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Improving and deploying markers
for biotic stresses in cassava
GCP Project #: G7010.01.02
Chiedozie Egesi
NRCRI, Nigeria
 Biotic constraints of cassava in Africa
 Mapping and new QTLs for cassava mosaic disease
(CMD)
 Pyramiding of QTLs for CMD
 Validating QTLs for cassava brown streak disease
(CBSD)
 Mining for resistance genes for cassava bacterial
blight (CBB) and cassava green mite (CGM)
 Summary
Outline
Cassava brown streak diseaseCassava bacterial blight
Cassava mosaic disease Cassava green mite
Each could
cause yield
losses of
30 to 100%
Major Biotic Constraints in African Cassava Productivity
 To develop mapping populations for CMD
 To identify and map QTLs for new sources of CMD
 To develop populations for validation of QTLs for CBSD
 To identify sources of resistance to CGM and CBB
Specific Objectives
New QTLs for CMD
Umudike: 97/2205 x 30555
N=340
Frequency distribution of severity scores for CMD in 2
mapping populations in Umudike and Otobi
Otobi: 96/1089A x 30555
Otobi: 97/2205 x 30555
Umudike: 96/1089A x 30555
N=141
Disease severity scores from 1 to 5.
Plants with scores 1-2 are considered resistant.
Mean symptom severity scores for CMD in 2 mapping
populations in Umudike and Otobi
Family Trial
Severity scores of
parents
Severity scores of
progenies
30555 97/2205 Check Lowest Highest F-value
97/2205x30555 Otobi 3 1 3.82 1 5 4.31***
N = 340 Umudike 3 1 2.76 1 4.04 2.72***
30555 96/1089A Check Lowest Highest F-value
96/1089Ax30555 Otobi 4 1 4.08 1 4 5.14***
N = 141 Umudike 2.6 1 2.5 1 4.08 1.39*
Linkage group size for SNP markers from family
97/2205 x 30555
Linkage group
Number of
markers
Average marker
interval (cM)
Size
(cM)
1 48 2.13 102.3
2 35 3.57 125.1
3 37 3.59 132.8
4 51 1.98 100.9
5 46 2.48 114.2
6 34 1.28 43.5
7 40 2.93 117.0
8 41 1.94 79.6
9 37 3.09 114.3
10 35 3.96 138.6
11 34 3.34 113.4
12 32 3.63 116.1
13 25 5.43 135.7
14 18 4.52 81.4
15 14 2.16 30.3
16 13 4.47 58.1
17 29 3.01 87.3
18 8 2.21 17.7
Total/Average* 577 3.1* 94.9*
SNP genetic linkage map of family 97/2205 x 30555
QTLs associated with resistance to CMD
Chr Position Left Marker Right Marker LOD
2 501 md076 md077 24.3743
4 1703 md168 md170 21.9322
8 636 md333 md334 18.4417
10 290 md402 md403 26.5707
13 358 md504 md506 23.5867
QTLs associated with
resistance to CMD
Pyramiding of QTLs for CMD
 Combining CMD2 and new QTLs to broaden resistance
 Crosses derived from parents with new QTLs already being
phenotyped
 ca. 100 progenies in multi-site trials for resistance to CMD
 Integration of SSR and SNP maps and markers for
consensus maps/QTLs
Pyramiding of QTLs for CMD
Validating QTLs for CBSD
Populations developed and segregating for CBSD in Tanzania
Parents
Number of F1
Seeds derived
Number of
seedlings
established
Resistant Susceptible
Namikonga AR37-80 5551 621
Kiroba 3C83-13 926 334
Muzege Cheupe 657 111
B2C20-65 AR37-80 302 150
Total 7436 1216
 Evaluation for the second year in Tanzania is nearing completion
 Markers derived from a BMGF project to be used for validation
