going to employ to get us there?
Intercropping
Weeds
Degraded soils
Traditional cultivation
Fundamental for food security
Low fertility
Low but stable yields
Development of management packages and new varieties
for high and efficient productivity has a history of almost
40 years in IARCs and longer in some NARS
Management
+ Genetic Improvement
Commercial planting in sub-
humid conditions
Commercial planting in acid soils
Well managed cassava
Fundamental for income
generation and rural development
1. Status of technology
• Applied breeding techniques well established
• Flow of improved varieties for many regions and
markets
• Optimum management packages (soils/agronomy)
defined for many regions and systems
• Steady yield increases in many countries
• Molecular tools advancing rapidly
Global yield trends (t/ha) for cassava
0.0
5.0
10.0
15.0
20.0
25.0
1961 1970 1980 1990 2000 2009
Asia
Americas
World
Africa
Source:
FAOSTAT
Yield trends (t/ha) in six
cassava-producing countries
0.0
5.0
10.0
15.0
20.0
25.0
30.0
35.0
40.0
1961 1970 1980 1990 2000 2009 Source:
FAOSTAT
India
Thailand
Brazil
Colombia
Nigeria
DR Congo
Yield trends - overview
• 30-40 t/ha is possible under very
good management in many
environments
• 70-80 t/ha is possible in
exceptional conditions
• Cassava is rapidly diverging into
a traditional crop for food security
and an industrial crop
However . . .
• Many people believed that by the 90s,
national programs would be able to take over
most breeding functions and IARCs could
focus on upstream and strategic research; trait
discovery for deployment by NARS.
• By the mid 90s, the effects of cutbacks in the
system were becoming evident
New Cassava pests and
diseases
• Mealy bug
• Whitefly
• Other
diseases
Emerging problems for Cassava in Asia:
The need for continued vigilance
Critical contributions of the Americas
• Diversity of cultivated cassava
• Diversity of wild species
• Diversity of pests and diseases
• Diversity of bio-control agents
New challenges: Impact of climate change
oncassava suitable environments
Global cassava suitability will increase
5.1% on average by 2050… but many major areas
of current production suffer negative impacts
Source: A. Jarvis, CIAT
2. Lessons learned
An overview
• Sustained investment in research pays off
• +/- 20-year lag between initial research investment and
substantial returns for breeding + management technology
• Genetic improvement and management contribute more or
less equally to yield gains
• Integration of production and market demand
. . . markets drive intensified management
• Most countries are not anywhere close to yield potential
• There is no status quo – the world evolves and research
efforts need to keep up
What do we want to be able to offer in
the next 20 years?
• to growers
• to processors and consumers
What do research organizations need
to do to deliver these products?
3. Where to from here?
3. What growers need
• High yield potential in a wide range of environments
• Effective management of biotic and abiotic constraints
• Cost-effective, eco-efficient crop and soil management
practices
• Plant traits that enable efficient
management
• Efficient propagation systems
• Root traits with a ready market
3. What processors and
consumers need
• Year-round access to a uniform, quality product at a
fair price
• Specific starch traits
• Good post-harvest storage
• Ease of processing (root form, peel traits, fibre
content)
• High efficiency of conversion (according to specific
end-uses)
4. How are we going to get there?
Challenges and Opportunities
• “Africa has only 70
scientists per million
inhabitants compared to
4380 scientists per million
inhabitants in Japan”
Dr Papa Abdoulaye Seck, Director General of the
Africa Rice Center (WARDA)
4. How are we going to get there?
Challenges and Opportunities for the research community
4. How are we going to get there?
Challenges and Opportunities for the research community
• Serious decline in funding in last 20 years
• Many once-strong NARS cassava programs have made
serious cutbacks in personnel and operations
• Training of the new generation has lagged
• Few national programs able to produce/manage crosses
(About 50,000 – 100,000 seeds managed for every successful
new variety developed)
