Beyond the EU: DORA and NIS 2 Directive's Global Impact
Positioning CIAT as leader in next generation breeding for roots, tubers and bananas
1. “Positioning CIAT as Leader in
Next-Generation Breeding for
Roots, Tubers and Bananas”
Becerra Lopez-Lavalle L.A.,
CIAT’s Senior Scientist and CGIAR-RTB Leader for Variety
Development
CIAT Seminar Series – Cali
10 February 2014
20. pVA and Starch: Novel starches
Functional Genetic for high
quality cassava: pVA and Starch
synthase pathways
Waxy and small-granule cassava
Easy hydrolysis good for bioethanol and
bioplastic production
75% Amylopectin
DE
SBEII
SBEI
SSIII
SSII
SSI
X
Starch Synthase Pathway
ATP PPi
75% Amylopectin
G1P
DE
SBEII
SBEI
SSIII
SSII
SSI
ADPG
ADP
ATP PPi
G1P
GBSSI
ADPG
25% Amylose
ADP
GBSSI
25% Amylose
Amyloplast
Amyloplast
21. pVA and Starch: Novel starches
Functional Genetic for high
quality cassava: pVA and Starch
synthase pathways
Waxy and small-granule cassava
75% Amylopectin
DE
SBEII
SBEI
SSIII
SSII
SSI
Starch Synthase Pathway
ATP PPi
75% Amylopectin
G1P
DE
SBEII
SBEI
SSIII
SSII
SSI
ADPG
ADP
XGBSSI
ATP PPi
G1P
100% amylopectin
ADPG
25% Amylose
ADP
GBSSI
25% Amylose
Amyloplast
Amyloplast
22. pVA and Starch: Novel starches
Functional Genetic for high
quality cassava: pVA and Starch
synthase pathways
Waxy and small-granule cassava
Important to bear in mind:
Type and quality of the
amylopectin is control by the
starch-synthase pathway
75% Amylopectin
DE
SBEII
SBEI
SSIII
SSII
SSI
Starch Synthase Pathway
ATP PPi
75% Amylopectin
G1P
DE
SBEII
SBEI
SSIII
SSII
SSI
ADPG
ADP
XGBSSI
ATP PPi
G1P
ADPG
25% Amylose
ADP
GBSSI
25% Amylose
Amyloplast
Amyloplast
23. pVA and Starch: Novel starches
Functional Genetic for high
quality cassava: pVA and Starch
synthase pathways
Starch Synthase Pathway
75% Amylopectin
DE
SBEII
SBEI
SSIII
SSII
SSI
ATP PPi
G1P
ADPG
ADP
GBSSI
25% Amylose
Amyloplast
Waxy and small-granule cassava
24. pVA and Starch: Novel starches WAXY
Functional Genetic for high
quality cassava: pVA and Starch
synthase pathways
GBSSI: Responsible for Waxy cassava
Starch Synthase Pathway
75% Amylopectin
DE
SBEII
SBEI
SSIII
SSII
SSI
ATP PPi
G1P
ADPG
ADP
GBSSI
25% Amylose
Amyloplast
• GBSSI in cassava is ~3400 bp
• 2 to 4 allelic versions
• Among 7 different sources of the
mutation span 126 SNPs
• 3 are diagnostic of the trait
25. pVA and Starch: Novel starches WAXY
New-V
4Wx
-1Ne
w-V2
Wx
7-1N
ew-V
1Wx
70
AC2
7-1
New
CL
-V3
4 2Wx
3N
ew
77
CL
A-V
4 15W
40
6N
x
ew
CL
51
A-V
