5. Genetic variation – basis for QTL discovery
and marker-assisted breeding
Heat
Aphid
T
R
S
S
Root-knot
nematodes
Striga
R
S
R
S
Jean-Baptiste,
Burkina Faso
7. SNP database for germplasm collection
> 400 accessions from Africa and the world
1
5
3
6
S
N
P
s
SNP
1_1431
1_0721
1_1392
1_1157
1_0595
1_0741
1_0482
1_0791
1_1490
1_1033
1_0144
1_0328
1_0240
1_0985
1_0041
1_1470
1_1535
1_1230
1_1108
1_0670
TVu-9522
GG
CC
GG
AA
GG
AA
GG
AA
GG
GG
GG
GG
CC
AA
GG
AA
GG
AA
CC
AA
TVu-9556
GG
CC
GG
AA
GG
AA
CC
AA
GG
GG
GG
GG
CC
TT
GG
AA
GG
AA
CC
GG
TVu-9557
GG
CC
GG
AA
GG
AA
CC
AA
GG
GG
GG
GG
CC
TT
AA
AA
GG
AA
CC
GG
TVu-9620
GG
CC
GG
AA
GG
AA
GG
AA
GG
GG
GG
GG
CC
TT
GG
AA
GG
AA
CC
AA
TVu-9651
GG
CC
GG
AA
CC
AA
CC
AA
GG
GG
GG
GG
CC
TT
GG
AA
GG
AA
CC
AA
TVu-969
AA
CC
GG
AA
CC
AA
CC
AA
GG
GG
GG
GG
CC
AA
AA
AA
GG
AA
CC
AA
TVu-972
GG
CC
GG
AA
CC
GG
GG
GG
CC
AA
AA
GG
CC
AA
GG
AA
GG
AA
AA
GG
2013 The Plant Genome 6(3)
TVu-9749
GG
CC
GG
AA
CC
AA
CC
AA
GG
GG
GG
GG
CC
TT
GG
AA
-AA
CC
GG
TVu-9761
GG
CC
GG
AA
CC
AA
CC
AA
GG
GG
GG
GG
CC
AT
GG
AA
GG
AA
CC
AG
TVu-9801
AA
CC
GG
GG
CC
AA
GG
GG
GG
GG
AA
GG
CC
AA
GG
GG
AA
AA
CC
AA
TVu-9820
AA
CC
GG
GG
CC
AA
GG
GG
GG
AA
AA
AA
CC
AA
GG
GG
AA
AA
AA
AA
8. Select informative SNPs for a MAS project
Consensus map
QTL
SNP genotypes of parents
SNPs selected for MAS
BreedIt (breedit.org), GDMS (IBP tool, ICRISAT)
9. SNP genotyping (KASP platform-LGC Genomics)
1
2
3
8
Selection
Crossing
Planting
New genotyping
4
7
6
5
10. Employ marker-assisted backcrossing (MABC)
to improve local cowpea varieties
Country
11 MABC populations (Recurrent/Donor) Main donor Traits
Nigeria
IT93K-452-1/IT97K-499-35
IT89KD-288/IT97K-499-35
SuVita 2/IT97K-499-35
Striga
Striga
Drought, Striga
Burkina Faso
Moussa/IT93K-693-2
KVX745-11P/KVX414-22
Striga
Striga, Large Seed
Senegal
Melakh/IT97K-499-39
Striga
Mozambique
IT85F-3139/CB27
CB27/INIA-41
Large seed, Heat
Nematode, Drought
USA/
Mozambique
CB27/IT97K-556-6
CB46/IT97K-556-6
CB50/IT97K-556-6
Aphid
11. MABC example – Aphid resistance
Blackeyes
IT97K-556-6
(susceptible)
(resistant)
14. QTL introgression
Resistant RIL x Recurrent P
1
2
3
BCnF1 plants
Leaf sampling
04
AA
AB
AB
AB
AB
AA
AB
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AB
AA
AA
AA
AA
AA
AB
AB
AA
AA
AA
AA
AA
AA
AA
AA
05
AA
AB
AB
AB
AB
AA
AB
AB
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AB
AB
AA
AA
AA
AA
AA
AA
AA
AA
5
6
Backcrossing
11
AA
AA
AB
AB
AB
AA
AB
AB
AA
AA
AA
AA
AA
AA
AB
AA
AA
AA
AB
AB
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
12
AA
AB
AB
AB
AB
AA
AB
AB
AA
