Presentation by Dr Emmanuel Okogbenin, National Root Crops Research Centre, Umudike, Nigeria
Delivered at the B4FA Media Dialogue Workshop, Ibadan, Nigeria - September 2012
www.b4fa.org
Nightside clouds and disequilibrium chemistry on the hot Jupiter WASP-43b
B4FA 2012 Nigeria: Cassava Research in Nigeria - Emmanual Okogbenin
1. A case study of using molecular markers
to link African cassava farmers to the
crop’s center of origin for increased
diversity and productivity
Okogbenin E., Fregene, M, Ceballos H., Egesi, C. Fulton
T., and Alves, A.
5. 17 millions hectares
Basic food for more than 500
million people in the tropics
Cassava
In Africa, Nigeria, the DRC, and Ghana
alone account for two-thirds of total
production on the continent
6. The Plant
Foliage:
A Tropical vegetable
Stems:
Planting materials
(source of cellulose)
Roots:
Unique starch properties
8. Recent projections forecast even higher dependence for
food security and poverty alleviation
Cassava
Modified Starch
Pharmaceuticals,
Processing inputs
Livestock feed
Processed foods
Industrial Starch
(e.g., drilling)
EthanolFlour
Glue
9. Pilot plant for artificial drying of cassava
roots and leaves
Flours from
roots
and/or
leaves
Animal feed
Dry extraction
of starch
Direct production
of dextrines
Direct production
of adhesives
10. Yellow Garri
White Garri
Light Yellow Garri
Yellow Garri
Yellow garri has higher
price premium than white
or intermediate colour
garri by 30-60% in Nigeria!
Great Potentials for Cassava Products in Nigeria
11. Fried cassava chips Frozen croquettes
High value-added products with excelent
potential in the export markets
Healthy (less fat than equivalent products)
Exotic
Organic
12. Cassava in BrazilCassava in Brazil
Starch – “tapioca”, “farinha de tapioca”, “beiju ”, etc
AACA-28Apr2005Photos: A. Alves
15. Westwards and Southwards Expansion of the Severe
Cassava Mosaic Disease Pandemic (Africa)
• EACMV
• ACMV
• EACMV-Ug
Cassava Belt
Known CMD pandemic
Threatened areas
CMD ‘crisis’ zones
Cassava Belt
Known CMD pandemic
Threatened areas
CMD ‘crisis’ zones
Emerging Threats
16. Cassava mosiac diease
CMD is a serious
disease in Africa and
parts of Asia (India)
It does not exist in
Latin America. Latin
American cassava are
highly susceptible
20. Cassava breeding and evaluation schemes currently used at
CIAT
Elite germplasm recombined trough sexual
crosses (hand or open pollinations).
Thousands of botanical seeds are produced each year.
Seedlings from botanical seed are grown in
screenhouses and then transplanted to the field.
Plants from botanical seed are grown (avoiding selection)
for 10 months and 7-8 stakes are produced from each plant.
One row plot with 7 or 8 plants/plot
One replication – One location
2-rows plot with 10 plants
3 replications – one location
5-rows plot with 30 plants.
3 replications – 2-3 locations
F1 [ 6000 GENOTYPES]
Clonal Evaluation Trial [4000]
Preliminary Yield trial [800]
Advanced Yield Trial [300]
Regional Trial [90]
4-rows plot with 20 plants
3 replications – one location
Shipment to Target Environment
Centro Internacional de Agricultura Tropical
International Center for Tropical Agriculture
21. The challenges for Nigeria:
Solving problems and adding useful traits to the crop
Sustaining steady and stable yield levels
Enhancing cassava nutritional quality in vitamins
and protein contents for the malnourished poor
Creating an export-market driven cassava
industry
Transforming cassava into a major player for
economic development and wealth creation
23. Brazil (160)
Mean = 2.9 %
COL / VEN (184)
Mean = 3.0 %
PER / ECU (87)
Mean = 2.2 %
PAR / ARG (8)
Mean = 3.1 %
Caribbean (8)
Mean = 2.9%
Central America (26)
Mean = 4.8 %
MEX / USA (13)
Mean = 3.5 %
Frequencies for
protein content
in the roots from
landraces in the
germplasm collection
24. Commonly reported protein levels
0
2
4
6
8
10Crudeproteincontent(%)
MGUA91
MCOL2436
MGUA86
MCOL219
SM734-5
CM3236
MGUA76
MCOL2694
MCOL2459
MBRA300
MGUA79
MBRA101
MMEX108
SM1406-1
MMEX95
MCOL678
SM673-1
Crude protein content (%) in selected clones measured in 1999 and 2005
1999:quantification in Australia
2005: quantification in Colombia
25. Yield potential in cassava
Cultivar:
SM 1433-4
Yield:
84 t/ha
Area:
9.5 ha
Location:
Ciénaga de
Oro (Córdoba)
The challenge is to turn
this into the rule,
not the exception
In every Department
35. Traits that we hope to generate and identify variation for:
Starch quality:
Low or no amylose
Low or no amylopectin
Different granule size
Change in P-bound starch
“Sugary” cassava
Variation in starch quality
and distribution in cassava
roots from Brazilian
landraces
37. “Diversity”: What does it mean?