• In CGIAR – the trend away from interdisciplinary core-
funded teams to special projects
• Limited private sector support in most countries
4. How are we going to get there?
Challenges and Opportunities for the research community
• Train young staff with advanced degrees
• Commit to long term support for research
• A system that fully integrates management and
genetic improvement
• A system that fully integrates molecular tools with
plant breeding
• Work to develop market demand
Research efforts to increase cassava productivity
Genebanks: The principal resource for breeding
Cassava Biodiversity
Wild Manihot species are unique
sources of genes that could be
used through breeding with
marker assisted selection,
and/or genetic transformation
BUT:
search first in M. esculenta
M. Bonierbale
Cassava Genomics Tools
Mapping Tools
- Several mapping populations linked to breeding
- ~ 450SSRS, 301 AFLP-RFLPs, 17 Genes
- MAS for CMD and Post Harvest Deterioration
- New gene based microsatellite markers identified at CIAT (1391) in
2008 and at USDA –IITA (846) in 2009
- SNP markers being developed at CIAT, U. Arizona, U. Maryland and
U. Pretoria
BAC Libraries
- 3 libraries with 5X, 10X, and 11X coverage
- Deposited at Clemson Genome Center
- Used so far by CIAT and EMBRAPA
Cost of whole genome sequencing
View in 2009
1995
1998
2005
2010
2015
10,000,000,000
1,000,000,000
100,000,000
10,000,000
1,000,000
100,000
10,000
1,000
100
May 19, 2009: $1 Per Gene,
Knome Launches $24,500
Genome Service1000 $ Genome
Adopted from Chan(2005), Mutation research.573:23-50)
June, 2007: Watson Genome
-$2 Million. 454 technology
Complete Genomics (2009 )
- $5,000
• Organizational
• Technical
4. The way forward
4. Organizational
• Move from project mode to integrated program mode for core
activities (basic breeding, agronomy, pest management)
• Participatory centralization for germplasm management
• A world genebank that can be freely exchanged (also technical)
• Revitalize national program capacity in conservation, breeding and
“seed” systems
• A molecular platform that includes broad developing country
participation (e.g. the Integrated Breeding Platform of GCP)
• Involve private sector to a greater extent
Building capacity for sustainable success!
4. Technical
• Breeding capacity
• Phenotypic characterization
• Access to genomics facilities
• Bioinformatics capacities
• Low cost rapid propagation expertise
• Capacity to transfer genes from cassava to specific genotypes
(cisgenic products)
• Development of transgenic products and how to manage the
whole process
• Access to biosafety fields
Rapidly Evolving Technologies
Phenomics Genotyping GM Microarray Proteomics Sequencing
CGIAR and Regional Infrastructures
Reducing costs
Access to technologies
Accelerate breeding
Integration with
germplasm banks
Integration with
breeding
Breeding can be made much more efficient , but . . .
The need for multi-
location, multi-
year advanced
testing (3 yrs?)
places a lower
limit.
Traits for added value
Variation in crude protein content of roots of 133 cassava clones
Fuente: Teresa Sánchez
1.00
1.20
1.40
1.60
1.80
2.00
2.20
2.40
2.60
2.80
1 5 9 13 17 21 25 29 33 37 41 45 49 53 57 61 65 69 73 77 81 85 89 93 97 101 105 109 113 117 121 125 129 133
Sqrt(%protein)
Genotype
1.4
2.0
2.6
3.2
4.0
4.8
5.8
7.8
Crudeproteincontent(%)DMbasis
Farmers produce cassava with 30%
added value.
 Stronger market demand
Reducción en el deterioro fisiológico de postcosecha en
el híbrido inter-específico M. esculenta x M. walkerae
(14 días luego de la cosecha)
MCOL 1505: 27.8%
MBRA 337: 9.48%
CM 523-7: 51.9%
CW 429-1: 0%
Fuente: C. Egesi
3.1 session by hershey
Average % amylose in the
starch: 0.0-2.9%
Fuente: Fernando Calle / Nelson Morante
“Waxy” maize has an added value of
about 30% in the marketplace
Stems
“Waxy”
cassava
Fuente : José A. Arroyave
Normal grains
Small grains
Grains with cavities
Ease of access for enzymes
Reduction in fermentation costs
Summary:
What’s limiting progress in breeding?
• Low support to NARS/CGIAR for cassava R&D
• Constraints on international shipment of germplasm
(esp. LA to Africa)
• Integration of molecular tools with field breeding
• Success with dihaploid technology – trait discovery;
deleterious recessives; breeding systems
• Ability to induce flowering – produce more crosses
• Regulatory environment for transgenics
• Targeted gene insertion via cisgenics
How?
• Developing capacity in national programs
• A long-term vision within the CG
• Developing markets that drive demand
• Public-private alliances
• North-South collaboration
TEAMS + TOOLS + TIME
THE VISION: Harvesting the sun -- A multi-purpose crop that
meets the needs of food security and income generation for
growers . . . and food, feed, fuel and diverse industrial uses in
the marketplace, through eco-efficient management systems.
