Strides in Building collaborations for cassava breeding

A member of CGIAR consortium www.iita.org
Strides in Building Collaborations
for Cassava Breeding
SK Hahn, AGO Dixon and other members of the
IITA Cassava Breeding Family
IITA Crop Improvement Workshop, Ibadan Nigeria 8 September 2015
TMS-IBA121635TMS-IBA121634
including many
other National,
International
and Private
Partners with
women, men,
experienced
and new
farmers in
Africa

Cassava in Africa

Future Potential for Cassava –
The Rambo Crop?
From Rosenthal and Ort (2012)

Global Agricultural Trial Repository
1,410 agronomic variables
measured are mapped to
Crop Ontology
29,633 trials out of 34,329
described use the Crop
Ontology trait names.
CO terms used for
metadata and search
http://www.agtrials.org/
Cassava – 1654 trials uploaded with 1293 uploaded by CIAT and
361 by IITA with traits conforming to ontology

Cassava Source Sink (2015 – 2019)
Metabolic engineering of carbon pathways to
enhance yield of root and tuber crops
•Andreas Gisel lead
•Physiology of root yield
•Genotypes: TMEB419, TMEB693, IBA30572,
IBA980581, IBA010040, IBA980002
•Testing of transgenics in 2018-2019
Partners:
FAU
ETH
FIF
BTI
Univ. Illinois
IITA

Drought Tolerance in Cassava
Cassava drought tolerance experiment:
– Two treatments; irrigated control and drought stressed
– Two years; two sites in Kenya; Kibwezi and Kiboko
– Five drought tolerant and five drought susceptible varieties
Findings:
– 59% reduction in fresh root yield
– Main mechanism driving drought tolerance is stomata that
respond slowly, do not close immediately when relative
humidity drops, thereby allowing photosynthesis to
continue with increased fresh root weight
– Leaf retention assists assimilate accumulation for a few
weeks
– Selection for yield is a good proxy for drought tolerance
Orek et al. (in preparation)

Cassava Markets in Nigeria
1
Source: Context Network analysis based on field research, farmer interviews, and published source analysis
2
Garri: “CTA Presentation”, October 2014
3
Industrial and Other Processed Food: “Sahel Rapid Appraisal of Nigerian Markets for Cassava”, August 2013
Nigeria Market
Share
(by Usage)1,2,3
52.4 Million MT
Production (2011)
Boil and eat – fresh consumption
Garri
Other Food Products
(fufu, lafun and others)
Industry

Processing into High Quality
Cassava Peel (HQCP) Mashes
http://news.ilri.org/2015/07/09/from-food-waste-to-animal-feed-cassava-peels-potenti

Slides from Dr. Chareinsuk
Rojanaridpiched, Thai
Tapioca Development
Institute
Example of Impact from Thailand

Three generations of improved Thai varieties
increased starch content to 23% to 29%
Slides from Dr. Chareinsuk
Rojanaridpiched, Thai
Tapioca Development
Institute

Agronomic practices for research and
farming successfully implemented

IITA contributed 500
Anagyrus lopezi introduced
from Benin to TTDI in Oct.
2009 for biocontrol of
Phenacoccus manihoti. In
Jan 2010 was first release
to 600 ha. (tapiocathai.org)
IITA contribution to solve mealy bug
threat to Thai Cassava Industry

IITA contribution to development of
cassava genomic resources
Cassava ultra-high density
map
• 532.5 Mb (~770Mb) draft
genome in 12977 scaffolds
• Composite cassava map from
10 populations used to anchor
the fragments to 18 pseudo-
chromosomes
• Resulted in v5.1 reference
genome!
• IITA contributed 9/10 of the
populations
10 Populations; 22,403
SNPs
International Cassava
Genetic Map Consortium,
Genes|Genomes|Genetics
5:133–144.likely that the LGs should be joined in the two-LG component maps
to generate single LGs. Finally, three component LGs were not
included in themergingbecausethey could not beresolved into amap
An integrated frame
With the exception of
maps were colinear with
Figure
The sc
Our co
density
Previo
clear o
a Rom
creasin

Logofoddsratio
Rabbi et al.
(2014)
Crop
Science 54
QTLs underlying key traits
(TMS961089A x TMEB117)