Frequency distribution for CBSD in 4 mapping populations
0
20
40
60
80
100
120
1 2 3 4 5
Muzege x Cheupe CBSD 6 MAP
0
20
40
60
80
100
120
1 2 3 4 5
Muzege x Cheupe CBSD 3 MAP
0
20
40
60
80
100
120
1 2 3 4 5
B2C20-65xAR 37-80 CBSD 3 MAP
0
20
40
60
80
100
120
140
1 2 3 4 5
B2C20-65 x AR 37-80 CBSD 6 MAP
0
100
200
300
400
500
600
700
1 2 3 4 5
Namikonga x AR 37-80 CBSD 3 MAP
0
100
200
300
400
500
600
1 2 3 4 5
Namikonga x AR 37-80 CBSD 6MAP
0
50
100
150
200
250
300
1 2 3 4 5
Kiroba x 3C83-13 CBSD 3 MAP
0
50
100
150
200
250
300
1 2 3 4 5
Kiroba x 3C83-13 CBSD 6 MAP
0
20
40
60
80
100
120
1 2 3 4 5
Muzege x Cheupe CBSD 9 MAP
0
20
40
60
80
100
1 2 3 4 5
B2C20-65 x AR 37-80 CBSD 9 MAP
0
100
200
300
400
500
600
1 2 3 4 5
Namikong x AR 37-80 CBSD 9 MAP
0
50
100
150
200
250
300
1 2 3 4 5
Kiroba x 3C83-13 CBSD 9 MAP
Mining for resistance gene donors in African cassava to
cassava bacterial blight (CBB) and cassava green mite (CGM)
1. Leaf blighting, brownish vascular discoloration
2. Wilting
3. Die back & rapid defoliation=‘candle sticks’
1, 3 2
1 1
4
5
Cassava Bacterial Blight (CBB)
CGM
Cassava green mite (CGM) symptoms
 Field evaluation for two years
 Multi-site, replicated trials
Germplasm assessed for resistance to CBB and CGM
Population
Type
Number of
Accessions
Trait Assessed
Landraces 256 CBB, CGM
Improved 183 CBB, CGM
Total 439
23.0
74.2
2.7
0.0
10.0
20.0
30.0
40.0
50.0
60.0
70.0
80.0
R MS HS
Frequency(%)
R = Resistant; MS = Moderately susceptible; HS = Highly susceptible
21.46
52.79
25.75
0.00
10.00
20.00
30.00
40.00
50.00
60.00
R MS S
Frequency(%)
CBB CGM
Distribution of 256 African casssava landraces for resistance to cassava
bacterial blight (CBB) and cassava green mite (CGM)
13.4
59.3
27.3
0.0
10.0
20.0
30.0
40.0
50.0
60.0
70.0
R MS HS
Frequency(%)
30.2
46.1
23.5
0
5
10
15
20
25
30
35
40
45
50
R MS HS
Frequency(%)
CBB CGM
R = Resistant; MS = Moderately susceptible; HS = Highly susceptible
Distribution of 183 improved casssava genotypes for resistance to
cassava bacterial blight (CBB) and cassava green mite (CGM)
NRCRI
germplasm
CBB
score
CGM
score
IITA
germplasm
CBB
score
CGM
score
NR/8010 1 1 188/023543 1 1
74/2 1 2 189/00748 1 1
74/640 1 2 TME-226 1 1
73/30 1 2 T983/00016 1 1
73/192 1 2 188/01226 1 1
73/404 1 2 088/00623 1 1
75/647 1 2 TME-236 1 2
75/726 1 2 TME-478 1 2
77/169 1 2 088/00378 1 2
TMX4009 1 2 087/00183 1 2
Disease and pest severity scores on the basis of 1 to 5
where 1 is no symptom and 5 is very severe symptoms
Clones identified with combined resistance to cassava bacterial blight
(CBB) and cassava green mite (CGM)
 New mapping populations for CMD and CBSD formed and
evaluated
 QTLs for resistance to CMD identified
 Pyramiding of different sources of resistance to CMD
commenced
 New sources of resistance to CGM and CBB identified
Summary
Acknowledgements
NRCRI, Nigeria
Emmanuel Okogbenin
Joseph Onyeka
Others
CRI, Ghana
Elizabeth Parkes
Bright Peprah
Others
ARI, Tanzania
Geoffrey Mkamilo
Heneriko Kulembeka
Others
GCP
Xavier Delannay
Chunlin He
Others
Project Partners
Thank You!