42
5W
-3N
x
CL
ew
A-V
42
-3N
7W
ew
x
ACU
V4
AM B
W
2
20 9 x
6- V3
AM
5N NW
20
ew x
C
6-V
L4
5N
4W
1ew
6N
x
-V
ew
6W
Ax
V2
W
x
AC27
AC27-1
AC2
91
24
82
57
24
24
24
62
A-V2Wx
CL44-2N
ewA-V1
Wx
CL44-2New
CL41-6NewA-V7Wx
CL41-6NewA-V3Wx
4N
6-2
31
3
SM
24
24
24
24
24
24
24
24
_0
24
AC
75
V7
1C
AB
2
O
04 K958 639
C O TTO
49
55 33P
N
TT
14 O
O
CH PU
IC LU N
KP S
VE
EA
N3
09
aV
VE
3N
N3
Wx
09a
V2
VE
NW
N30
x
9aV
1NW
CUB
x
29-V
GBS
SJF
7089 6NWx
48N
Wx
CUB23
-V4N
Wx
VEN309
bV2NW
x
XP
24
24
46
99
24
66
99
87
24
24
24
26
26
24
24
CUB23-V
3NWx
TME-3NewV1PSg
NWx
24
24
18
18
25
24
66
24
36
24
24
24
27
21
99
73
24
81
22
VE
N2
NC
AU
72
VE XB4 9-V
1
N2 9-60 9N
9- V4NW W
V4 NWx x
VE
NW x
N2
9-V
x
CU
3N
B2
W
VE C
-V1
x
N3U
0Bb
NW
9 2V
-V4
1N
NW x
Wx
x
TMS30555V1r AM
50
evPSgNWx
CUB 6-5NW
2-V3
x
NW
CUB
x
2-V6
NWx
CU
VEN2B2-V5NWx
9-V2NW
x
IcD
All non-waxy landraces carried the
non-waxy allele(s), but waxy types
also carried non-waxy alleles
C4revV2PSgNWx
VEN29-V1NWx
GB
SS
96
95
85
26
34
34
81
18 49
39
84
Amyloplast
x
W
x
V5 Wx
1W x
AV4 W-xV
3W
ew A8A
ew A-V
6N ew A-V
w
2- 6N -24N ew
6
L4 41- 6Ne -24N
x
C
31 6
1W
CL SL43 331
M1
A-V
C
SM
ew
-3N
42
Wx
CL
2N
3-V 5NWx
B2
75
CU B23-V NWxWx
99
-V a
CU 58096 V4N
28
B
CU N3
VE
99
99
2PSgNWx
TME-3NewV
x
V2NW
CUB27NWx
CUB2-VV1PSgNWx
C4rev
2
24 5
GBSSI
25% Amylose
91
26
82
51
24
ADP
24
62
90
90
89
54
55
29
21
19
ADPG
VEN29-V7NWx
CL41-1NewAV3W
x
AM206-5
New-V1Wx
CUB29V5NW
24
x
CUB29
24
-V
CL4
2-3N 7NWx
ewA
CL4
-V3W
2
x
CL4 -3NewA
82
-V6
2-6
Wx
New
CL
42A-V
6N
CL
4W
53
ew
42
x
A-V
CL
75
2W
SM4 6New
x
11
A-V
SM 33-1 N
1W
e
33 6-3 wA
x
16 2N V4
CL
e W
-3
2N wA- x
CL 41V3
ew
42 6N
W
A-6 ew
x
V4
Ne AW
V6
wA
x
-V Wx
3W
x
24
24
24
G1P
PAN139-V6NWx
24
8
ATP PPi
24
24
11
DE
SBEII
SBEI
SSIII
SSII
SSI
CUB29-V2NWx
VEN29-V6NWx
8NWx
VEN29-V
x
-V1NW x
W
PAN139PSgN
5V2rev
2Wx
3055
wA-V
TMS
Wx
2N e
-V1
316-3
ewA
SM3
-32N
x
316
S
5NWY
SM3
9-V NE
A
N13 M
0
PA416
7
Wx
IX
6N
SS
3-V NWx
GB
B2
1
CU 23-V NWx
4
x
B
CU 58-V NW x
B
V5 W
CU 29- 4N Wx
N
-V N
VE 139 10
N
-V
PA N29
VE
x
CUB58-V3NW
24
24
47
75% Amylopectin
24
24
CUB58-V1NWx
Starch Synthase Pathway
x
W
V1
x
A3W
ew
-V
x
W
wA
V2
1
Ne
x
A-5
33
w
5
4W
Ne
31
-V
SM
5
3
A
5ew
S M 33 1
x
-5N
2W
15
SM
-V
33
x
wA
SM
1W
Ne
A-V
2-3
86
4
w
Wx
Ne
CL
-V5
1-6
ew
L4
C
-5N
x
94
206
V1W
71
AM
wA
Ne
1-1
CL4
Wx
2N
58-V
x
CUB
1NW
29-V
2Wx
CUB
ew-V
6-5N
AM20
Wx
9-V2N
PAN13
36
24
3NWx
76
PAN139-V
5N
5-
24
A-V
ew
All waxy types
carried the waxy
allele(s)
67
AC
J1
1
x
3W
w-V
x
Ne
-V2W
6-5
ewAx
