Positioning CIAT as leader in next generation breeding for roots, tubers and bananas

“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

DevelopmentCIAT Seminar Series – Cali

10 February 2014

Core - Team: 2009 - 2010Tissue Culture Mol. Biology Breeding

06 Collaborators

02 Researchers02 Agronomist

Molecular Markers Technology efective but time-consuming

Core - Team: 2011 - 2014Tissue Culture Mol. Biology Bioinformatic & Data Management Post Harvest BreedingWhiteFly Res. VIGS

06 Collaborators

10 Researchers02 Agronomist02 Support Staff

Staff Professional Deveploment Tissue Culture Mol. Biology Bioinformatic & Data Management Post Harvest BreedingWhiteFly Res. VIGS

03 Supervisors

3 Master Students

THANK YOU!!!!!!!Tissue Culture Mol. Biology Bioinformatic & Data Management Post Harvest BreedingWhiteFly Res. VIGS

06 Collaborators

10 Researchers02 Agronomist02 Support Staff

Current ResearchFunctional Genetic for high

quality cassava: pVA and Starch synthase pathways

Whitefly control: a durable solution to cassava-disease pandemics (Africa and Asia)

Bemisia tabaci J N410741


Bemisia tabaci biotypeB KF059959 CIAT

Bemisia tabaci biotypeA KF059958 CIAT

Bemisia tabaci AY521259

Aleurolobus marlatti J Q340188

Siphoninus philyreae J Q340199

Aleurocanthus inceratus HM150621

Aleurocanthus spiniferus J Q340176

Crenidorsum micheliae J Q340190

Aleurotrachelus trachoides KF059957 CIAT

Aleurothrachelus socialis KF059953 CIAT

Aleurothrixus floccosus KF059956 CIAT

Aleuroclava sp J Q340187

Dialeuropora J Q340197

Dialeurodes citri J Q340193

Dialeurodes hongkongensis J Q340195

Trialeurodes variabilis KF059962 CIAT

Trialeurodes vaporiariorum KF192508 CIAT

Trialeurodes vaporariorum AY521265

Aleuronudus melzeri KF059955 CIAT

Aleurodicus dugessi AY521251

Lecanoideus floccissimus KF059960 CIAT

Aleurodicus dispersus KF059954 CIAT

Aleurodicus dispersus EU581838


Drosophila melanogaster ADW61439


Drosophila melanogaster AGE13862

100

100

75

99

46

95

99

99

99

81

100

99

88

99

89

98

93

98

97

96

73

68

45

30

0.000.050.100.150.20

Asia / Asia-Minor

New World

Ale

uro

dic

inae

Ale

yro

din

ae

A

B

C

D

E

F

G

H

I

New World

G-I

G-I

I

Asia

Asia

G-I

II

G-I

VG

-V

G-V

I

Asia

New World

New World

Asia

CMC-40

MEcu 72

A B

C D

Whitefly resistance

Whitefly molecular identification

α-carotene

PDS + Z-ISOZDS + CRTISO

LCYB

Phytoene

15µg

25 µg Total Carotenoid Content

Chromoplast

GGPPPSY

ζ-carotene

Lycopene

β-caroteneLCYB + LCYE

β+ε-OHase

Lutein

β-OHaseZeaxanthin

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast

Starch Synthase Pathway

Carotenoid Synthase Pathway

Enhancing Cassava productivity through more targeted use of

global genetic diversity

Next-generation sequencing

Metabolomic profiling

pVA and Starch: WhyFunctional Genetic for high


α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPPPSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast



Challenge: Malnutrition – Secure Source of Incomefor poor small-holder farmers

pVA and Starch: HypothesisFunctional Genetic for high


α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPPPSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast



Amyloplast vs. Chromoplast

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast

pVA and Starch: InfrastructureFunctional Genetic for high


α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPPPSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast



Equipment needed:

pVA and Starch: Plant materialsFunctional Genetic for high


α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPPPSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast



PEDIGREE:

pVA and Starch: PhenotypingFunctional Genetic for high


α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPPPSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast



BIOCHEMICAL TEST:

pVA and Starch: Data consistencyFunctional Genetic for high


α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPPPSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin


Three years evaluation 2011, 2012 and 2013

y = 1.0899x - 0.0065R² = 0.8194

0

2

4

6

8

10

12

14

16

0 2 4 6 8 10 12 14

2012

2011

β-carotene content (HPLC method)

b-carotene content (HPLC method) Linear (b-carotene content (HPLC method))

y = 1.0007x + 1.7402R² = 0.821

0

5

10

15

20

25

30

0 5 10 15 20 25

2012

2011

Total Carotenoid Content(HPLC method)

Total Carotenoid Content (HPLC method) Linear (Total Carotenoid Content (HPLC method))

pVA and Starch: The potentialFunctional Genetic for high


α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPPPSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin



0

5

10

15

20

25

30

35

40

45

GM

3732

-28

GM

3736

-78

GM

3736

-84

GM

3736

-29

GM

3732

-19

GM

3732

-22

GM

3736

-75

GM

3736

-40

GM

3736

-56

GM

3736

-26

GM

3736

-45

GM

3736

-37

GM

3736

-34

GM

3732

-02

GM

3732

-05

GM

3732

-34

GM

3736

-17

GM

3736

-16

GM

3732

-17

GM

905-

57G

M37

36-3

2G

M37

36-1

5G

M37

32-1

8G

M37

36-5

8G

M37

36-5

9G

M37

32-1

1G

M37

32-0

8G

M37

36-7

7G

M37

36-2

0G

M37

36-6

9G

M90

5-60

GM

3732

-29

GM

3732

-30

GM

3736

-66

GM

3736

-38

GM

3736

-36

GM

3732

-01

GM

3736

-76

GM

3732

-21

GM

3736

-51

GM

3736

-43

GM

3732

-16

GM

3736

-18

GM

3736

-85

GM

3736

-12

GM

3736

-44

GM

3732

-37

GM

3732

-13

GM

3736

-13

GM

3736

-02

GM

3736

-06

GM

3736

-48

GM

3736

-53

GM

3736

-54

GM

3736

-74

GM

3732

-23

GM

3732

-36

GM

3736

-72

GM

3732

-31

GM

3736

-57

GM

905-

52G

M37

36-5

2G

M37

36-0

3G

M37

36-0

8G

M37

32-2

5G

M37

36-1

9G

M37

36-1

1G

M37

32-2

7G

M37

36-2

3G

M37

36-8

0G

M37

32-1

2G

M37

32-3

5G

M37

36-0

5G

M37

36-7

9G

M37

32-1

4G

M37

32-0

4G

M37

36-6

3G

M37

32-2

0G

M37

32-3

2G

M37

32-0

9G

M37

36-2

4G

M37

36-2

5G

M37

36-4

1G

M37

32-3

3G

M37

36-7

3G

M37

32-0

3G

M37

36-1

0G

M37

32-0

6G

M37

36-2

2G

M37

36-6

1G

M37

36-3

5G

M37

36-4

7G

M37

36-2

1G

M37

36-3

0G

M37

36-2

7G

M37

36-7

0G

M37

32-0

7G

M37

36-3

9G

M37

32-1

5G

M37

36-4

9G

M37

36-8

1G

M37

32-1

0G

M37

36-0

9G

M37

36-3

3G

M37

36-5

0G

M37

32-2

4G

M37

36-2

8G

M37

36-7

1G

M37

36-6

4G

M37

36-1

4G

M37

36-5

5G

M37

36-8

2G

M37

36-4

2G

M37

36-4

6G

M37

36-6

2G

M37

36-6

7G

M37

36-0

1G

M37

36-8

3

PTFN 2012

PTH 2012

TCH 2012

Car

ote

no

id

Gai

ne

dC

aro

ten

oid

P

ote

nti

al

IPP

Geranylgeranyl diphosphate

Phytoene

Lycopene

-carotene(vitamin A precursor)

Phytoene synthase

Phytoene desaturase

Lycopene-beta-cyclase

ξ-carotene desaturase

pVA and Starch: No Lycopene Functional Genetic for high


α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPPPSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin



Car

ote

no

id

Gai

ne

dC

aro

ten

oid

P

ote

nti

al

0

5

10

15

20

25

30

35

40

45

GM

3732

-28

GM

3736

-78

GM

3736

-84

GM

3736

-29

GM

3732

-19

GM

3732

-22

GM

3736

-75

GM

3736

-40

GM

3736

-56

GM

3736

-26

GM

3736

-45

GM

3736

-37

GM

3736

-34

GM

3732

-02

GM

3732

-05

GM

3732

-34

GM

3736

-17

GM

3736

-16

GM

3732

-17

GM

905-

57G

M37

36-3

2G

M37

36-1

5G

M37

32-1

8G

M37

36-5

8G

M37

36-5

9G

M37

32-1

1G

M37

32-0

8G

M37

36-7

7G

M37

36-2

0G

M37

36-6

9G

M90

5-60

GM

3732

-29

GM

3732

-30

GM

3736

-66

GM

3736

-38

GM

3736

-36

GM

3732

-01

GM

3736

-76

GM

3732

-21

GM

3736

-51

GM

3736

-43

GM

3732

-16

GM

3736

-18

GM

3736

-85

GM

3736

-12

GM

3736

-44

GM

3732

-37

GM

3732

-13

GM

3736

-13

GM

3736

-02

GM

3736

-06

GM

3736

-48

GM

3736

-53

GM

3736

-54

GM

3736

-74

GM

3732

-23

GM

3732

-36

GM

3736

-72

GM

3732

-31

GM

3736

-57

GM

905-

52G

M37

36-5

2G

M37

36-0

3G

M37

36-0

8G

M37

32-2

5G

M37

36-1

9G

M37

36-1

1G

M37

32-2

7G

M37

36-2

3G

M37

36-8

0G

M37

32-1

2G

M37

32-3

5G

M37

36-0

5G

M37

36-7

9G

M37

32-1

4G

M37

32-0

4G

M37

36-6

3G

M37

32-2

0G

M37

32-3

2G

M37

32-0

9G

M37

36-2

4G

M37

36-2

5G

M37

36-4

1G

M37

32-3

3G

M37

36-7

3G

M37

32-0

3G

M37

36-1

0G

M37

32-0

6G

M37

36-2

2G

M37

36-6

1G

M37

36-3

5G

M37

36-4

7G

M37

36-2

1G

M37

36-3

0G

M37

36-2

7G

M37

36-7

0G

M37

32-0

7G

M37

36-3

9G

M37

32-1

5G

M37

36-4

9G

M37

36-8

1G

M37

32-1

0G

M37

36-0

9G

M37

36-3

3G

M37

36-5

0G

M37

32-2

4G

M37

36-2

8G

M37

36-7

1G

M37

36-6

4G

M37

36-1

4G

M37

36-5

5G

M37

36-8

2G

M37

36-4

2G

M37

36-4

6G

M37

36-6

2G

M37

36-6

7G

M37

36-0

1G

M37

36-8

3

PTFN 2012

PTH 2012

TCH 2012

IPP


Phytoene

Lycopene


Phytoene synthase

Phytoene desaturase



pVA and Starch: Unknown carotenoidsFunctional Genetic for high


α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPPPSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin



Car

ote

no

id

Gai

ne

dC

aro

ten

oid

P

ote

nti

al

0

5

10

15

20

25

30

35

40

45

GM

3732

-28

GM

3736

-78

GM

3736

-84

GM

3736

-29

GM

3732

-19

GM

3732

-22

GM

3736

-75

GM

3736

-40

GM

3736

-56

GM

3736

-26

GM

3736

-45

GM

3736

-37

GM

3736

-34

GM

3732

-02

GM

3732

-05

GM

3732

-34

GM

3736

-17

GM

3736

-16

GM

3732

-17

GM

905-

57G

M37

36-3

2G

M37

36-1

5G

M37

32-1

8G

M37

36-5

8G

M37

36-5

9G

M37

32-1

1G

M37

32-0

8G

M37

36-7

7G

M37

36-2

0G

M37

36-6

9G

M90

5-60

GM

3732

-29

GM

3732

-30

GM

3736

-66

GM

3736

-38

GM

3736

-36

GM

3732

-01

GM

3736

-76

GM

3732

-21

GM

3736

-51

GM

3736

-43

GM

3732

-16

GM

3736

-18

GM

3736

-85

GM

3736

-12

GM

3736

-44

GM

3732

-37

GM

3732

-13

GM

3736

-13

GM

3736

-02

GM

3736

-06

GM

3736

-48

GM

3736

-53

GM

3736

-54

GM

3736

-74

GM

3732

-23

GM

3732

-36

GM

3736

-72

GM

3732

-31

GM

3736

-57

GM

905-

52G

M37

36-5

2G

M37

36-0

3G

M37

36-0

8G

M37

32-2

5G

M37

36-1

9G

M37

36-1

1G

M37

32-2

7G

M37

36-2

3G

M37

36-8

0G

M37

32-1

2G

M37

32-3

5G

M37

36-0

5G

M37

36-7

9G

M37

32-1

4G

M37

32-0

4G

M37

36-6

3G

M37

32-2

0G

M37

32-3

2G

M37

32-0

9G

M37

36-2

4G

M37

36-2

5G

M37

36-4

1G

M37

32-3

3G

M37

36-7

3G

M37

32-0

3G

M37

36-1

0G

M37

32-0

6G

M37

36-2

2G

M37

36-6

1G

M37

36-3

5G

M37

36-4

7G

M37

36-2

1G

M37

36-3

0G

M37

36-2

7G

M37

36-7

0G

M37

32-0

7G

M37

36-3

9G

M37

32-1

5G

M37

36-4

9G

M37

36-8

1G

M37

32-1

0G

M37

36-0

9G

M37

36-3

3G

M37

36-5

0G

M37

32-2

4G

M37

36-2

8G

M37

36-7

1G

M37

36-6

4G

M37

36-1

4G

M37

36-5

5G

M37

36-8

2G

M37

36-4

2G

M37

36-4

6G

M37

36-6

2G

M37

36-6

7G

M37

36-0

1G

M37

36-8

3

PTFN 2012

PTH 2012

TCH 2012

IPP


Phytoene

Lycopene


Phytoene synthase

Phytoene desaturase



Unknown Carotenoids

pVA and Starch: DMC do not matterFunctional Genetic for high


α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPPPSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin


Carotenoids vs Dry Matter Content (DMC)