Major locus underlying carotenoid
accumulation in cassava roots
0
20
40
60
80
linkage group
lod
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
2011
2012
combined
PULPCOLS7520_912057
Rabbi et al. Crop Science vol. 54:

Multiple sequence alignment featuring
C/T and A/C SNP polymorphism

6128 clones genotyped and
phenotyped
West Africa, East Africa
~90K SNPs
GWAS supports narrow genetic base for
major gene resistance to CMD
CMD2 Locus
(Wolfe et al. unpublished)

Molecular markers for CBSD tolerance
in three mapping populations
Above LOD 3 is significant
1,000x more likely to be linked than independent assortment
5
Chromosome scale for a 20
MB chromosome
Var1, Site 1, Year 1 (LOD 3.92; 8.2%)
Var1, Site 1, Year 2 (LOD 3.92; 8.2%)
Var1, Site 2, Year 1 (LOD 5.07; 11.6%)
Mb 2010 15Mb 5
Var2, Site 1, Year 1 (LOD 10.75; 25.8%)
Var2, Site 1, Year 2 (LOD 6.06; 21.4%)
Var2, Site 2, Year 1 (LOD 3.91; 8.6%)
Var2, Site 2, Year 2 (LOD 3.62; 8.4%)
Var3, Site 1, Year 1
(LOD 3.56; 10.6%)
Var3, Site 2, Year 2 (LOD 4.33; 12.2%)
Tolerant parents are related: Namikonga (Kaleso), NDL06/132
and Nachinyaya
(Ferguson and students, unpublished)

Resistance to cassava green mite

Germplasm management
GRC core(256+24)
TMEB(831+59)
669 duplicates
501 unique

ADMIXTURE plots from
~4000 cassava
accessions, including
CIAT.
All samples (includes
accessions with one or
more clonal relationships
were included in the
analysis).
Below: Within individual
inbreeding coefficient (F)

Tracking of improved varieties in
Ghana using DNA fingerprinting
Individual ancestry estimated
Hierarchical clustering

Projection of
identified clones
on the Ghana
map.

Farmer-elicited variety names often
do not match specific genotypes
182 different names recorded for the entire sample collection and
here only names that occurred > 9 times are represented.
I"
II"
III"
IX "
V "
V I"
V II"
V III" X " X I" K O T EE"
A M P EN K Y EN E"
T U A K A "
A FIA 0K O FIE"
ESIA B A Y A A "
B O SO M EN SIA "
A B EN W O H A "
D EB O R "
B A N K Y E0"
K O K O O "
A N K R A "

Cassava Breeding Methods
1. Phenotypic Recurrent Selection – pedigree
selection
2. Genomic selection
3. Marker discovery leading to marker
assisted selection
4. Hybrid breeding focused on development
of inbred lines and strategies for
exploitation of heterosis
5. Polyploid Breeding

Progress in genomic-selection
breeding at IITA
SeedlingsCross
Select Genotype
Predict
Breeding
Value
Clonal
PYT
AYT
UYT
Dramatic reduction in cassava
breeding cycle length from 5 to 1
year through genomic selection
Conventional
phenotype-based
selection (> 5 years)

Genomic selection:
Prediction using many markers
Meuwissen et al. 2001: “It was concluded that selection on
genetic values predicted from markers could substantially
increase the rate of genetic gain in animals and plants.”
GEBV = Genomic Expected Breeding Value = predicted quality as a parent