20
4N49W
-2
AM
316 089 x
SM3SJ-F7 NW
S58 V5
GBB
6Wx
wA-V
CU
-2Ne
3Wx
CL44 2NewA-V
x
CL44wA-V5W
44-2Ne
CL
AV2Wx
CL41-1New
CL44-2NewA-V4Wx
Waxy and small-granule cassava
x
4W
Functional Genetic for high
quality cassava: pVA and Starch
synthase pathways
26. pVA and Starch: Novel starches WAXY
New-V
4Wx
-1Ne
w-V2
Wx
7-1N
ew-V
1Wx
70
AC2
7-1
New
CL
-V3
4 2Wx
3N
ew
77
CL
A-V
4 15W
40
6N
x
ew
CL
51
A-V
42
5W
-3N
x
CL
ew
A-V
42
-3N
7W
ew
x
ACU
V4
AM B
W
2
20 9 x
6- V3
AM
5N NW
20
ew x
C
6-V
L4
5N
4W
1ew
6N
x
-V
ew
6W
Ax
V2
W
x
AC27
AC27-1
AC2
91
24
82
57
24
24
24
62
A-V2Wx
CL44-2N
ewA-V1
Wx
CL44-2New
CL41-6NewA-V7Wx
CL41-6NewA-V3Wx
4N
6-2
31
3
SM
24
24
24
24
24
24
24
24
_0
24
AC
75
V7
1C
AB
2
O
04 K958 639
C O TTO
49
55 33P
N
TT
14 O
O
CH PU
IC LU N
KP S
VE
EA
N3
09
aV
VE
3N
N3
Wx
09a
V2
VE
NW
N30
x
9aV
1NW
CUB
x
29-V
GBS
SJF
7089 6NWx
48N
Wx
CUB23
-V4N
Wx
VEN309
bV2NW
x
XP
24
24
46
99
99
87
26
26
24
24
24
66
24
36
24
24
24
27
21
99
73
24
81
22
VE
N2
NC
AU
72
VE XB4 9-V
1
N2 9-60 9N
9- V4NW W
V4 NWx x
VE
NW x
N2
9-V
x
CU
3N
B2
W
VE C
-V1
x
N3U
0Bb
NW
9 2V
-V4
1N
NW x
Wx
x
TMS30555V1r AM
50
evPSgNWx
CUB 6-5NW
2-V3
x
NW
CUB
x
2-V6
NWx
CU
VEN2B2-V5NWx
9-V2NW
x
All non-waxy landraces carried the
non-waxy allele(s), but waxy types
also carried non-waxy alleles
C4revV2PSgNWx
VEN29-V1NWx
GB
SS
x
W
x
V5 Wx
1W x
AV4 W-xV
3W
ew A8A
ew A-V
6N ew A-V
w
2- 6N -24N ew
6
L4 41- 6Ne -24N
x
C
31 6
1W
CL SL43 331
M1
A-V
C
SM
ew
-3N
42
Wx
CL
2N
3-V 5NWx
B2
75
CU B23-V NWxWx
99
-V a
CU 58096 V4N
28
B
CU N3
VE
99
99
2PSgNWx
TME-3NewV
x
V2NW
CUB27NWx
CUB2-VV1PSgNWx
C4rev
96
95
85
26
34
34
81
18 49
39
IcD
91
26
82
51
84
Amyloplast
24
62
2
24 5
GBSSI
25% Amylose
VEN29-V7NWx
CL41-1NewAV3W
x
AM206-5
New-V1Wx
CUB29V5NW
24
x
CUB29
24
-V
CL4
2-3N 7NWx
ewA
CL4
-V3W
2
x
CL4 -3NewA
82
-V6
2-6
Wx
New
CL
42A-V
6N
CL
4W
53
ew
42
x
A-V
CL
75
2W
SM4 6New
x
11
A-V
SM 33-1 N
1W
e
33 6-3 wA
x
16 2N V4
CL
e W
-3
2N wA- x
CL 41V3
ew
42 6N
W
A-6 ew
x
V4
Ne AW
V6
wA
x
-V Wx
3W
x
24
24
24
ADP
PAN139-V6NWx
24
90
90
89
54
55
29
21
19
ADPG
x
CUB58-V3NW
24
24
24
G1P
CUB29-V2NWx
VEN29-V6NWx
8NWx
VEN29-V
x
-V1NW x
W
PAN139PSgN
5V2rev
2Wx
3055
wA-V
TMS
Wx
2N e
-V1
316-3
ewA
SM3
-32N
x
316
S
5NWY
SM3
9-V NE
A
N13 M
0
PA416
7
Wx
IX
6N
SS
3-V NWx
GB
B2
1
CU 23-V NWx
4
x
B
CU 58-V NW x
B
V5 W
CU 29- 4N Wx
N
-V N
VE 139 10
N
-V
PA N29
VE
24
8
ATP PPi
24
11
DE
SBEII
SBEI
SSIII
SSII
SSI
24
24
47
75% Amylopectin
24
24
18
18
25
24
Starch Synthase Pathway
Is cassava really
diploid (2X)?