AA
AA
AA
AA
AA
AB
AA
AA
AA
AB
AA
AA
AA
AA
AA
AA
AB
AA
AA
AA
AA
AA
AA
AA
AA
AA
24
AA
AA
AB
AB
AB
AA
AA
AA
AA
AA
AA
AA
AA
AA
AB
AA
AA
AA
AB
AB
AA
AA
AA
AA
AA
AB
AB
AA
AA
AA
AA
AA
AA
AA
AA
26
AA
AB
AB
AB
AB
AA
AB
AA
AA
AA
AA
AA
AA
AA
AB
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AB
AA
AA
AA
AA
AA
AA
AA
AA
35
AA
AB
AB
AB
AB
AA
AA
AB
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AB
AB
AA
AA
AA
AA
AA
AB
AB
AA
AA
AA
AA
AA
AA
AA
AA
38
AA
AB
AB
AB
AB
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AB
AB
AA
AA
AA
AA
AA
AB
AB
AA
AA
AA
AA
AA
AA
AA
AA
40
AA
AB
AB
AB
AB
AA
AA
AB
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AB
AB
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
-AA
46
AA
AB
AB
AB
AB
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AB
AB
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
48
AA
AB
AB
AB
AB
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AB
AB
AA
AA
AA
AA
AA
AA
AA
AA
53
AA
AB
AB
AB
AB
AA
AB
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
57
AA
AB
AB
AB
AB
AA
AB
AB
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
62
AA
AA
AB
AB
AB
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
63
AA
AB
AB
AB
AB
AA
AA
AA
AA
AA
AA
AA
AA
AA
AB
AA
AA
AA
AB
AB
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
66
AA
AB
AB
AB
AB
AA
AB
AB
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AB
AB
AA
AA
AA
AA
AA
AB
AB
AA
AA
AA
AA
AA
AA
AA
AA
SNP genotyping
67
AA
AB
AB
AB
AB
AA
AB
AB
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AB
AA
AA
AA
AA
AA
AB
AB
AA
AA
AA
AA
AA
AA
AA
AA
69
AA
AB
AB
AB
AB
AA
AB
AB
AA
AA
AA
AA
AA
AA
AB
AA
AA
AA
AB
AB
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
71
AA
AB
AB
AB
AB
AA
AA
AA
AA
AA
AA
AA
AA
AA
AB
AA
AA
AA
AB
AB
AA
AA
AA
AA
AA
AB
AB
AA
AA
AA
AA
AA
AA
AA
AA
Background selection
79
AA
AB
AB
AB
AB
AA
AA
AB
AA
AA
AA
AA
AA
AA
AB
AA
AA
AA
AB
AB
AA
AA
AA
AA
AA
AA
AB
AA
AA
AA
AA
AA
AA
AA
AA
80
AA
AB
AB
AB
AB
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
CB46A
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
AA
4
Resistant
genotypes
Foreground selection
15. Parent 1 × Parent 2
QTL
Recombination
Population
development
F1
F2
Multilocation
phenotyping
QTL detection –estimate marker effects
Cycle 1
Cycle 2
Cycle 3
A B C D E
F1
F1
F G H
4 populations
Traits
Burkina Faso
(Issa Drabo et al.)
F1
F1
Ideotype
Line
development
Genotyping
F3
Employ marker-assisted
recurrent selection (MARS) to
develop improved breeding lines
Yield, Drought,
Striga, Macrophomina
Nigeria
(Ousmane Boukar et al.)