Annual Breeding Cycle

Popn. Trial
Name
Locations # of plots
Ubiaja Ibadan Ikenne Mokwa
Local
germplasm
Local
Germplasm
[907plots, 1row,
5plants, unrep] 907
Genetic
Gain
Genetic Gain [764plots, 1row,
10plants,unrep]
[764plots, 1row,
10plants, unrep] 1528
Genomic
Selection
Cycle 0
GS.C0.PYT88
(from genetic
gain)
[88plots, 1row,
10plants, 2reps]
[88plots, 1row, 10plants,
2reps]
[88plots, 1row,
10plants, 2reps]
[88plots, 1row,
10plants, 2reps] 704
Genomic
Selection
Cycle 1
GS.C0.C1
Crossing Block
C0 = 86; C1 = 158
[244plots, 4rows,
20plants, unrep]
244
GS.C1
Expanded CET
[293plots, 4rows,
20plants, unrep]
[331plots, 4rows,
20plants, unrep]
[329plots, 4rows,
GS.C1.CET
(Ungenotyped)
[226plots, 1row,
10plants, unrep]
GS.C1
Expanded CET
(Ungenotyped)
[120plots, 1row,
20plants, unrep]
GS.C1.AYT40
(Ungenotyped)
[40plots, 4rows,
20plants, 3reps] 120
Genomic
Selection
Cycle 2
GS.C2 Crossing
Block
[173plots, 1row,
GS.C2.CET [381plots, 1row, 5plants,
unrep]
[447plots, 1row,
5plants, unrep]
[432plots, 1row,
GS.C2 Extra
Selections
[884plots, 1row,
5plants, unrep] 884
GS.C2 Rescued
CET
[151plots, 1row, 5plants,
unrep] 151
GS.C2.CET
(Ungenotyped)
[195plots, 1row,

Broad-sense Heritability estimates
from different trial designs
Trial Traits
Carotenoids
(calorimetric)
DM FYLD RTNO MCMDS Average
(env)
PYT88_2013.2015 0.793 0.55 0.23 0.18 0.73 0.50
Genetic Gain_Historical NA 0.26 0.14 0.14 0.59 0.28
Genetic Gain_2013.2015 NA 0.57 0.25 0.27 0.56 0.41
GS.C1.CET_2013.2014 NA 0.47 0.44 0.33 0.86 0.52
GS.C1.Expanded.CET_2014.20
15
0.730 0.68 0.75 0.64 0.67 0.69
GS.C1.CET_2013.2015 0.730 0.64 0.53 0.38 0.86 0.63
GS.C2.CET_2014.2015 0.943 0.64 0.71 0.61 0.93 0.77
GS.C1.C2.CET_2013.2015 0.721 0.44 0.47 0.43 0.82 0.58
Average (trait) 0.783 0.53 0.44 0.37 0.75 0.56

Population
Improvement
after three
cycles of
GS-based
recombination

Principal
Components
Analysis
using
filtered
SNPs

Global GCP cassava reference set
CIAT Breeders
CIAT Genebank
IITA Genebank
IITA Breeders
SEC Africa
Level-2 OTU
Sample
Size
Gene
Diversity
(He)
CIAT breeders 121 0.3465
CIAT genebank 91 0.3433
IITA breeders 102 0.3190
IITA genebank 101 0.3375
SEC Africa 123 0.3410
0 0.1
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537538
Ghana, Sierra Leonne, Togo
Muzege, Bwana Mrefu,
Nyaraboke…
“Cassava Potato”,
Kigoma
1125 SNPs

Doubled Haploid Project (2010 – 2017)
Objectives
•Development of doubled haploid technology
•Partially inbred genetic stocks – IITA role
Partners:
CIAT
NaCRRI
IITA
Consultants

Cassava Doubled Haploid Project
IITA Contribution – Development of Parially Inbred
Genetic Stocks
Seedling nursery (SN)
4,741 inbred plants from 199
families
Clonal evaluation (CE)
Ubiaja, Ibadan, Ikenne: ~500
Preliminary yield trial (PYT)
256
New Seeds
2013-2014 – 27,189
2014-2015 – 20,013

Genetic Stock Groups
1 agronomic traits Drought tolerance
2 High dry matter
3 Early Bulking
4 breeders traits Selected CASTOR progenies
5 Polyploids
6 High flowering
7 Male sterile source
8 disease/pest resistance White root CBSD resistance/tolerance
9 CMD resistance
10 CGM resistance
11 Hairy apical leaves (CGM biocontrol)
12 Multiple pest resistance, yield and dry matter
13 Genetic root necrosis
14 Yellow root CBSD Population
15 geographic location CIAT lines
16 East African lines
17 morphological traits Deep red color
18 quality High HCN potential
19 High carotenoids
20 Poundability
21 Post harvest physiological deterioration
22 High protein
23 Yellow/white roots