24
24
CUB58-V1NWx
24
66
CUB23-V
3NWx
TME-3NewV1PSg
NWx
x
W
V1
x
A3W
ew
-V
x
W
wA
V2
1
Ne
x
A-5
33
w
5
4W
Ne
31
-V
SM
5
3
A
5ew
S M 33 1
x
-5N
2W
15
SM
-V
33
x
wA
SM
1W
Ne
A-V
2-3
86
4
w
Wx
Ne
CL
-V5
1-6
ew
L4
C
-5N
x
94
206
V1W
71
AM
wA
Ne
1-1
CL4
Wx
2N
58-V
x
CUB
1NW
29-V
2Wx
CUB
ew-V
6-5N
AM20
Wx
9-V2N
PAN13
36
24
3NWx
76
PAN139-V
5N
5-
24
A-V
ew
All waxy types
carried the waxy
allele(s)
67
AC
J1
1
x
3W
w-V
x
Ne
-V2W
6-5
ewAx
20
4N49W
-2
AM
316 089 x
SM3SJ-F7 NW
S58 V5
GBB
6Wx
wA-V
CU
-2Ne
3Wx
CL44 2NewA-V
x
CL44wA-V5W
44-2Ne
CL
AV2Wx
CL41-1New
CL44-2NewA-V4Wx
Waxy and small-granule cassava
x
4W
Functional Genetic for high
quality cassava: pVA and Starch
synthase pathways
27. Whitefly research: WHY
Whitefly control: a durable
solution to cassava-disease
pandemics (Africa and Asia)
Whiteflies have been called
Whitefly resistance
A
B
CMC-40
“The pest of 21st Century”
Tomato
C
Citrus
D
MEcu 72
Whitefly molecular identification
Bemisia tabaci JN410741
Asia /
Asia-Minor
Bemisia tabaci JN410738
Bemisia tabaci biotypeB KF059959 CIAT
100
A
Bemisia tabaci biotypeA KF059958 CIAT
96
99
30
New World
G-I
99
81
Bemisia tabaci AY521259
Aleurolobus marlatti JQ340188
Asia
Siphoninus philyreae JQ340199
Aleurocanthus inceratus HM150621
45
B
Asia
Crenidorsum micheliae JQ340190
97
C
Aleurotrachelus trachoides KF059957 CIAT
98
Aleurothrachelus socialis KF059953 CIAT
89
88
New World
G-II
Aleurocanthus spiniferus JQ340176
D
Aleurothrixus floccosus KF059956 CIAT
Aleuroclava sp JQ340187
Dialeurodes citri JQ340193
98
93
G-III
Dialeuropora JQ340197
73
Asia
Dialeurodes hongkongensis JQ340195
E
New World
Trialeurodes variabilis KF059962 CIAT
Trialeurodes vaporiariorum KF192508 CIAT
99
G-IV
68
New World
G-V
Aleyrodinae
99
F
100 Trialeurodes vaporariorum AY521265
Aleurodicinae
Aleuronudus melzeri KF059955 CIAT
G
Aleurodicus dugessi AY521251
46
99
Lecanoideus floccissimus KF059960 CIAT
H
Aleurodicus dispersus KF059954 CIAT
95
99
Aleurodicus dispersus EU581838
I
75 Aleurodicus dispersus EU581837
100
Drosophila melanogaster ADW61333
Drosophila melanogaster AGE13862
0.20
0.15
0.10
0.05
0.00
G-VI
Drosophila melanogaster ADW61439
Asia
Cotton
Zucchini
Palm
28. Whitefly research
Whitefly control: a durable
solution to cassava-disease
pandemics (Africa and Asia)
Whitefly Pest response Bio-assay
Whitefly resistance
A
A
B
B
CMC-40
C
D
C
MEcu 72
Whitefly molecular identification
Bemisia tabaci JN410741
Asia /
Asia-Minor
Bemisia tabaci JN410738
Bemisia tabaci biotypeB KF059959 CIAT
A
Bemisia tabaci biotypeA KF059958 CIAT
96
99
30
New World
G-I
99
81
100
Bemisia tabaci AY521259
Aleurolobus marlatti JQ340188
Asia
Siphoninus philyreae JQ340199
Aleurocanthus inceratus HM150621
45
B
Asia
Crenidorsum micheliae JQ340190
97
C
Aleurotrachelus trachoides KF059957 CIAT
98
Aleurothrachelus socialis KF059953 CIAT
89
88
New World
G-II
Aleurocanthus spiniferus JQ340176
D
Aleurothrixus floccosus KF059956 CIAT
Aleuroclava sp JQ340187
Dialeurodes citri JQ340193
98
93
G-III
Dialeuropora JQ340197