Earliness, Striga, Heat
Senegal
(Ndiaga Cisse et al.)
Drought, Striga, Nematode,
Macrophomina
Mozambique
(Rogerio Chiulele et al.)
Heat, Large seed, Grain
quality
F1
F1
F1
F2
F3
Single seed
descent
F3:4
Multilocation phenotyping
16. Burkina Faso – MARS example
• Developed F2 from elite parents (Suvita 2, IT97K-499-35).
• Genotyped 300 F2s with 164 poly SNPs every 2 cM interval.
• Phenotyped F2:3 families
₋ Pobe (low-yielding site)
Pope
300 mm
₋ Saria (high-yielding site)
Saria
1000 mm
19. QTL combination
1
2
3
10 members per family/cross
Leaf sampling
5
6
Plant ID Cycle MS
Yield QTLs
KASP genotyping
Kernel-size QTLs Striga
YLD-4 YLD-6 YLD-8 GDW-3 GDW-11 Rsg 3
Selected
71
0.83
1.00
1.00
0.50
1.00
0.50
1.00
71-03
F4
0.92
1.00
1.00
0.50
1.00
1.00
1.00
Yes
71-02
F4
0.92
1.00
1.00
1.00
1.00
0.50
1.00
Yes
71-10
F4
0.92
1.00
1.00
1.00
1.00
0.50
1.00
Yes
71-01
F4
0.75
1.00
1.00
0.52
1.00
0.00
1.00
No
71-04
F4
0.75
1.00
1.00
0.00
1.00
0.50
1.00
No
71-05
F4
0.75
1.00
1.00
0.50
1.00
0.00
1.00
No
71-07
Intercrossing
F2
F4
0.67
1.00
1.00
0.00
1.00
0.00
1.00
Plant
Cycle 1_0853 1_0447 1_0146 1_0937 1_0031
2010-057-190
F2
GG
GG
AA
GG
GG
2010-057-190-01 F4
GG
GG
AA
GG
GG
2010-057-190-02 F4
GG
-AA
-GG
2010-057-190-03 F4
GG
GG
AA
GG
GG
2010-057-190-04 F4
GG
GG
AA
GG
GG
2010-057-190-05 F4
GA
GC
GA
GC
GA
2010-057-190-06 F4
GG
GG
AA
GG
GG
2010-057-190-07 F4
GG
GG
AA
GG
GG
2010-057-190-08 F4
GG
GG
AA
GG
GG
2010-057-190-09 F4
GG
GG
AA
GG
GG
2010-057-190-10 F4
GA
GC
GA
GC
GA
4
No
OptiMAS to select best plants
Outcrosses eliminated
20. OptiMAS summary: Frequency of favorable alleles at different
selection steps in Burkina Faso MARS (on average and for each QTL)
C2
C1
F5
F4
F2
F1
P
21. MARS activities in Burkina Faso (Issa Drabo et al.)
Leaf sample
for genotyping
Intercross to
recombine QTLs
Intercross progeny
“Ideotype”
Local check
22. University of California,
Riverside
Roberts, Philip A.
Close, Timothy J.
Huynh, Bao Lam
Wanamaker, Steve
Lucas, Mitchell
Ndeve, Arsenio
Jansen Santos
Xu, Shizhong
Ehlers, Jeff D.
Diop, Ndeye N.
Muchero, Wellington
Pottorff, Marti
Hu, Zhiqiu
Acknowledgements
National Agricultural Research System (NARS)
Cisse, Ndiaga, ISRA-Senegal
Drabo, Issa, INERA-Burkina Faso
Tignegre, Jean-Baptiste, INERA-Burkina Faso
Joseph, Batieno T. Benoît – WACCI
Chiulele , Rogerio, EMU-Mozambique
International Inst. of Tropical Agriculture (IITA)
Boukar, Ousmane
Fatokun, Christian
Ofodile, Sam
IBP-GCP
Delannay, Xavier et al.
LGC Genomics
Vyas, Darshna et al.
22