Car

ote

no

id

Gai

ne

dC

aro

ten

oid

P

ote

nti

al

IPP


Phytoene

Lycopene


Phytoene synthase

Phytoene desaturase



0

5

10

15

20

25

30

35

40

45

50

GM

3732

-28

GM

3736

-78

GM

3736

-84

GM

3736

-29

GM

3732

-19

GM

3732

-22

GM

3736

-75

GM

3736

-40

GM

3736

-56

GM

3736

-26

GM

3736

-45

GM

3736

-37

GM

3736

-34

GM

3732

-02

GM

3732

-05

GM

3732

-34

GM

3736

-17

GM

3736

-16

GM

3732

-17

GM

905-

57G

M37

36-3

2G

M37

36-1

5G

M37

32-1

8G

M37

36-5

8G

M37

36-5

9G

M37

32-1

1G

M37

32-0

8G

M37

36-7

7G

M37

36-2

0G

M37

36-6

9G

M90

5-60

GM

3732

-29

GM

3732

-30

GM

3736

-66

GM

3736

-38

GM

3736

-36

GM

3732

-01

GM

3736

-76

GM

3732

-21

GM

3736

-51

GM

3736

-43

GM

3732

-16

GM

3736

-18

GM

3736

-85

GM

3736

-12

GM

3736

-44

GM

3732

-37

GM

3732

-13

GM

3736

-13

GM

3736

-02

GM

3736

-06

GM

3736

-48

GM

3736

-53

GM

3736

-54

GM

3736

-74

GM

3732

-23

GM

3732

-36

GM

3736

-72

GM

3732

-31

GM

3736

-57

GM

905-

52G

M37

36-5

2G

M37

36-0

3G

M37

36-0

8G

M37

32-2

5G

M37

36-1

9G

M37

36-1

1G

M37

32-2

7G

M37

36-2

3G

M37

36-8

0G

M37

32-1

2G

M37

32-3

5G

M37

36-0

5G

M37

36-7

9G

M37

32-1

4G

M37

32-0

4G

M37

36-6

3G

M37

32-2

0G

M37

32-3

2G

M37

32-0

9G

M37

36-2

4G

M37

36-2

5G

M37

36-4

1G

M37

32-3

3G

M37

36-7

3G

M37

32-0

3G

M37

36-1

0G

M37

32-0

6G

M37

36-2

2G

M37

36-6

1G

M37

36-3

5G

M37

36-4

7G

M37

36-2

1G

M37

36-3

0G

M37

36-2

7G

M37

36-7

0G

M37

32-0

7G

M37

36-3

9G

M37

32-1

5G

M37

36-4

9G

M37

36-8

1G

M37

32-1

0G

M37

36-0

9G

M37

36-3

3G

M37

36-5

0G

M37

32-2

4G

M37

36-2

8G

M37

36-7

1G

M37

36-6

4G

M37

36-1

4G

M37

36-5

5G

M37

36-8

2G

M37

36-4

2G

M37

36-4

6G

M37

36-6

2G

M37

36-6

7G

M37

36-0

1G

M37

36-8

3

Dry Matter Content (2012)

High β-carotene has no penalty on DMC

Gains from 2010/12 to 2013From 25ug to 29ug in TCCFrom 15ug to 22ug in TBC

pVA and Starch: During 2014Functional Genetic for high


α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPPPSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin


SSR and SNPs

pVA and Starch: Which Molecular MarkersFunctional Genetic for high


α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPPPSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin


Unraveling the genetics of high pVA61003 Mapping Pop.

CIR00030.0RGA-8A-1c2.9

CIR000966.6

CIR0199a86.4BNL169399.8

BNL0256232.8

BNL1160250.8

CIR0171c272.4

BNL1161315.1

CIR0166a338.0A1110349.4

BNL2960377.3

qF

5-VB

S

qF

4-VB

S

qF

5-VB

S

A10-Chr10

BNL40590.0CIR0272b6.3

BNL1673110.9

CIR0148140.5BNL1045a146.9CIR0293160.2BNL3537a172.8BNL0598b188.4

BNL0598a215.1BNL3537c218.0

CIR0272a248.9

BNL3537b274.7

BNL1045b310.4BNL2495326.3CIR0085b330.8

qF

3-FG

AW

6b

qF

3-FG

AW

6a qF

3-VB

Sa

qF

3-VB

Sb

qF

4-VB

S

qF

5-VB

Sq

F3-F

GA

W5

qF

3-FG

AW

6

qF

3-VB

S

A12-Chr12

61003 Mapping Pop.

BNL11450.0

CIR012148.7BNL383849.3BNL394863.4CIR0171b77.9BNL094688.8BNL399393.9CIR0171d104.2BNL0169128.7

CIR0166b149.8

qF

3-FG

AW

3

qF

3-FG

AW

4

qF

3-FG

AW

5

qF

3-FG

AW

6

qF

3-VB

S

qF

3-FG

AW

3

qF

3-FG

AW

4

qF

3-FG

AW

5

qF

3-FG

AW

6

qF

3-VB

S

D10-Chr20

Unig22B10b0.0Gate1AC11a12.3BNL019315.0BNL254420.5

BNL2652b61.9BNL107975.1BNL347987.1BNL3280b95.8

CIR0277158.7

qF

3-W3

qF

4-VB

S

qF

5-VB

S

qF

4-VB

S

D13-Chr18

pVA and Starch: Novel starchesFunctional Genetic for high


GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast


Waxy and small-granule cassava

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast

X

Easy hydrolysis good for bioethanol and bioplastic production



GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast



GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast

X

100% amylopectin



GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast



GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast

X

Important to bear in mind:Type and quality of the amylopectin is control by the starch-synthase pathway



GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast



http://www.google.com.co/url?sa=i&source=images&cd=&cad=rja&docid=1C-foD45sxTHoM&tbnid=7jqujX6Fb7VQhM:&ved=0CAgQjRw&url=http://4vector.com/free-vector/check-mark-symbol-clip-art-115329&ei=UI6qUq-tII6qkAeXo4CYDw&psig=AFQjCNGEH6_o0mVlE-IVGJVfRA9cgpLJ2Q&ust=1386995664589117



pVA and Starch: Novel starches WAXYFunctional Genetic for high


GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast


GBSSI: Responsible for Waxy cassava

• 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



GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast



SM

3316

-24N

ewA

-V4W

x

AM

206-

5New

-V3W

x

24

CU

B58

-V5N

Wx

24

GB

SS

JF70

8949

Wx

24

SM

3316

-24N

ewA

-V2W

x

24

CL4

4-2N

ewA

-V6W

x

24

CL

44-2

New

A-V

3Wx

CL

44-

2N

ew

A-V

5W

x

67

24

CL

41

-1N

ew

AV

2W

x

24

CL

44

-2N

ew

A-V

4W

x

24

CL

41

-6N

ew

A-V

3W

x

CL

41

-6N

ew

A-V

7W

x91

24

CL

44

-2N

ew

A-V

2W

xC

L4

4-2

Ne

wA

-V1

Wx

70

24

AC

27-1

New

-V4W

xA

C27

-1N

ew-V

2Wx

AC

27-1

New

-V1W

xA

C27

-1N

ew-V

3Wx

514077

24

CL4

2-3N

ewA

-V5W

x

24

CL4

1-6N

ewA

-V5W

x

24

CL4

2-3N

ewA

-V7W

x

CL4

2-3N

ewA

-V4W

x

CU

B29

-V3N

Wx

5782

24

AM20

6-5N

ew-V

4Wx

AM20

6-5N

ew-V

6Wx

62

24

CL41-

6New

A-V2W

x

24

SM33

15-5NewA-V

1Wx

SM3315-5NewA-V

3Wx

86SM3315-5NewA-V

2Wx

SM3315-5NewA-V4Wx

7194

24

CL42-3NewA-V2Wx

24

CL41-6NewA-V1Wx

24

AM206-5New-V5Wx

24

CL41-1NewAV1Wx

CUB58-V2NWx

CUB29-V1NWx

AM206-5New-V2Wx

PAN139-V2NWx

PAN139-V3NWx76

CUB58-V3NWx

PAN139-V6NWx

VEN29-V7NWx

CL41-1NewAV3WxAM206-5New-V1WxCUB29-V5NWxCUB29-V7NWx

24

24

24

24

24

24

24

24

2424

3624

CL42-3NewA-V3WxCL42-3NewA-V6Wx

82

24

CL42-6NewA-V4Wx

CL42-6NewA-V2Wx

CL42-6NewA-V1Wx

75

53

24

CL41-1NewAV4Wx

SM3316-32NewA-V3Wx

SM3316-32NewA-V4Wx

82

26

36

CL41-6NewA-V6Wx

CL42-6NewA-V3Wx

CL42-6NewA-V5Wx

CL41-6NewA-V4Wx

CL41-6N

ewA-V8W

x

75

SM3316-24N

ewA-V1W

x

SM

3316-24New

A-V

3Wx

9999

2899

51

62

CL42-3N

ewA

-V1W

x

91

CU

B23-V

2NW

x

CU

B23-V

5NW

x

96

90

CU

B58-V

6NW

x

90

VE

N309aV

4NW

x

8954

CU

B2-V

2N

Wx

CU

B2

-V7

NW

x

9555

TM

E-3

Ne

wV

2P

Sg

NW

x

29C

4re

vV1

PS

gN

Wx

C4 rev V

2PS

g NW

x85

21

VE

N2

9-V

1N

Wx

TM

S3

05

55

V1

revP

Sg

NW

x

VE

N2

9-V

2N

Wx

34

26

19

CU

B2-

V5N

Wx

CU

B2-

V6N

Wx

34

CU

B2-

V3N

Wx

81

AM

506-

5NW

x

VE

N30

9bV

1NW

x

49

CU

B2-

V4N

Wx

CU

B2-

V1N

Wx

84 39 18

8

VE

N29

-V3N

Wx

11

GBS

SIcD

NAX

7416

0NW

x

VEN29

-V4N

Wx

25

CUB29-V

4NW

x

24

VEN29-V

9NW

x

24

VEN29-V10NW

x

24

PAN139-V4NW

x

22

VEN29-V5NW

x

CUB58-V4NWx

CUB23-V1NWx

CUB23-V6NWx

81

GBSSIX74160MANESYPAN139-V5NWx

SM3316-32NewA-V1WxSM3316-32NewA-V2Wx 99

TMS30555V2revPSgNWx 73

PAN139-V1NWxVEN29-V8NWxVEN29-V6NWx

CUB29-V2NWx

CUB58-V1NWx

TME-3NewV1PSgNWx

CUB23-V3NWx

VEN309bV2NWx

CUB23-V4NWx

GBSSJF708948NWx

CUB29-V6NWx 26

26

24

24

24

24

24

2518

18

24

2424

2424

2127

47

VEN309aV1NWx

VEN309aV2NWx

VEN309aV3NWx

87

99

66

XP_004495514CHICKPEA

ABK95833POPULUS

ACV72639COTTON

ACJ11751COTTON

99

46

66

All non-waxy landraces carried the non-waxy allele(s), but waxy types also carried non-waxy alleles

All waxy types carried the waxy allele(s)



GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast



SM

3316

-24N

ewA

-V4W

x

AM

206-

5New

-V3W

x

24

CU

B58

-V5N

Wx

24

GB

SS

JF70

8949

Wx

24

SM

3316

-24N

ewA

-V2W

x

24

CL4

4-2N

ewA

-V6W

x

24

CL

44-2

New

A-V

3Wx

CL

44-

2N

ew

A-V

5W

x

67

24

CL

41

-1N

ew

AV

2W

x

24

CL

44

-2N

ew

A-V

4W

x

24

CL

41

-6N

ew

A-V

3W

x

CL

41

-6N

ew

A-V

7W

x91

24

CL

44

-2N

ew

A-V

2W

xC

L4

4-2

Ne

wA

-V1

Wx

70

24

AC

27-1

New

-V4W

xA

C27

-1N

ew-V

2Wx

AC

27-1

New

-V1W

xA

C27

-1N

ew-V

3Wx

514077

24

CL4

2-3N

ewA

-V5W

x

24

CL4

1-6N

ewA

-V5W

x

24

CL4

2-3N

ewA

-V7W

x

CL4

2-3N

ewA

-V4W

x

CU

B29

-V3N

Wx

5782

24

AM20

6-5N

ew-V

4Wx

AM20

6-5N

ew-V

6Wx

62

24

CL41-

6New

A-V2W

x

24

SM33

15-5NewA-V

1Wx

SM3315-5NewA-V

3Wx

86SM3315-5NewA-V

2Wx

SM3315-5NewA-V4Wx

7194

24

CL42-3NewA-V2Wx

24

CL41-6NewA-V1Wx

24

AM206-5New-V5Wx

24

CL41-1NewAV1Wx

CUB58-V2NWx

CUB29-V1NWx

AM206-5New-V2Wx

PAN139-V2NWx

PAN139-V3NWx76

CUB58-V3NWx

PAN139-V6NWx

VEN29-V7NWx

CL41-1NewAV3WxAM206-5New-V1WxCUB29-V5NWxCUB29-V7NWx

24

24

24

24

24

24

24

24

2424

3624

CL42-3NewA-V3WxCL42-3NewA-V6Wx

82

24

CL42-6NewA-V4Wx

CL42-6NewA-V2Wx

CL42-6NewA-V1Wx

75

53

24

CL41-1NewAV4Wx

SM3316-32NewA-V3Wx

SM3316-32NewA-V4Wx

82

26

36

CL41-6NewA-V6Wx

CL42-6NewA-V3Wx

CL42-6NewA-V5Wx

CL41-6NewA-V4Wx

CL41-6N

ewA-V8W

x

75

SM3316-24N

ewA-V1W

x

SM

3316-24New

A-V

3Wx

9999

2899

51

62

CL42-3N

ewA

-V1W

x

91

CU

B23-V

2NW

x

CU

B23-V

5NW

x

96

90

CU

B58-V

6NW

x

90

VE

N309aV

4NW

x

8954

CU

B2-V

2N

Wx

CU

B2

-V7

NW

x

9555

TM

E-3

Ne

wV

2P

Sg

NW

x

29C

4re

vV1

PS

gN

Wx

C4 rev V

2PS

g NW

x85

21

VE

N2

9-V

1N

Wx

TM

S3

05

55

V1

revP

Sg

NW

x

VE

N2

9-V

2N

Wx

34

26

19

CU

B2-

V5N

Wx

CU

B2-

V6N

Wx

34

CU

B2-

V3N

Wx

81

AM

506-

5NW

x

VE

N30

9bV

1NW

x

49

CU

B2-

V4N

Wx

CU

B2-

V1N

Wx

84 39 18

8

VE

N29

-V3N

Wx

11

GBS

SIcD

NAX

7416

0NW

x

VEN29

-V4N

Wx

25

CUB29-V

4NW

x

24

VEN29-V

9NW

x

24

VEN29-V10NW

x

24

PAN139-V4NW

x

22

VEN29-V5NW

x

CUB58-V4NWx

CUB23-V1NWx

CUB23-V6NWx

81

GBSSIX74160MANESYPAN139-V5NWx

SM3316-32NewA-V1WxSM3316-32NewA-V2Wx 99

TMS30555V2revPSgNWx 73

PAN139-V1NWxVEN29-V8NWxVEN29-V6NWx

CUB29-V2NWx

CUB58-V1NWx

TME-3NewV1PSgNWx

CUB23-V3NWx

VEN309bV2NWx

CUB23-V4NWx

GBSSJF708948NWx

CUB29-V6NWx 26

26

24

24

24

24

24

2518

18

24

2424

2424

2127

47

VEN309aV1NWx

VEN309aV2NWx

VEN309aV3NWx

87

99

66

XP_004495514CHICKPEA

ABK95833POPULUS

ACV72639COTTON

ACJ11751COTTON

99

46

66

All non-waxy landraces carried the non-waxy allele(s), but waxy types also carried non-waxy alleles

All waxy types carried the waxy allele(s)

Is cassava really diploid (2X)?

Whitefly research: WHYWhitefly control: a durable

solution to cassava-disease pandemics (Africa and Asia)






























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0.000.050.100.150.20

Asia / Asia-Minor

New World

Ale

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Ale

yro

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ae

A

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C

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G-I

I

Asia

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G-I

II

G-I

VG

-V

G-V

I

Asia

New World

New World

Asia

CMC-40

MEcu 72

A B

C D

Whitefly resistance


Whiteflies have been called

“The pest of 21st Century”

Tomato Citrus Palm

Cotton Zucchini

Whitefly researchWhitefly control: a durable































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C

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New World

G-I

G-I

I

Asia

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G-I

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G-I

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-V