73
Asia
Dialeurodes hongkongensis JQ340195
E
New World
Trialeurodes variabilis KF059962 CIAT
Trialeurodes vaporiariorum KF192508 CIAT
99
G-IV
68
New World
G-V
Aleyrodinae
99
F
100 Trialeurodes vaporariorum AY521265
Aleurodicinae
Aleuronudus melzeri KF059955 CIAT
G
Aleurodicus dugessi AY521251
46
99
Lecanoideus floccissimus KF059960 CIAT
H
Aleurodicus dispersus KF059954 CIAT
95
99
Aleurodicus dispersus EU581838
I
75 Aleurodicus dispersus EU581837
100
Drosophila melanogaster ADW61333
Drosophila melanogaster AGE13862
0.20
0.15
0.10
0.05
0.00
G-VI
Drosophila melanogaster ADW61439
Asia
29. Whitefly research
Whitefly control: a durable
solution to cassava-disease
pandemics (Africa and Asia)
Whitefly resistance
A
B
CMC-40
C
D
MEcu 72
Whitefly molecular identification
Bemisia tabaci JN410741
Asia /
Asia-Minor
Bemisia tabaci JN410738
Bemisia tabaci biotypeB KF059959 CIAT
A
Bemisia tabaci biotypeA KF059958 CIAT
96
99
30
New World
G-I
99
81
100
Bemisia tabaci AY521259
Aleurolobus marlatti JQ340188
Asia
Siphoninus philyreae JQ340199
Aleurocanthus inceratus HM150621
45
B
Asia
Crenidorsum micheliae JQ340190
97
C
Aleurotrachelus trachoides KF059957 CIAT
98
Aleurothrachelus socialis KF059953 CIAT
89
88
New World
G-II
Aleurocanthus spiniferus JQ340176
D
Aleurothrixus floccosus KF059956 CIAT
Aleuroclava sp JQ340187
Dialeurodes citri JQ340193
98
93
G-III
Dialeuropora JQ340197
73
Asia
Dialeurodes hongkongensis JQ340195
E
New World
Trialeurodes variabilis KF059962 CIAT
Trialeurodes vaporiariorum KF192508 CIAT
99
G-IV
68
New World
G-V
Aleyrodinae
99
F
100 Trialeurodes vaporariorum AY521265
Aleurodicinae
Aleuronudus melzeri KF059955 CIAT
G
Aleurodicus dugessi AY521251
46
99
Lecanoideus floccissimus KF059960 CIAT
H
Aleurodicus dispersus KF059954 CIAT
95
99
Aleurodicus dispersus EU581838
I
75 Aleurodicus dispersus EU581837
100
Drosophila melanogaster ADW61333
Drosophila melanogaster AGE13862
0.20
0.15
0.10
0.05
0.00
G-VI
Drosophila melanogaster ADW61439
Asia
Whitefly SSR and AFLP genetic map
SNP markers are underway
30. Whitefly research
Whitefly control: a durable
solution to cassava-disease
pandemics (Africa and Asia)
Whitefly resistance
A
B
CMC-40
C
D
MEcu 72
Whitefly molecular identification
Bemisia tabaci JN410741
Asia /
Asia-Minor
Bemisia tabaci JN410738
Bemisia tabaci biotypeB KF059959 CIAT
A
Bemisia tabaci biotypeA KF059958 CIAT
96
99
30
New World
G-I
99
81
100
Bemisia tabaci AY521259
Aleurolobus marlatti JQ340188
Asia
Siphoninus philyreae JQ340199
Aleurocanthus inceratus HM150621
45
B
Asia
Crenidorsum micheliae JQ340190
97
C
Aleurotrachelus trachoides KF059957 CIAT
98
Aleurothrachelus socialis KF059953 CIAT
89
88
New World
G-II
Aleurocanthus spiniferus JQ340176
D
Aleurothrixus floccosus KF059956 CIAT
Aleuroclava sp JQ340187
Dialeurodes citri JQ340193
98
93
G-III
Dialeuropora JQ340197
73
Asia
Dialeurodes hongkongensis JQ340195
E
New World
Trialeurodes variabilis KF059962 CIAT
Trialeurodes vaporiariorum KF192508 CIAT
99
G-IV
68
New World
G-V
Aleyrodinae