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GRM 2013: Improving and deploying markers for biotic stresses in cassava -- C Egesi

  • 1. Improving and deploying markers for biotic stresses in cassava GCP Project #: G7010.01.02 Chiedozie Egesi NRCRI, Nigeria
  • 2.  Biotic constraints of cassava in Africa  Mapping and new QTLs for cassava mosaic disease (CMD)  Pyramiding of QTLs for CMD  Validating QTLs for cassava brown streak disease (CBSD)  Mining for resistance genes for cassava bacterial blight (CBB) and cassava green mite (CGM)  Summary Outline
  • 3. Cassava brown streak diseaseCassava bacterial blight Cassava mosaic disease Cassava green mite Each could cause yield losses of 30 to 100% Major Biotic Constraints in African Cassava Productivity
  • 4.  To develop mapping populations for CMD  To identify and map QTLs for new sources of CMD  To develop populations for validation of QTLs for CBSD  To identify sources of resistance to CGM and CBB Specific Objectives
  • 6. Umudike: 97/2205 x 30555 N=340 Frequency distribution of severity scores for CMD in 2 mapping populations in Umudike and Otobi Otobi: 96/1089A x 30555 Otobi: 97/2205 x 30555 Umudike: 96/1089A x 30555 N=141 Disease severity scores from 1 to 5. Plants with scores 1-2 are considered resistant.
  • 7. Mean symptom severity scores for CMD in 2 mapping populations in Umudike and Otobi Family Trial Severity scores of parents Severity scores of progenies 30555 97/2205 Check Lowest Highest F-value 97/2205x30555 Otobi 3 1 3.82 1 5 4.31*** N = 340 Umudike 3 1 2.76 1 4.04 2.72*** 30555 96/1089A Check Lowest Highest F-value 96/1089Ax30555 Otobi 4 1 4.08 1 4 5.14*** N = 141 Umudike 2.6 1 2.5 1 4.08 1.39*
  • 8. Linkage group size for SNP markers from family 97/2205 x 30555 Linkage group Number of markers Average marker interval (cM) Size (cM) 1 48 2.13 102.3 2 35 3.57 125.1 3 37 3.59 132.8 4 51 1.98 100.9 5 46 2.48 114.2 6 34 1.28 43.5 7 40 2.93 117.0 8 41 1.94 79.6 9 37 3.09 114.3 10 35 3.96 138.6 11 34 3.34 113.4 12 32 3.63 116.1 13 25 5.43 135.7 14 18 4.52 81.4 15 14 2.16 30.3 16 13 4.47 58.1 17 29 3.01 87.3 18 8 2.21 17.7 Total/Average* 577 3.1* 94.9*
  • 9. SNP genetic linkage map of family 97/2205 x 30555
  • 10.
  • 11. QTLs associated with resistance to CMD Chr Position Left Marker Right Marker LOD 2 501 md076 md077 24.3743 4 1703 md168 md170 21.9322 8 636 md333 md334 18.4417 10 290 md402 md403 26.5707 13 358 md504 md506 23.5867
  • 14.  Combining CMD2 and new QTLs to broaden resistance  Crosses derived from parents with new QTLs already being phenotyped  ca. 100 progenies in multi-site trials for resistance to CMD  Integration of SSR and SNP maps and markers for consensus maps/QTLs Pyramiding of QTLs for CMD
  • 16. Populations developed and segregating for CBSD in Tanzania Parents Number of F1 Seeds derived Number of seedlings established Resistant Susceptible Namikonga AR37-80 5551 621 Kiroba 3C83-13 926 334 Muzege Cheupe 657 111 B2C20-65 AR37-80 302 150 Total 7436 1216  Evaluation for the second year in Tanzania is nearing completion  Markers derived from a BMGF project to be used for validation