Challenge 1: Improve Starch Yield
• Break the dry matter content barrier to
reliably produce starch of 23 to 29%.
• TMEB419 is the standard for high starch
production in Nigeria and many countries with
starch yield near 23%. Few have
exceptionally high starch yield.
• Seasonal time of harvest is a key constraint
to starch yield with best starch production in
the dry season
– Few year round harvest datasets to document
this

Root weight vs Dry matter content
Ibadan
2− 1− 0 1 2 3
−4−202
rtwt_plant
dm
Ikenne
2− 1− 0 1 2 3
−4−3−2−1012
rtwt_plant
dm

High Starch Genotypes in Advanced Testing
High Starch set A – 7 locations, 2 years

Partnership with FMARD and NRCRI
High Starch set B, 7 locations, 2 years

Challenge 2: Reaching needs of
important beneficiaries
• Cassava breeding research must be
gender responsive and address needs of
all groups of farmers.
• Extension information reaches men easier
than women
• 2015 Cassava Monitoring Study of 2500
households in Nigeria will be very helpful
for guiding new strategies.

Gender Differentiated Cassava Preferences
• Nextgeneration Cassava Breeding Project
• Results from a pilot study in the four communities in SW and SE
Nigeria
• Focus group discussions and individual interviews were held with
women, men and youth (women and men separately)
• Results were analyzed using qualitative methods
• Questions included:
– Characteristics of Respondents
– The varieties grown
– Traits preferred (implications to the Breeding program)
– Access to resources
– Marketing and Processing
– Decision making

Preferred Traits of Dangaria

Preferred Traits of IITA

Challenge 3: Meeting end user
preferences
• Over 80% of cassava is consumed as food
• While income can purchase nutrition security,
adoption of cassava varieties in many situations
will depend on providing desired end user
characteristics.
• Includes functional properties of cassava
starches, leaf harvest, biofortification and time of
harvest/in ground storage.
• Industrial traits will have specific target niches
and will address specific markets. Do not
assume one variety will meet all needs.

Challenge 4: Breeding methods need to
be accessible to all breeders in Africa
• Improved phenotyping methods for key traits
• Field designs and analysis methods to maximize
heritability and address GxE
• Successfully implement databases and secure
and accurate data collection
• Determine the appropriate roles of genomic and
phenotypic selections with efficient use of
appropriate markers.

Cassavabase:
A global open
access resource
All Data Available with Open Access with agreement to observe the
Toronto Protocol regarding use of unpublished data

195 Traits in Cassava Ontology
Agronomic 47
Morphological 61
Physiological 3
Quality 33
Stress 51
Total 195

Challenge 5 – addressing the challenge
of dual resistance to CMD and CBSD
• Appropriate use of of different modes of
resistance and tolerance
• Production and dissemination of clean planting
materials
• Effective hybridization sites for international
exchange of botanic seed
• Safe and efficient germplasm exchange of tissue
culture clones

Effect of CMD on yield in
TMEB117 and TMEB693

Planting material Tubers Starch Ethanol
Poor quality
No
management
Poor yield
Crop
Management Increase in yieldGood quality
Quality planting material is fundamental to increase and
sustain cassava productivity
Quality planting material to manage biotic threats
Invest in clean seed systems

Production & distribution of pest-free
germplasm
Transfer to pots in isolated
growth chamber.
Disease monitoring
Screenhouse propagation of
healthy plants in treated soil.
International distribution with
Germplasm Health Statement,
Phytosanitary Certificate,
Material Transfer Agreement
and Import Permit
Plants produced by meristem-tip culture;
indexed, multiplication in vitro
Harvest material (stems,
tubers, suckers) cleaned of
soil/dirt, treated before
despatch with fungicide or
hot-water treatment.