3.1 session by hershey

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3.1 session by hershey

  • 2. Genetic tools and knowledge for cassava productivity and special uses 1. What is the status of cassava production and how did we get here? 2. Lessons learned along the way 3. Where do we want to go from here? 4. What are the tools, knowledge and systems that we going to employ to get us there?
  • 3. Intercropping Weeds Degraded soils Traditional cultivation Fundamental for food security Low fertility Low but stable yields
  • 4. Development of management packages and new varieties for high and efficient productivity has a history of almost 40 years in IARCs and longer in some NARS Management + Genetic Improvement
  • 5. Commercial planting in sub- humid conditions Commercial planting in acid soils Well managed cassava Fundamental for income generation and rural development
  • 6. 1. Status of technology • Applied breeding techniques well established • Flow of improved varieties for many regions and markets • Optimum management packages (soils/agronomy) defined for many regions and systems • Steady yield increases in many countries • Molecular tools advancing rapidly
  • 7. Global yield trends (t/ha) for cassava 0.0 5.0 10.0 15.0 20.0 25.0 1961 1970 1980 1990 2000 2009 Asia Americas World Africa Source: FAOSTAT
  • 8. Yield trends (t/ha) in six cassava-producing countries 0.0 5.0 10.0 15.0 20.0 25.0 30.0 35.0 40.0 1961 1970 1980 1990 2000 2009 Source: FAOSTAT India Thailand Brazil Colombia Nigeria DR Congo
  • 9. Yield trends - overview • 30-40 t/ha is possible under very good management in many environments • 70-80 t/ha is possible in exceptional conditions • Cassava is rapidly diverging into a traditional crop for food security and an industrial crop
  • 10. However . . . • Many people believed that by the 90s, national programs would be able to take over most breeding functions and IARCs could focus on upstream and strategic research; trait discovery for deployment by NARS. • By the mid 90s, the effects of cutbacks in the system were becoming evident
  • 11. New Cassava pests and diseases • Mealy bug • Whitefly • Other diseases Emerging problems for Cassava in Asia: The need for continued vigilance
  • 12. Critical contributions of the Americas • Diversity of cultivated cassava • Diversity of wild species • Diversity of pests and diseases • Diversity of bio-control agents
  • 13. New challenges: Impact of climate change oncassava suitable environments Global cassava suitability will increase 5.1% on average by 2050… but many major areas of current production suffer negative impacts Source: A. Jarvis, CIAT
  • 14. 2. Lessons learned An overview • Sustained investment in research pays off • +/- 20-year lag between initial research investment and substantial returns for breeding + management technology • Genetic improvement and management contribute more or less equally to yield gains • Integration of production and market demand . . . markets drive intensified management • Most countries are not anywhere close to yield potential • There is no status quo – the world evolves and research efforts need to keep up
  • 15. What do we want to be able to offer in the next 20 years? • to growers • to processors and consumers What do research organizations need to do to deliver these products? 3. Where to from here?
  • 16. 3. What growers need • High yield potential in a wide range of environments • Effective management of biotic and abiotic constraints • Cost-effective, eco-efficient crop and soil management practices • Plant traits that enable efficient management • Efficient propagation systems • Root traits with a ready market
  • 17. 3. What processors and consumers need • Year-round access to a uniform, quality product at a fair price • Specific starch traits • Good post-harvest storage • Ease of processing (root form, peel traits, fibre content) • High efficiency of conversion (according to specific end-uses)
  • 18. 4. How are we going to get there? Challenges and Opportunities
  • 19. • “Africa has only 70 scientists per million inhabitants compared to 4380 scientists per million inhabitants in Japan” Dr Papa Abdoulaye Seck, Director General of the Africa Rice Center (WARDA) 4. How are we going to get there? Challenges and Opportunities for the research community
  • 20. 4. How are we going to get there? Challenges and Opportunities for the research community • Serious decline in funding in last 20 years • Many once-strong NARS cassava programs have made serious cutbacks in personnel and operations • Training of the new generation has lagged • Few national programs able to produce/manage crosses (About 50,000 – 100,000 seeds managed for every successful new variety developed) • In CGIAR – the trend away from interdisciplinary core- funded teams to special projects • Limited private sector support in most countries
