grm 2011: improving cassava to withstand drought and disease in africa ‒ e okogbenin
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Cassava CI projects Project 1: Development of a genetic resources base
for drought and biotic stress improvement in cassava – M. Ferguson
Project 2: Improving and Deploying Markers for Biotic Stresses in Cassava – C. Egesi
Project 3: Implement MAS Project for drought tolerance – E. Okogbenin
Project 4: Project 4: QTL analysis of drought tolerance in South America – A. Alves
Project 5: A Cassava Breeding Community of Practice in Africa for Accelerated Production and Dissemination of Farmer-Preferred Cassava Varieties Resistant to Pests and Diseases – E. Okogbenin
Overall objective Overall objective: To deliver a set of germplasm to NARS breeders that encompasses diversity per se as well as trait-based diversity to be incorporated into breeding programs to broaden the genetic base for enhanced genetic gain.
Observations: 1. Breeders germplasm in many NARS
breeding programs in SEC Africa had a narrow genetic base
2. Breeders found it difficult to acquire new germplasm. What germplasm to request?
0 0.5
DRC
Kenya
Madagascar
Rwanda
Tanzania
Mozambique
Uganda
Project1: Development of a genetic resources base for drought and biotic stress improvement in cassava
Morag
• 250 accessions
• The number of accessions selected per cluster was proportional to the log of the number of accessions in that cluster. The methodology used was thought to represent diversity yet minimise population structure.
• Of 250, 102 from IITA, 144 from CIAT and 4 from EMBRAPA
• Represents 82.5% of alleles of composite set
• 29 of 46 countries represented (63%)
• The reference sets have been placed in vitro
GCP Phase 1: (2) Selection of CIAT/IITA/EMBRAPA Reference Set 2306 accessions, 48 countries
Americas 1273 (1139 from S. America) Asia 36 SEC Africa 61 West Africa 884 Unknown 24 Wild 28
<2% germplasm in IITA genebank from SEC.
GCP Phase II: Definition of trait-based global reference set
Southern eastern and central Africa (100)
IITA breeders germplasm (100)
IITA genebank (102)
CIAT breeders germplasm (100)
CIAT genebank (148)
GCP Phase II: (1) Definition of SEC Africa Reference Set
100 Genotypes Methodology Breeders in seven countries selected 10 varieties
with traits of specific interest, all with SSR genotyping data (70 accessions)
30 accessions selected, in relation to the 70, to maximise diversity
Characteristics:
1401 Varieties 100 Reference set
Total number of alleles 192 157
Average gene diversity 0.6439 0.6556
Effective number of
alleles (Ae)
3.2613 3.2788
GCP Phase II: (2) Definition of 100 IITA breeders lines
Trait Number of genotypes
Multiple pest resistance
51
CMD Resistance 39
Stay green 32
High yield 31
High dry matter 25
High β-carotene 24
Future
AA AB BB
Genotyped using 1,536 SNPs on Illumina’s GoldenGate platform
Selection of ~ 250 genotypes to make up GCP Reference Set
?
Project 2: Biotic stresses
Hybridizations of parents in a bi-parental crossing design for the development of two CMD mapping populations for 2 putative resistance genes
Resistant (♀) x Susceptible (♂)
1. 97/2205 x 30555 (CMD3)
2. 96/1089A x 30555 (CMD4)
Egesi
Preliminary Phenotype Data: CMD
0
10
20
30
40
50
60
70
80
1 2 3 4 5
CMD 3 MAP: 97/2205 x 30555
0
10
20
30
40
50
60
70
80
1 2 3 4 5
CMD 4 MAP: 97/2205 x 30555
0
20
40
60
80
100
1 2 3 4 5
CMD 3 MAP: 96/1089A x 30555
0
10
20
30
40
50
60
70
80
1 2 3 4 5
CMD 4 MAP: 96/1089A x 30555