99
F
100 Trialeurodes vaporariorum AY521265
Aleurodicinae
Aleuronudus melzeri KF059955 CIAT
G
Aleurodicus dugessi AY521251
46
99
Lecanoideus floccissimus KF059960 CIAT
H
Aleurodicus dispersus KF059954 CIAT
95
99
Aleurodicus dispersus EU581838
I
75 Aleurodicus dispersus EU581837
100
Drosophila melanogaster ADW61333
Drosophila melanogaster AGE13862
0.20
0.15
0.10
0.05
0.00
G-VI
Drosophila melanogaster ADW61439
Asia
Grant to be approved in 2014
31. Whitefly research
Whitefly control: a durable
solution to cassava-disease
pandemics (Africa and Asia)
Grant to be approved in 2014
Whitefly resistance
A
B
CMC-40
C
D
MEcu 72
Whitefly molecular identification
Bemisia tabaci JN410741
Asia /
Asia-Minor
Bemisia tabaci JN410738
Bemisia tabaci biotypeB KF059959 CIAT
A
Bemisia tabaci biotypeA KF059958 CIAT
96
99
30
New World
G-I
99
81
100
Bemisia tabaci AY521259
Aleurolobus marlatti JQ340188
Asia
Siphoninus philyreae JQ340199
Aleurocanthus inceratus HM150621
45
B
Asia
Crenidorsum micheliae JQ340190
97
C
Aleurotrachelus trachoides KF059957 CIAT
98
Aleurothrachelus socialis KF059953 CIAT
89
88
New World
G-II
Aleurocanthus spiniferus JQ340176
D
Aleurothrixus floccosus KF059956 CIAT
Aleuroclava sp JQ340187
68
Dialeurodes citri JQ340193
98
93
G-III
Dialeuropora JQ340197
73
Asia
Dialeurodes hongkongensis JQ340195
E
Trialeurodes variabilis KF059962 CIAT
New World
Trialeurodes vaporiariorum KF192508 CIAT
99
F
G-IV
Aleyrodinae
99
100 Trialeurodes vaporariorum AY521265
G
Aleurodicus dugessi AY521251
46
99
Lecanoideus floccissimus KF059960 CIAT
H
Aleurodicus dispersus KF059954 CIAT
95
99
Aleurodicus dispersus EU581838
I
75 Aleurodicus dispersus EU581837
100
Drosophila melanogaster ADW61333
Drosophila melanogaster AGE13862
0.20
0.15
0.10
0.05
0.00
G-VI
Drosophila melanogaster ADW61439
New World
Asia
G-V
Aleurodicinae
Aleuronudus melzeri KF059955 CIAT
Dr. Adriana Bohorquez
Post Doctoral Fellow
32. Lesson learned:
Cassava genetic resource are critical to advance crop
development. Understanding them fully is imperative
A
B
CMC-40
C
MEcu 72
D
33. Positioning CIAT as a Leader in RTB
Improvement
By 2012
Cassava Genetics / Molecular breeding
working like Swiss clock
Tissue Culture
Mol. Biology
WhiteFly Res.
VIGS
Bioinformatic & Data Management
The Best Team
Post Harvest
Breeding
35. Global Cassava Diversity: Cross-Cutting
Enhancing Cassava productivity
through more targeted use of
global genetic diversity
Next-generation sequencing
Metabolomic profiling
36. Global Cassava Diversity: Strategy
Enhancing Cassava productivity
through more targeted use of
global genetic diversity
Next-generation sequencing
Metabolomic profiling
mGWAS and GWAS
High pVA
Waxy
37. Global Cassava Diversity: OMICS
Enhancing Cassava productivity
through more targeted use of
global genetic diversity
Data generation and analysis pipeline
Next-generation sequencing
Sampling
• Selection of
relevant
breeding
genotypes
Metabolomic profiling
• Geographic
distribution
RAD-SEQ
Bioinformatic
Pipeline
Pop.