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Asia

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New World

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MEcu 72

A B

C D

Whitefly resistance


Whitefly Pest response Bio-assay

A

B

C
































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H

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New World

G-I

G-I

I

Asia

Asia

G-I

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G-I

VG

-V

G-V

I

Asia

New World

New World

Asia

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MEcu 72

A B

C D

Whitefly resistance


Whitefly SSR and AFLP genetic map

SNP markers are underway
































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G-I

G-I

I

Asia

Asia

G-I

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New World

Asia

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MEcu 72

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C D

Whitefly resistance


Grant to be approved in 2014
































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D

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G

H

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New World

G-I

G-I

I

Asia

Asia

G-I

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G-I

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-V

G-V

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Asia

New World

New World

Asia

CMC-40

MEcu 72

A B

C D

Whitefly resistance


Grant to be approved in 2014

Dr. Adriana Bohorquez Post Doctoral Fellow

Lesson learned:

Cassava genetic resource are critical to advance crop development. Understanding them fully is imperative

CMC-40

MEcu 72

A B

C D

Positioning CIAT as a Leader in RTB

Improvement

Cassava Genetics / Molecular breeding working like Swiss clock

By 2012

The Best Team

Tissue Culture Mol. Biology Bioinformatic & Data Management Post Harvest BreedingWhiteFly Res. VIGS

RTB Leader for Development of Varieties

Global Cassava Diversity: Cross-CuttingEnhancing Cassava productivity

through more targeted use of global genetic diversity



Global Cassava Diversity: StrategyEnhancing Cassava productivity



Metabolomic profiling mGWAS and GWAS

High pVAWaxy

Global Cassava Diversity: OMICSEnhancing Cassava productivity




Data generation and analysis pipeline

Sampling

RAD-SEQBioinformatic

Pipeline

Pop. GENOMICS

Whole Genome Region/Window

SNP-KIT

Genotype validation/

Identification

•Selection of relevant breeding genotypes

•Geographic distribution

•Mapping to REF-GENOME

•Adequate data filtering

• Variant detection and genotyping (NGSEP)

•Pop. Structure

•Pop. diversity

•Differential and random matting estimates

•Nucleotide diversity

•Tajima’s D

•Kernell smoothed FSTs

• Identification of highly informative SNPs to discriminate among cassava accessions





• 1,900 Experimental nurseries

• Nearly 15’000,000 data points





• Identification of the 139 founders CIAT’s cassava breeding program

• Important genotypes: MCol22, MCol1505, MCol1684, MBra12.

• Identification of 25 trait-specific genotypes to construct the Cassava-Basic Metabolome Profile

Genotypes

Fo

un

der

fre

q.

X





CIAT’s cassava collection compositions

• Founders CIAT’s breeding program 0139• CIAT’s Core collection 0429• Other Landraces 0163• Wild Manihot species 0054• Improved Cassava Materials 0170• African materials 0300

1255

SAMPLING:

Cassava Agro-biodiversityEnhancing Cassava productivity




NextGen sequencing: RAD-seq

820 acc.435 acc.





NextGen sequencing: Whole genome

11 acc.06 acc.





NGSEP





1. Sequence Analysis using NGSEP on 346 cassava specimens

• 292 Cassava accessions

from LAC

• 054 Wild Manihot species2. Strong differentiation between wild and cultivated specimens

• 614,000 SNPs were used to

trace for the closest wild

relatives to cassava3. Complex patterns of population structure within M. esculenta

• 99,037 SNPs were used.