Disease scores of 1 – 5 where 1: no symptoms; 5: severe symptoms
# D
ise
ased
pla
nts
S/No Parent
Resistance
Status
# SNP Polymorphic
markers
1 97/2205 Resistant 619
2 96/1089A Resistant 623
3 30555 Susceptible 636
SNP Polymorphisms
S/No Mother Father
# SNP Polymorphic
markers
1 97/2205 30555 984
3 96/1089A 30555 927
SUMMARY OF SEEDS GENERATED FOR CBSD
Parents
Number
of F1
Seeds
Established
mapping
population
Resistant Susceptible
Namikonga AR37-80 5551
Kiroba 3C83-13 926
Muzege Cheupe 657
B2C20-65 AR37-80 302
Project 3: MARS
IAR – Kano, Nigeria SARI, Tamale, Ghana
Trial sites:
0
10
20
30
40
50
60
TMS 419 TMS
92/0326
TMS
95/0289
TMS
98/0505
TMS
98/0510
TMS
98/0581
DMC (%)
Tolerant
Susceptible Check
Established progenies on the field
Pedigree Progeny size in field
Polymorphic markers
TMS 98/0505 X TMS 98/0510 192 856
TMS 98/0505 X TMS 98/0581 278 871
TMS 98/0505 X TMS 91/02324 162 960
Phenotyping site Improvement
Pump house and deep well system currently under construction
Irrigation system
Trial sites at advanced stages in development
Weather station provided by GCP
Project 4: QTL mapping for drought tolerance
Physiological traits
• Partial closure/ less stomatal openings
• Less stomatal conductance
• More chlorophyll content during drought
• Decline of photosynthetic efficiency
Stomatal conductivity in cassava genotypes
MCOL 1468 76% reduction STC susceptible V3
CM4403 68% reduction STC susceptible V1
CG 1141-1 46% reduction STC tolerant V2
Effect of drought on biomass production in cassava
30-40% biomass reduction due to drought in cassava
http://www.cassavacop.org/cbcopa/
Sharing knowledge and technology among
research partners
Project 5 : Cassava
breeeding CoP
MAB based programmes Validation of stability of CMD resistance in CMD2
genotypes MAS developed CMD resistant variety released in
Nigeria Genotypes combining CBSD and CMD resistance
developed in Tanzania Genetic stock fixed for CMD2 and CGM alleles
developed Genetic diversity of breeding lines analyzed Genetic mapping for early bulking and high protein
conducted Breeding populations for key traits developed Introgression of novel traits into CMD resistance
genetic background achieved – Protein, delayed PPD, drought tolerance.
Genetic diversity
Esuma, 2011
Co002/C
OL1734
AR
C02
8/A
R12
.37
Co0
17
/CO
L2
2
Ug0
27
/And
iteku
Gh023/B
ankyeB
ota
n
Ug086/U
nknow
n/T
oro
ro
Ni0
38/T
MS
98/0
505
Ni0
43/T
MS
4/2
1425
Gh030/A
W36
Kz0
37/T
ype3.3
AR
C014/M
SA
F1
Kz0
35/T
ype3.1
AR
C012/S
M707.1
7
Co023/C
M2177/C
M2177-2
Kz0
17/C
lone5.3
Kz0
25/C
lone7.3
Br0
13/B
GM
0063
Br0
60/B
GM
0890
Co0
01/V
EN
77
Ug0
88/U
nkno
wn2
/Kak
umiro
Ug0
90/A
lado
-Ala
do
Ug0
13/L
ugw
ara
Ug0
89/U
nkno
wn1
/Mas
indi
Ug0
22/O
budu
gavu
Ug0
26/N
amun
yura
Ug0
07/K
akwal
e
Ug021/K
ajali
Ug019/Lya
horole
Gh022/U
CC
Gh006/Ess
iabaya
Gh015/Tuaka
ARC018/MOZ
Kz011/Clone7.1
Kz014/Clone7.4
Kz039/Clone6.1
Kz041/Clone6.3
Ug018/NjuleRed
Ug025/NjuleWhite
Ug003/Bao
Ug001/Nyaraboke
Ug002/Egabu
ARC019/Hombolo954
Ug036/MM96/4271
Ug039/52/TME14
ARC001/01/1649
Ni069/TMS01/1442
Br061/Col2215
ARC013/SM1053.23
Ni006/TMS94/0330Gh058/KwaseabediawuNi058/NR01/0161Ni064/NR8082Ug087/Unknown2/HoimaBr050/BGM0260Ug067/YellowR
Kz002/FemaleCKz027/TypeC1Kz030/TypeC4Kz031/TypeA1
Ni015/TMS87/0052
ARC022/AR40.17
ARC030/AR37.99
ARC025/AR42.3
ARC026/CR25.4
Ug020/Magana
Gh017/Agbelifia
ARC011/AR23.1
Ug085/Unknown/Luwero
Ni008/CR41-10
Ug074/CR36-2/1
ARC020/Mkondezi21
Kz006/FemaleD
Gh020/Essam
Bankye
Ni025/TM
S99/2123
Ni040/TM
S96/1089A
Ni010/Z97/0474