GENOMICS
Whole Genome
Region/Window
• Mapping to
REF-GENOME
• Pop.
Structure
• Adequate
data filtering
• Pop. diversity
• Variant
detection and
genotyping
(NGSEP)
• Differential
and random
matting
estimates
• Nucleotide
diversity
• Tajima’s D
• Kernell
smoothed
FSTs
SNP-KIT
Genotype
validation/
Identification
• Identification
of highly
informative
SNPs to
discriminate
among
cassava
accessions
38. Global Cassava Diversity: OMICS
Enhancing Cassava productivity
through more targeted use of
global genetic diversity
Next-generation sequencing
•
Metabolomic profiling
1,900 Experimental nurseries
•
Nearly 15’000,000 data points
39. Global Cassava Diversity: OMICS
Enhancing Cassava productivity
through more targeted use of
global genetic diversity
•
•
Important genotypes: MCol22, MCol1505,
MCol1684, MBra12.
•
Next-generation sequencing
Identification of the 139 founders CIAT’s
cassava breeding program
Identification of 25 trait-specific genotypes
to construct the Cassava-Basic
Metabolome Profile
Founder freq.
Metabolomic profiling
X
Genotypes
40. Global Cassava Diversity: OMICS
Enhancing Cassava productivity
through more targeted use of
global genetic diversity
CIAT’s cassava collection compositions
Next-generation sequencing
Metabolomic profiling
SAMPLING:
•
•
•
•
•
•
Founders CIAT’s breeding program
CIAT’s Core collection
Other Landraces
Wild Manihot species
Improved Cassava Materials
African materials
0139
0429
0163
0054
0170
0300
1255
41. Cassava Agro-biodiversity
Enhancing Cassava productivity
through more targeted use of
global genetic diversity
NextGen sequencing: RAD-seq
Next-generation sequencing
Metabolomic profiling
820 acc.
435 acc.
42. Cassava Agro-biodiversity
Enhancing Cassava productivity
through more targeted use of
global genetic diversity
Next-generation sequencing
Metabolomic profiling
NextGen sequencing: Whole genome
11 acc.
06 acc.
44. Cassava Agro-biodiversity
Enhancing Cassava productivity
through more targeted use of
global genetic diversity
Next-generation sequencing
1. Sequence Analysis using NGSEP on
346 cassava specimens
• 292 Cassava accessions from LAC
• 054 Wild Manihot species
2. Strong differentiation between wild
and cultivated specimens
Metabolomic profiling
• 614,000 SNPs were used to trace
for the closest wild relatives to
cassava
3. Complex patterns of population
structure within M. esculenta
• 99,037 SNPs were used.
45. Cassava Agro-biodiversity
FLA PER ALT
FLA PER TST
FLA CTH GUT
AES ALT
Wild Manihots
WKE
K1 Southern South America
K2 Caribbean
K3 Mesoamerican
K4 Andean Cordillera (High lands)
K5 Savanna
K6 Amazon and Eastern Brazil
47. Cassava Agro-biodiversity
High level of genetic
diversity found in
Mesoamerican landraces
7%
70%
K1 Southern South America
K2 Caribbean
K3 Mesoamerican
K4 Andean Cordillera (High lands)
K5 Savanna
K6 Amazon and Eastern Brazil
48. Cassava Agro-biodiversity
K2
K1
K3 K5
K4
Cassava has a geographical
sub-population distribution
that suggest northward southward movement.
K6
K1
K1 Southern South America
K2 Caribbean
K3 Mesoamerican
K4 Andean Cordillera (High lands)
K5 Savanna
K6 Amazon and Eastern Brazil
50. Signs of selection in cassava
Cassava
Wild
Cassava Chromosomes much needed
51. Global Cassava Diversity: Genomics
DEVELOPING A CORE SET OF SNPs FOR VALIDATION AND
IDENTIFICATION OF CASSAVA ACCESSIONS
High Quality SNPs
Technical criteria
for SNPtype™
Assays in
Fluidigm.