Variability among living organisms
Biological Diversity, genetic diversity
Genomic diversity - on a whole genome scale
Cowpea at IITA, Nigeria
38. Levels of diversity
Among species; within ecosystems
Within a species: among populations or individuals
Intra-species variation
(within a species)
Inter-species variation
(between species)
39. Allelic diversity
Alleles are variants of a particular gene or DNA segment
Example: eye color
Image from Discovermagazine.com
40. Gregor Mendel
In >30,000 crosses, Mendel
studied the inheritance of 7 traits
In Peas (Pisum sativum)
41.
42. DNA: the most basic level of
diversity
Each DNA strand is composed of a string of
nucleotides, which are formed from a pentose
sugar, a phosphate group, and either adenine,
guanine, thymine or cytosine (abbreviated as A,
G, T, or C).
The order of the four bases in the DNA sequence
of each individual organism is unique.
It carries all the genetic information needed for
the organism to function.
These illustrations from the Human Genome Project Information site
(http://www.doegenomes.org/) show two views of the structure of DNA.
43. Morphological markers versus Molecular markers
I. Morphological markers
• mutations normally in exons
• usually gene knockouts
• often deleterious
• usually recessive (lose half information for
genome mapping)
• attached to function
ª epistasis a problem
• low natural polymorphism, often mono-allelic
II. Molecular markers
microsatellites polymorphism among maize inbreds
Chlorophyll mutant in pepper
• any part of genome
• often neutral
• codominant (maximum info for
mapping)
• usually no function attached
• no epistasis
• high natural variation, multi allelic
mC A C IN/DEL
44. Molecular markers -- detection of genetic variation at the protein
or DNA level
Protein level:
• Isozymes analysis using non-denaturing gel electrophoresis and enzyme activity stains
DNA level:
•Restriction fragment length polymophism (RFLP)
•Random amplified polymorphic DNA (RAPD)
•Amplified fragment length polymorphism (AFLP)
•Microsatellites (simple sequence repeat, SSR) detection
•Cleaved amplified polymorphisms (CAP); also called Sequence characterized amplified
polymorphisms (SCAR)
•Single stand conformational polymorphism (SSCP)/ Denaturing gradient Gel
electrophoresis (DGGE)
•Denaturing high pressure liquid chromotography (cHPLC)
•Single nucleotide polymorphism (SNP) detection
• DNA chips (allele specific arrays)
•Taqman assays
•Invader technology
•DNA TILLING
46. The complete set of DNA that an individual inherits from its
parents
The genotype of an individual remains unchanged throughout its life,
regardless of the environment surrounding and affecting it
Although DNA is the basis of a genotype, we can study genotypes
without knowing the DNA sequence
Genotype
47. ManihotManihot
esculentaesculenta
• Genome : 770Mbp
• Genetic resources
• Extensive knowledge on the
genetic diversity
• Different tools :
- genetic maps
- markers
- BAC librairies
- ESTs, microarrays
- transformation
- silencing (VIGS)
• Pests and diseases
Cassava : crop of the futureCassava : crop of the future
48. RAPD Bulk Segregant Analysis of
Resistance to Whitefly
RR11 SS11 RR22 SS22 RR33 SS33 RR44 RR55
R1 and S1: CG 489-34 x MCol 2026
R2 and S2: MBra 12 x MCol 2026
R3 and S3: CG 489-34 x MCol
1505 R4: Ecu 72; R5:Ecu 72
progeny.