Cassava Agro-biodiversity

K1 Southern South AmericaK2 CaribbeanK3 MesoamericanK4 Andean Cordillera (High lands)K5 SavannaK6 Amazon and Eastern Brazil

Mesoamerica

And

ean

Ran

ges

Sav

anna

Amazon & Eastern Brazil

Sothern South America

Wild Manihots

Car

ibbe

an

FLA PER ALT

FLA PER TST

FLA CTH GUT

AES ALT

WKE


Southern South America

Caribbean Mesoamerica Savanna Andean Ranges Amazon & Eastern Brazil



7%

70%

High level of genetic diversity found in Mesoamerican landraces



K1

K1

K6

K5

K4

K3

K2

Cassava has a geographical sub-population distribution that suggest northward - southward movement.


Southern South America

Caribbean Mesoamerica Savanna Andean Ranges Amazon & Eastern Brazil

High pVA WF resistance

Signs of selection in cassava

Cassav

aW

ild

Cassava Chromosomes much needed

Global Cassava Diversity: Genomics

High Quality SNPs

SNPs shared between WGS and RAD-seq

Filters:Repetitive regions and CNVs

Quality Score: Higher than 40

DEVELOPING A CORE SET OF SNPs FOR VALIDATION AND IDENTIFICATION OF CASSAVA ACCESSIONS

Application: SNP-kit for variety ID

96 SNPs

96 DNAs

48 SNPs

48 DNAs

9,216 data points

2,304 data pointsHOM

HET

HOM

CIAT’s germplasm

Unknown germplasm

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.

Global Cassava Diversity: MetabolomicsEnhancing Cassava productivity




Genotype Trait Clones1 BRA488 High Cianide Content 62 DOM2 High Dry Matter Content 63 COL2017 High Sugar Content 64 PAR36 High Amilose Content 65 MPER183 High PPD Tolerance/Frog Skin disease/Low Carotene 66 MCOL2436 High Carotene/Trips Susceptible 67 MECU72 WF Resistance/Bacteriosis Susceptible 68 MCUB74 High Culinary Quality/Z06 adaptation 69 CUB23 Waxi Potential 6

10 PAN139 Trips Resistance 611 TMS604444 Transformacion 612 TME3 CMD 613 TMS305555 CMD 614 BRA1A High carotene 615 MCOL1505 Z01 nd Z04 adaptation 616 MCOL1522 Z05 adaptation 617 GUA35 Low Sugar Content 618 CUB25 Low Amilose Content 619 MVEN25 Low Culinary Quality 620 MCOL22 PPD susceptible 621 MGUA85 Adaptation Z02 622 MVEN77 Drought tolerance 623 MCOL113 Adaptation Z06 624 MCOL638 Bacteriosis resistance 625 MCOL1684 Z03 adaptation 6

150

Materials for Metabolomic profiling

Global RTB Diversity for breeding APPSEnhancing RTB productivity through more targeted use of




• 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.

Why Metabolomics

Global RTB Diversity for breeding APPSEnhancing RTB productivity through more targeted use of




• Genome-scale metabolic networks provide a comprehensive structural framework for qualitative and quantitative measure of genotype-phenotype relationships.

Why Metabolomics

Breeding Applications: Statistical “omics” Enhancing RTB productivity through more targeted use of




Non-target Profiling

Making sense of the data

http://www.sciencedirect.com/science/article/pii/S0375960106006530#gr003

Enhancing RTB productivity through more targeted use of




Analytical Challenge

http://www.genengnews.com/Media/images/Article/UnivVA_MetabolicNetwork7514635831.jpg

System Biology Analysis for Breeding

RegulomicsRegulome

Breeding Applications: Statistical “omics”





Future of Genetic Gain??

http://www.embl.de/research/units/scb/patil/

Regulome






Future of Genetic Gain??

http://www.embl.de/research/units/scb/patil/

Regulome

pVA

carotenoid biosynthetic pathways






Metabolite clusters-traits

Hoekenga Lab Pipeline: LC/MS Fingerprinting


Metabolomics: TeamEnhancing RTB productivity through more targeted use of




Post-Doctoral fellow and PhD candidate appointed

Elisabete Barros-Carvalho (PhD)

Elliot Price (PhD candidate)

Paul Fraser (PhD)

RTB Transformational Breeding

DNA

RNA

Proteins

Metabolites

Phenotype

Trait

Genome Transcriptome Proteome Metabolome Phenome

QTL - GWAS & GSmQTL - mGWASpQTL eQTL

MWAS

Genotype Molecular networks Phenotype

System Biology Analysis for Breeding with high genetic gains

Positioning CIAT as a Leader in RTB breeding in 2nd CRP Phase

RTB Transformational Breeding Platform

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

Positioning CIAT as a Leader in RTB breeding in 2nd CRP Phase

Acknowledgment

THANK YOU

AD1 – 800BC

AD1 – 800BC

AD800- 1000AD630

Positioning CIAT as leader in next generation breeding for roots, tubers and bananas

Education

Transcript of Positioning CIAT as leader in next generation breeding for roots, tubers and bananas