Highly Informative
SNPs shared
between WGS
and RAD-seq
No SNPs
around 40bp
SNP/Scaffold
Filters:
Repetitive
regions and
CNVs
GC content
from 40 to 65
Mínimum MAF
0.2
Quality Score:
Higher than 40
More than 10
homozygous
differences
52. Application: SNP-kit for variety ID
This core set of 181 SNPs enabled:
• Accurate identifications of CIAT’s Cassava
materials, and
• Allowed for the assessment of the diversity
of uncharacterized cassava collected in
Amazonian native communities
A set of the most 181 informative SNPs
discovered by RAD-seq were validated by
Fluidigm SNP-type chip technology.
9,216 data points
96 SNPs
96 DNAs
Unknown germplasm
CIAT’s germplasm
48 SNPs
48 DNAs
2,304 data points
HOM
HET
HOM
54. Global RTB Diversity for breeding APPS
Enhancing RTB productivity
through more targeted use of
global genetic diversity
Next-generation sequencing
Metabolomic profiling
Why Metabolomics
• It has been determined that there
are approximately 31,000 genes in
cassava, 37,000 in banana, and
39,000 in potato. For sweetpotato
and yams is still unknown.
• However how these gene interact
with each or in other words how
are they connected in networks is
UNKNOWN.
• The big challenge is: TO MEASURE
HOW these genes interact in
networks – METABOLOMICS is the
best approach.
55. Global RTB Diversity for breeding APPS
Enhancing RTB productivity
through more targeted use of
global genetic diversity
Next-generation sequencing
Metabolomic profiling
Why Metabolomics
• Genome-scale metabolic networks
provide a comprehensive
structural framework for qualitative
and quantitative measure of
genotype-phenotype relationships.
56. Breeding Applications: Statistical “omics”
Enhancing RTB productivity
through more targeted use of
global genetic diversity
Next-generation sequencing
Non-target Profiling
Making sense of the data
Metabolomic profiling
http://www.sciencedirect.com/science/article/pii/S0375960106006530#gr003
57. Breeding Applications: Statistical “omics”
Enhancing RTB productivity
through more targeted use of
global genetic diversity
Analytical Challenge
Next-generation sequencing
Metabolomic profiling
System Biology Analysis for Breeding
Regulome
Regulomics
http://www.genengnews.com/Media/images/Article/UnivVA_MetabolicNetwork7514635831.jpg
58. Breeding Applications: Statistical “omics”
Enhancing RTB productivity
through more targeted use of
global genetic diversity
Future of Genetic Gain??
Next-generation sequencing
Regulome
Metabolomic profiling
http://www.embl.de/research/units/scb/patil/
59. Breeding Applications: Statistical “omics”
Enhancing RTB productivity
through more targeted use of
global genetic diversity
Future of Genetic Gain??
Next-generation sequencing
Regulome
Metabolomic profiling
pVA
carotenoid biosynthetic pathways
http://www.embl.de/research/units/scb/patil/
60. Breeding Applications: Statistical “omics”
Enhancing RTB productivity
through more targeted use of
global genetic diversity
Next-generation sequencing
Metabolomic profiling
Metabolite clusters-traits
Hoekenga Lab Pipeline: LC/MS Fingerprinting
61. Metabolomics: Team
Enhancing RTB productivity
through more targeted use of
global genetic diversity
Next-generation sequencing
Post-Doctoral fellow and PhD
candidate appointed
Metabolomic profiling
Elisabete
Barros-Carvalho (PhD)
Paul Fraser (PhD)
Elliot
Price (PhD candidate)
62. RTB Transformational Breeding
Positioning CIAT as a Leader in RTB breeding in 2nd CRP Phase
MWAS
DNA
RNA
Genome Transcriptome
eQTL
Genotype
Proteins
Metabolites
Phenotype
Proteome
Metabolome
Phenome
pQTL
Molecular
mQTL - mGWAS
Trait
QTL - GWAS & GS
networks
Phenotype
System Biology Analysis for Breeding with high genetic gains
63. RTB Transformational Breeding Platform
Positioning CIAT as a Leader in RTB breeding in 2nd CRP Phase
Rich a consensus on
GENETIC GAIN in
RTBs
RTB genetic gains
means: On the one
hand, increasing the
frequency of
favorable alleles and
opposing their
losses through drift.
On the other,
reducing the
frequency of
deleterious alleles,
which can result in
an excess of genetic
load