  • 17. Frequency distribution for CBSD in 4 mapping populations 0 20 40 60 80 100 120 1 2 3 4 5 Muzege x Cheupe CBSD 6 MAP 0 20 40 60 80 100 120 1 2 3 4 5 Muzege x Cheupe CBSD 3 MAP 0 20 40 60 80 100 120 1 2 3 4 5 B2C20-65xAR 37-80 CBSD 3 MAP 0 20 40 60 80 100 120 140 1 2 3 4 5 B2C20-65 x AR 37-80 CBSD 6 MAP 0 100 200 300 400 500 600 700 1 2 3 4 5 Namikonga x AR 37-80 CBSD 3 MAP 0 100 200 300 400 500 600 1 2 3 4 5 Namikonga x AR 37-80 CBSD 6MAP 0 50 100 150 200 250 300 1 2 3 4 5 Kiroba x 3C83-13 CBSD 3 MAP 0 50 100 150 200 250 300 1 2 3 4 5 Kiroba x 3C83-13 CBSD 6 MAP 0 20 40 60 80 100 120 1 2 3 4 5 Muzege x Cheupe CBSD 9 MAP 0 20 40 60 80 100 1 2 3 4 5 B2C20-65 x AR 37-80 CBSD 9 MAP 0 100 200 300 400 500 600 1 2 3 4 5 Namikong x AR 37-80 CBSD 9 MAP 0 50 100 150 200 250 300 1 2 3 4 5 Kiroba x 3C83-13 CBSD 9 MAP
  • 18. Mining for resistance gene donors in African cassava to cassava bacterial blight (CBB) and cassava green mite (CGM)
  • 19. 1. Leaf blighting, brownish vascular discoloration 2. Wilting 3. Die back & rapid defoliation=‘candle sticks’ 1, 3 2 1 1 4 5 Cassava Bacterial Blight (CBB)
  • 20. CGM Cassava green mite (CGM) symptoms
  • 21.  Field evaluation for two years  Multi-site, replicated trials Germplasm assessed for resistance to CBB and CGM Population Type Number of Accessions Trait Assessed Landraces 256 CBB, CGM Improved 183 CBB, CGM Total 439
  • 22. 23.0 74.2 2.7 0.0 10.0 20.0 30.0 40.0 50.0 60.0 70.0 80.0 R MS HS Frequency(%) R = Resistant; MS = Moderately susceptible; HS = Highly susceptible 21.46 52.79 25.75 0.00 10.00 20.00 30.00 40.00 50.00 60.00 R MS S Frequency(%) CBB CGM Distribution of 256 African casssava landraces for resistance to cassava bacterial blight (CBB) and cassava green mite (CGM)
  • 23. 13.4 59.3 27.3 0.0 10.0 20.0 30.0 40.0 50.0 60.0 70.0 R MS HS Frequency(%) 30.2 46.1 23.5 0 5 10 15 20 25 30 35 40 45 50 R MS HS Frequency(%) CBB CGM R = Resistant; MS = Moderately susceptible; HS = Highly susceptible Distribution of 183 improved casssava genotypes for resistance to cassava bacterial blight (CBB) and cassava green mite (CGM)
  • 24. NRCRI germplasm CBB score CGM score IITA germplasm CBB score CGM score NR/8010 1 1 188/023543 1 1 74/2 1 2 189/00748 1 1 74/640 1 2 TME-226 1 1 73/30 1 2 T983/00016 1 1 73/192 1 2 188/01226 1 1 73/404 1 2 088/00623 1 1 75/647 1 2 TME-236 1 2 75/726 1 2 TME-478 1 2 77/169 1 2 088/00378 1 2 TMX4009 1 2 087/00183 1 2 Disease and pest severity scores on the basis of 1 to 5 where 1 is no symptom and 5 is very severe symptoms Clones identified with combined resistance to cassava bacterial blight (CBB) and cassava green mite (CGM)
  • 25.  New mapping populations for CMD and CBSD formed and evaluated  QTLs for resistance to CMD identified  Pyramiding of different sources of resistance to CMD commenced  New sources of resistance to CGM and CBB identified Summary
  • 26. Acknowledgements NRCRI, Nigeria Emmanuel Okogbenin Joseph Onyeka Others CRI, Ghana Elizabeth Parkes Bright Peprah Others ARI, Tanzania Geoffrey Mkamilo Heneriko Kulembeka Others GCP Xavier Delannay Chunlin He Others Project Partners