Cassava Challenge

Initiative

ARI

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