49. 2SSR and 2 SCAR marker explains between 90 -
100% of phenotypic variance for CMD resistance
Dist Marker
cM Name
rGY115
7.9
rGY9
15.6
rGY1
16.1
rSSRY28
11.3
Ai19
CMD2
R
CMD Resistance F1 progeny CMD Susceptible F1 progeny
150bp
RP/SP/RB/SB
200bp
175bp
Akano et al 2001 Theor and Appl Genet 105:521-525
Gene Tagging: Resistance to the
Cassava Mosaic Disease (CMD)
Funding: Rockefeller Foundation
51. 144 F1s144 F1s
Resistant to ACMV
Resistant to CBB
Early Bulking
Resistant to ACMV
Resistant to CBB
Early Bulking
Good Cooking Quality
Resistant to CBB
High Photosynthesis
Good Cooking Quality
Resistant to CBB
High Photosynthesis
XX
TMS30572TMS30572
Female ParentFemale Parent Male ParentMale Parent
CM2177-2CM2177-2
60. MAS for CMD Resistance at CIAT
Sexual Seeds
Embryo Rescue
PCR Amplificatión
Shipment to partners To Breeding scheme
S S S R S S R R S R S S S S R S S S S R S S R S R R R R S S S S R C R R S S R S S S
R S R R R R R S R R R R S S S S S S R R R R S R S R S S R R R S S S S S R R S R S R S S
Progenies of TME3 x CIAT Elite parents
62. MAS: CMD and CGM
SCAR in
agarose
gel
NS 158 in
acrilamide
1014NO15RS
MCOL
2206C-243CR53-411
1013YES14RR
MCOL
2206C-243CR53-310
1012NO13SR
MCOL
2206C-243CR53-29
1010NO12S´C-243SM1219-9CR-52B-18
1009YES11RRSM1219-9C-243CR52A-437
1007YES9RRSM1219-9C-243CR52A-416
1006YES8RRSM1219-9C-243CR52A-405
1005YES7RRSM1219-9C-243cr52a-394
1004NO6SRSM1219-9C-243CR52A-383
1003YES5RRSM1219-9C-243CR52A-372
998NO1S-SM1219-9C-243CR52A-321
TEJIDO
CAMPO/ENVI
ONo.SCAR RME 1SSRY 158FRASCOS CC
CÓDIGOPARAPOSOEVALUACIÓN
EVALUACIÓ
NNÚMERODEPADREMADRECODIGOITEM
PLACANo9CMD
EVALUACI
ÓN:FORMATOEVALUACIÓNPARA MAS.
1014NO15RS
MCOL
2206C-243CR53-411
1013YES14RR
MCOL
2206C-243CR53-310
1012NO13SR
MCOL
2206C-243CR53-29
1010NO12S´C-243SM1219-9CR-52B-18
1009YES11RRSM1219-9C-243CR52A-437
1007YES9RRSM1219-9C-243CR52A-416
1006YES8RRSM1219-9C-243CR52A-405
1005YES7RRSM1219-9C-243cr52a-394
1004NO6SRSM1219-9C-243CR52A-383
1003YES5RRSM1219-9C-243CR52A-372
998NO1S-SM1219-9C-243CR52A-321
TEJIDO
CAMPO/ENVI
ONo.SCAR RME 1SSRY 158FRASCOS CC
CÓDIGOPARAPOSOEVALUACIÓN
EVALUACIÓ
NNÚMERODEPADREMADRECODIGOITEM
PLACANo9CMD
EVALUACI
ÓN:FORMATOEVALUACIÓNPARA MAS.