  • 21. 4. How are we going to get there? Challenges and Opportunities for the research community • Train young staff with advanced degrees • Commit to long term support for research • A system that fully integrates management and genetic improvement • A system that fully integrates molecular tools with plant breeding • Work to develop market demand
  • 22. Research efforts to increase cassava productivity Genebanks: The principal resource for breeding
  • 23. Cassava Biodiversity Wild Manihot species are unique sources of genes that could be used through breeding with marker assisted selection, and/or genetic transformation BUT: search first in M. esculenta M. Bonierbale
  • 24. Cassava Genomics Tools Mapping Tools - Several mapping populations linked to breeding - ~ 450SSRS, 301 AFLP-RFLPs, 17 Genes - MAS for CMD and Post Harvest Deterioration - New gene based microsatellite markers identified at CIAT (1391) in 2008 and at USDA –IITA (846) in 2009 - SNP markers being developed at CIAT, U. Arizona, U. Maryland and U. Pretoria BAC Libraries - 3 libraries with 5X, 10X, and 11X coverage - Deposited at Clemson Genome Center - Used so far by CIAT and EMBRAPA
  • 25. Cost of whole genome sequencing View in 2009 1995 1998 2005 2010 2015 10,000,000,000 1,000,000,000 100,000,000 10,000,000 1,000,000 100,000 10,000 1,000 100 May 19, 2009: $1 Per Gene, Knome Launches $24,500 Genome Service1000 $ Genome Adopted from Chan(2005), Mutation research.573:23-50) June, 2007: Watson Genome -$2 Million. 454 technology Complete Genomics (2009 ) - $5,000
  • 27. 4. Organizational • Move from project mode to integrated program mode for core activities (basic breeding, agronomy, pest management) • Participatory centralization for germplasm management • A world genebank that can be freely exchanged (also technical) • Revitalize national program capacity in conservation, breeding and “seed” systems • A molecular platform that includes broad developing country participation (e.g. the Integrated Breeding Platform of GCP) • Involve private sector to a greater extent Building capacity for sustainable success!
  • 28. 4. Technical • Breeding capacity • Phenotypic characterization • Access to genomics facilities • Bioinformatics capacities • Low cost rapid propagation expertise • Capacity to transfer genes from cassava to specific genotypes (cisgenic products) • Development of transgenic products and how to manage the whole process • Access to biosafety fields
  • 29. Rapidly Evolving Technologies Phenomics Genotyping GM Microarray Proteomics Sequencing CGIAR and Regional Infrastructures Reducing costs Access to technologies Accelerate breeding Integration with germplasm banks Integration with breeding
  • 30. Breeding can be made much more efficient , but . . . The need for multi- location, multi- year advanced testing (3 yrs?) places a lower limit.
  • 32. Variation in crude protein content of roots of 133 cassava clones Fuente: Teresa Sánchez 1.00 1.20 1.40 1.60 1.80 2.00 2.20 2.40 2.60 2.80 1 5 9 13 17 21 25 29 33 37 41 45 49 53 57 61 65 69 73 77 81 85 89 93 97 101 105 109 113 117 121 125 129 133 Sqrt(%protein) Genotype 1.4 2.0 2.6 3.2 4.0 4.8 5.8 7.8 Crudeproteincontent(%)DMbasis Farmers produce cassava with 30% added value.  Stronger market demand
  • 33. Reducción en el deterioro fisiológico de postcosecha en el híbrido inter-específico M. esculenta x M. walkerae (14 días luego de la cosecha) MCOL 1505: 27.8% MBRA 337: 9.48% CM 523-7: 51.9% CW 429-1: 0% Fuente: C. Egesi
  • 35. Average % amylose in the starch: 0.0-2.9% Fuente: Fernando Calle / Nelson Morante “Waxy” maize has an added value of about 30% in the marketplace Stems “Waxy” cassava
  • 36. Fuente : José A. Arroyave Normal grains Small grains Grains with cavities Ease of access for enzymes Reduction in fermentation costs
  • 37. Summary: What’s limiting progress in breeding? • Low support to NARS/CGIAR for cassava R&D • Constraints on international shipment of germplasm (esp. LA to Africa) • Integration of molecular tools with field breeding • Success with dihaploid technology – trait discovery; deleterious recessives; breeding systems • Ability to induce flowering – produce more crosses • Regulatory environment for transgenics • Targeted gene insertion via cisgenics
  • 38. How? • Developing capacity in national programs • A long-term vision within the CG • Developing markets that drive demand • Public-private alliances • North-South collaboration TEAMS + TOOLS + TIME
  • 39. THE VISION: Harvesting the sun -- A multi-purpose crop that meets the needs of food security and income generation for growers . . . and food, feed, fuel and diverse industrial uses in the marketplace, through eco-efficient management systems.