Gh031/K
25
Co024/N
GA2
Gh016/A
fisiafi
Gh057/S
isipe166
Ni013/T
MS30572
Co018/M
ex17
AR
C015/9
7/4
763
Ni0
51/T
MS
96/1
431
Ni0
52/T
MS
01/1
413
Ni0
44/T
MS
97/2
205
Ni0
50/T
MS
97/2
205
AR
C023/A
R9.1
8
Ni0
03/N
R87/1
84
Ug047/A
R9-2
4
Ug076/C
R97x-1
Ni0
34/M
M96/JW
1N
i042/M
H94/4
041
Ug030/N
ase12
Gh0
29
/AW
3
Ni0
56/N
R82
12
Kz0
07
/Fem
ale
EK
z0
19
/Typ
eB
1
AR
C00
2/9
2B
/00
06
1N
i02
8/T
MS
01
/14
12
Br0
08/B
GM
09
24
Ni0
45/T
ME
1
Gh007/N
yam
ebekye
re270
Ni0
32/T
ME
9
Br0
03/B
GM
0001
Ni0
48/T
MS
01/0
040
AR
C005/I9
2/0
057
Ni0
68/T
MS
98/0
002
AR
C029/A
R17.2
Ni0
47/T
MS
98/2
132
Ni0
17/T
MS
00/0
355
Ni0
62/T
MS
99/0
558
Gh019/D
oku
Duade
AR
C007/M
M96/1751
Ug043/T
ME
204
Co016/T
ME-3
Gh021/N
kabom
ARC
006/TM
E7
Gh012/S
isipe290
Ni027/M
98/0115
Ug065/M
M96/0469
Co0
15/M
ven3
0q
ARC01
0/L9
/304/
1616
Kz009/C
lone9
Br026/B
GM
0931
Br012/B
GM
0456
Br054/S
M1438-2
Ug097/MH04/3123
Br035/BGM0211
Co009/MCol1468
Gh028/NK26
Kz001/FemaleF
ARC003/94/0026
ARC021/Maunjili6
Ni067/TMS92/0325
Ni024/TMS94/0561
Ni035/TMS01/1371
Ug082/95/SE-00036
ARC027/AR42.4ARC004/98/0581
ARC016/14/48Br055/TAI16Kz003/Male1Br021/BGM1269Co019/GUA76Br025/BGM1318Br045/BGM2017
Br036/BGM0249
Br049/BGM1696
Br051/BGM0384
Br029/BGM0070
Br046/BGM2019
Br056/TAI8
Br031/BGM2018
Br034/BGM1810
ARC008/MM96/5280
Br042/BGM0120
Br037/BGM1694
Br038/BGM0867
Br048/BGM0876
Gh001/Dagarti
Gh005/AgricBankye
Br001/BGM1148
Br018/BGM1693
Br023/BGM1811
Br005/BGM0549
Co008/BRA255
Br041/BGM
0600
Br016/BGM
0255
Br052/BGM
0195
Br059/BG
M0086
Br040/B
RA997
ARC024/S
M1433.4
Br024/B
GM
1153
Br014/B
GM
0021
Br043/B
GM
1672
Br011/B
GM
1627
AR
C009/P
1/16
Br028/B
GM
1697
AR
C017/B
847
Br0
19/B
GM
0537
Gh014/T
ME
11
Co020/B
RA
12
Ni0
16/T
MS
96/1
432
0.05
Melissa
Based on 48 SNPs
SSR markers
Response profile of CMD2 genotypes
0
0.5
1
1.5
2
2.5
3
3.5
4
4.5
1 MAP 3 MAP 6 MAP 9 MAP 12 MAP
Months After Planting
CM
D s
ev
erit
y S
co
re
(1
-5
)
A R 1- 8 2
C R 14 A - 1
C R 52 A - 4 1
C R 3 6 - 2C R 3 6 - 5
0
0.5
1
1.5
2
2.5
YEAR 1 YEAR 2 YEAR 3 YEAR 4
Years
CM
D s
ev
erit
y S
co
re
(1
-5)
A R 9 - 5
A R 14 - 10
A R 15- 5
C R 10 0 - 15
C R 10 0 - 2 15
MAS Scheme to Improve Cassava
Germplasm
Seedling trial
Crossing block
Polycross design
(MAS)
Combining
ability studies
Farmer participatory trial
Field trials
Local varieties
(selected by farmers) Improved
introductions
Variety release:MAS develop Latin American genotype
New generation of cassava
breeders
Country - Uganda Nigeria Ghana Ghana Ghana Tanzania Name - Mr. Esuma Dr. Olasanmi Mr. Peprah Ms. Prempeh Mr. Danquah Ms. Kimata Degree - M.Sc. Ph.D. M. Phil Ph.D. Ph.D. M.Sc. Status On-going Completed On-going On-going On-going Ongoing
Gene pool development
Inbred line development (six families)
Root Weight(kg)
0 2 4 6 8 10 12 14
No
of G
enot
ypes
0
20
40
60
80
100
120
Harvest Index
0.0 0.2 0.4 0.6 0.8
No o
f G
enoty
pes
0
20
40
60
80
Plant Height(cm)
50 100 150 200 250 300 350 400
No
of
Ge
no
typ
es
0
10
20
30
40
Vigour
1 2 3 4 5
No o
f G
enoty
pes
0
20
40
60
80
100
120
Selection index based on two year data for for Latin America germplasm
0
5
10
15
20
25
30
35
40
45
50
CW
52
5-1
sp p
lot
AR
9-5
TMS9
1/0
23
24
CW
45
0-7
5
CW
45
1-8
0
TMS9
8/0
58
1
CR
14
B-1
80
NR
87
/18
4
TME4
19
TMS3
05
72
TMS9
5/0
28
9
CR
14
B-2
18
CR
20
A-2
CW
45
0-1
06
TMS9
2/0
06
7
AR
14
-4
AR
9-4
5
CW
45
1-1
3
TMS9
8/0
51
0
CW
45
0-4
6
CW
45
0-3
6
CR
15
B-9
CR
52
A-1
AR
9-1
9
CR
10
0-1
5
CR
15
B-7
CW
48
2-1
6
CW
48
2-3
TMS9
7/0
05
7
Dak
ata
FRY(ton/ha)
Potentials
Local ch
eck