CoP has effectively integrate MAS with field-based strategies
63. A SCAR marker RME1 and an SSR marker,
NS158, could predict CMD resistance >90% of the
time
MAS provides an efficiency gain of up to 20%
over phenotypic selection, could be much higher
where disease pressure is lower
MAS for CMD Resistance:
S S S R S S R R S R S S S S R S S S S R S S R S R R R R S S S S R C R R S S R S S S
R S R R R R R S R R R R S S S S S S R R R R S R S R S S R R R S S S S S R R S R S R S S
67. From conventional to MAB schemes
Figure 1. Germplasm selection scheme of cassava
Crossing Block(s)
Source population for
target ecology
Seedling nursery
50,000-100,000
seedlings
(no replication)
Clonal evaluation
500-3,000 clones
(1 replication)
Preliminary yield trial
100-200 clones
(2 replications)
Advanced yield trial
about 50 clones
(4 replications)
Uniform yield trial
15-25 clones
(4 replications)
On-farm trials (2-5 elite clones),
multiplication and release
NARS
Year 5
Year 4
Year 3
Year 2
Year 1
NARS
Screen for:
resistance to diseases and
pests, root conformation (pre-
and post-harvest handling)
and plant characteristics
Further screen for:
resistance to diseases and pests,
root conformation (pre- and
post-harvest handling) and plant
characteristics
Evaluate for yield and food quality
characteristics
Further screen for:
resistance to diseases and pests, root
conformation (pre- and post-harvest
handling) and plant characteristics
Further evaluate for
yield and food quality
characteristics
Evaluate for yield, food
quality and adaptation in
multilocations
Selection
scheme
Feedback
69. The Molecular Genetic Diversity of
Cassava Network (MOLCAS)
SSR diversity of Cassava Land Races
-20
-15
-10
-5
0
5
10
15
20
-20 -15 -10 -5 0 5 10 15 20 25 30
PC1 (36%)
PC2
(28%)
Tanzania Mtwara
Tanz. Kibaha
Tanz. Naliendele
Argentina
Brazil
Colombia
Mexico
Peru
Venezuela
Nigeria
Thailand
Guatemala
Differentiation of
Genotypes From Latin
America and Africa
Automated and
Silver-stained
SSR analysis of
Cassava Diversity
http://www.ciat.cgiar.org/molcas
Supported by IPICs/SAREC amd CIAT
71. MAS bred varietiesMAS bred varieties
Three genotypes at farmers
level, four additional
selected for national wide
testing in Nigeria
Yield 57.5 t/ha in Uganda;
58 t/ha in Ghana; 48t/ha
Nigeria
Multiplication of best CMD
resistant and CGM tolerant
CR 37-108 CR 36-2
CR 14A-1
CR 36-5
74. MAB varieties
UMUCASS33 released in
Nigeria in 2010
Another variety is under
process for release in
Nigeria
Tanzania released two
varieties in 2012
Ghana has four entries in
pre-release trials
77. Bringing the Benefits of
Modern Science to Farmer’s
Fields
Demonstrate superior yield
and quality to farmers and
processors for accelerated
adoption of new pest and
disease resistant cassava
varieties
Disseminate farmer-preferred
varieties by integrating formal
(scientist-led) and farmer-
driven multiplication of
improved materials
78. Cassava Value Chains
7
8
HQCF
High Quality Cassava Flour (HQCF)
Principal market –replacement of up to 10% wheat flour in bread; others – food industry, adhesive
industry, dextrins. Demand is over 400,000 tons per year.
Starch
Native and modified starches
We have two functional starch mills in Nigeria with a combined capacity of 27,000 tons (although
they currently operate below capacity).
Demand is 230,000 tons per year currently met by corn starch imports.
Chips
Dried Chips
Principal market – to meet internal and external demand of cassava for industrial use. China’s
demand is expected to exceed 12 mill tons by 2015/16 due to their large ethanol production. Demand
is 520,000 tons per year from China and 400,000 tons
HFCS
Sweeteners - High Fructose Cassava Syrup (HFCS)
The total sugar requirement for soft drink bottlers and juice manufacturers in Nigeria is estimated at
200,000 tons of sugar p/a. A replacement of half of this by HFCS from cassava, would create a
100,000 ton demand.
Ethanol
Fuel Ethanol (E10)
Nigeria has adopted the policy of blending gasoline with 10% ethanol, the E-10 policy. This
represents a potential one billion liter per year market of fuel ethanol and 3.75billion for cooking fuel,
assuming 50% of feedstock comes from cassava, a raw material requirement of over 3 million tons of
dried chips is required.