Challenge 6 – Set and reach our
impact targets
• Set targets for each regions and design
programs to reach those targets
• Work together as a team across regions
avoiding unnecessary duplication of effort
– Breeders meetings
– Regional training workshops
• Position resources where they are needed
• Expand regional trials beginning with 5CP in
East Africa and Harvest Plus in West Africa
• Monitor results and adjust methods and targets

Regional Updates
• Set targets for each regions and design
programs to reach those targets
• Work together as a team across regions
avoiding unnecessary duplication of effort
– Breeders meetings
– Regional training workshops
• Position resources where they are needed
• Expand regional trials beginning with 5CP in
East Africa and Harvest Plus in West Africa
• Monitor results and adjust methods and targets

Suitability area for cassava in SADC
Source:
(IITA GPS lab)

Participatory Variety Selection leading to
variety release in Southern Africa
• Malawi: Mlora (83350), Phoso (LCN801),
Sagonja CH92/082 ); Chiombola (TME 6);
Kalawe (CH02/0066); Mpale (NDL90/34); and
Chamandanda (01/1313)
• Mozambique: Colicanana, Nziva, Okhumelela,
Orera and Eyope
• Zambia: Three varieties submitted for variety
release to Seed Control and Certification
Institute -SCCI)
• Biofortified clones introduced in evaluation in
Malawi, Mozambique, Zambia and Swaziland.

Cassava Breeding Achievements in East
Africa
• Tanzania: with ARI released 8 varieties for the coastal lowlands of
Tanzania in the past 5 years.
• Uganda: with NARO two breeding lines submitted for release as the
first varieties with dual resistance to CMD (especially, EACMV-UG)
and tolerance to both CBSD and UCBSD for the mid-altitude areas
of East Africa bordering Lake Victoria
• Dozens of highly promising breeding lines in advanced stages of
evaluation
• Under 5CP facilitating exchange and cooperative testing of 25 elite
clones among 5 NARS breeding programs: Malawi, Mozambique,
Kenya, Tanzania and Uganda.
• Botanical seeds from CBSD tolerant parents sent to Burundi
(6,000), Rwanda (6,000) and DR Congo (10,000) to initiate national
selection programs for specific adaptation to their agro-ecologies.

Cassava Breeding Achievements in DR
Congo
• With INERA released and registration of 21 improved varieties with
harvest period from 12 to 20 months and root yield between 21 to 47
t/ha.
• New selection approach for cassava brown streak disease (CBSD)
comprising evaluation of maturity time every 3 months and in
ground storage to 24 MAP maintaining high starch yield
• Selection for new industrial traits including dietary fibre in leaves,
amylose free starch for pasting industry and sugary cassava for
ethanol
• In partnership with INERA and HarvestPlus new biofortified
genotypes have been selected with total carotene content (TCC) up
to 15µg/g fresh weight and more than the released check TMS-
IBA01/1661 (9.5 µg/g)

Building National Programs in Sierra Leone
and Liberia
• Introduce and characterize local and advanced germplasm using
morphological, biochemical and biotechnology tools
• Generate improved and adapted populations with desired
characteristics for different agro-ecologies targeting different end
uses (farming systems, food, feed and industry) and markets
• Establish special backup populations
• Conserve a core set of local cultivars and improved germplasm
• Fast track on farm evaluation through participatory evaluation using
innovation platforms
• Expedite farmer access to quality planting materials on sustainable
basis
• Improve NARs capacity and facilities (human, financial,
infrastructure) for effective execution of germplasm development,
deployment and communication

IITA Cassava Breeding Trials in Nigeria
TRIAL TYPE 2011/2012 2012/2013 2013/2014 2014/2015
Seedling Nursery 3 4 3 4
Clonal Evaluation 2 4 9 8
Preliminary Yield Trials (PYT) 10 13 17 19
Advanced Yield Trials (AYT) 32 45 22 15
Uniform Yield Trials (UYT) 10 28 44 29
Additional Trials:
Genomic Selection Trials 1 10 18
Student Trials 14
Mapping populations/biotech 1 6 5 5
Germplasm (local
germplasm/genetic resources) 1 3 2 2
Genetic gain & Genetic stocks 2 3 4 6
Overall Total 61 107 116 120
Current program is about 50% white root and 50% biofortified

• First large scale distribution of 1st
Wave Vitamin A
Cassava in Nigeria to about 700,000 farmers in 2015
• Release in Nigeria with NRCRI of IITA-TMS-IBA070593,
IITA-TMS-IBA070539 and NR070220 with significantly
higher beta carotene levels
Pro-Vitamin A Cassava

Regional Trials and Breeders
Meeting – West Africa and DRC

Strides in Building collaborations for cassava breeding

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Editor's Notes