Tanzania
Cont’d
Screen shot captures the implementation of cassava trait ontology with 125 traits defined. www.cropontology-curationtool.org
Trait Ontology Tree
FOCUS FOR 2012
• Upload datasets into ICASS
• Curate cassava pedigrees
• Collaborate with partners to continuously add new
traits to ontology
• Annotation cassava datasets using ontology-based tool
• Harmonize cassava ontologies with other ontologies
– Submit cassava specific terms to Gramene trait
ontology (TO)
– Begin cassava plant ontology to describe plant
structure, anatomy and growth stages
Finger printing project There are 270 genotypes fingerprinted with
1740 SNPs Finger printing project is a new opportunity to
finger print more accessions Is this a project targeting CI countries or open to
others Considerations for countries like Mozambique,
Liberia and Sierra Leone were suggested for inclusion in the project We have a broader list of accession earlier
submitted by breeders in Africa (six countries) and Brazil. A possible list from which accesssions could be chosen from List to be compiled by Oct 15.
CoP DM
WUR led CoP for DM and technical trainers
Identification of appropriate candidates and minimum eligibility criteria for particpants
Structured over three years to handle germplasm mgt and evaluation, field trial mgt system, update on tools, molecular analysis, genotyping data mgt system, data analysis, analytical pipeline, breeding decision, and decision support system
Resource persons with experience in cassava canvassed – tailored to meet crop needs and NOT generalized applications
CoPs after GCP
IBP sustainability crucial to CoP
Relevant to regional development
CoP to transform to self-sustainable entities: functionality critical for attracting funding support from donor bodies
Seek institutional and public funding support
Must be willing to pay for services
Cassava Information Resources
Germplasm and its documentation – ICASS (DMS, GMS, GeMS)
Molecular resources and sequence information – cassava genome sequence, transcriptome datasets, MOLCAS, PlanTFDB, PlnTFD
Four main areas for consideration • (1) Information related to accessions stored in genebanks
• (2) Information relating to breeding material • (3) Information related to genetic markers, genetic linkage
maps, QTLs, expression data and transformation
• (4) Geographic information.
Ideally information from these broad areas should be interconnected.
In addition: • supplementary sites and tools are proposed such as
decision-making tools and a cassava community site.
To enable the cassava community to work efficiently, a means of connecting researchers to relevant data is
essential. Communities for other species have developed integrated data sites to combat this problem, notably
SOLgenomics, TAIR and SoyBase.
One advantage of this approach is the ability to integrate publicly available data with private data through the use
of user accounts, which also allows sharing of pre-published data between users.
Acknowledgement
Y. Baguma A. Pariyo B. Kimata C. Sichalwe C. Egesi E. Parkes B. Peprah G. Mkamilo J. Onyeka M. Fregene S. Rounsley E. Lotsu M.D. Quain P. Rabinowicz Z. Myburg P. Kulakow H. Murtah X. Delannay Ndeye Ndack Diop Luis Augusto BecerraLopez lavalle Hernan ceballos
K. Ogundapo
F. Ewa
B. Olasanmi
E. Okogbenin
H. Gomez
C. de Vicente
M. Gedil
A. Dixon
H. Kulembeka
A. Mbanaso
R. Thompson
P. Boateng
O. Akinbo
M. Reynolds
A. Okono
N.C. Ezebuiro
Larry Butler
Ismail Rabbi
Dominique Dumet
Franco Jorge