true-to-type fingerprinting: implications towards cocoa

A member of CGIAR consortium ww.iita.org

True-to-type Fingerprinting: Implications towards cocoa and

chocolate economy and sustainability

Ranjana BhattacharjeeMolecular Geneticist

[email protected]

2016 Next Generation Cocoa Research Symposium


- Nene Akwetey-Kodjoe- Desire Pokou- Olivier Sounigo- Francis Padi- Festus Olasupo- Ives Bruno Efombagn- Mathias Tahi- Stephan Opoku- Abu Dadzie- Anna Muyiwa- Peter Aikpokpodion- Honorine Brigitte

Guiraud- Komivi Ametafe- Sona Ebai

Co-Authors



Cocoa Growing Countries



Cocoa Producers and Chocolate Consumers


Chocolate Consumption Kilos per person 2010

Belgium 10.74 Austria 8.33

Switzerland 10.14 Denmark 7.13

UK 9.94 Sweden 6.97

Norway 9.19 Finland 6.43

Germany 8.96 USA 5.58


Source: Mitchell (2007a, 2007b and 2007c); Faostat (2012)

Cocoa: World Production (1895-2010)

A member of CGIAR consortium ww.iita.org2016 Next Generation Cocoa Research Symposium


Cocoa and Chocolate: The Changing Patterns

Several factors influence the consumption of chocolate products throughout time:- price of cocoa beans (price elasticity of demand is relatively low)- income (income elasticity of demand is higher) - taste and preference differences- climate (people in cooler climates consume more chocolate)- availability of substitutes (cocoa beans/cocoa butter)- availability of other products on the market (tea, coffee, other sugar confectionery)- changing consumer patterns (increasing population and preferences)

An increase in processing in country X does not necessarily means an increase in consumption:

‘apparent domestic cocoa consumption’= amount of cocoa beans used into final

chocolate goods that are actually consumed in a country or region

In last decade: some changing tastes and preferences (11% increase in consumption) invention of new chocolate products:

- premium chocolates: dark, organic and single-origin chocolate bars (themed products)- more socially conscious products: fair trade2016 Next Generation Cocoa Research Symposium


Both Cocoa and Chocolate is in Crisis

Productivity is not keeping up with demand (demand increasing at 2% per year

Pest and disease pressure is increasing

Soils in cocoa growing areas are depleted

Heavily populated countries like India and China are demanding more

Many cocoa producing countries are affected by war and political unrest

Both Ivory Coast and Ghana are in environmental crisis

Ageing farmers and ageing tree stocks: low investment on rehabilitation

Young farmers equate cocoa bean crops with poverty

Cocoa is one of the major driver of deforestation



IITA and Cocoa Networks


Objectives:- Sorting out the true identity of cocia genotypes used in West and CentralAfrica

- Defining the extent of diversity present in the breeders’ collection and seedgardens in each country

- Identify a set of true-to-type core accessions/genotypes which could be shared among all countries within the region

ITRA, Togo

African Cocoa Breeders’ Group




Objective: DNA fingerprinting of cocoa genotypes from West and Central Africa

Country Accessions Presence of Duplicates

Nigeria 2000 None

Ghana 2551 YES

Cote d'Ivoire 2550 YES

Cameroon 2070 NoneTogo 869 YES

Total number of genotypes = 10,040

genotypes (seed gardens and breeding

materials) from five participating

countries

SNP-chip of 100 SNPs (from both Criollo

and Matina) distributed across 10 linkage

groups

Genotyping completed using 89 SNPs

using whole genome amplification (WGA)

method

Cocoa: ACI Project



ACI project: Results

Statistical analysis of individual country data

True-to-type genotyping through visualization of data using FlapJack

software

Data analysis using R-software

Minimum number of markers for diversity analysis




NanayIquitos

Gu

ian

a

Tri

nit

ari

o

Pu

rus

Ma

ran

on

A1/154 A1/197

ACU 85

AMAZ 15-15

AMAZ 3-2AMAZ 5-2

APA 4

B5/3

B5/7BE 10BE 3BE 8

CAS 3C-SUL 7

DOM 4

EET 400

EET 59HEQX 3338 EQX 3360-3EQX 78

GU 123 CGU 125 C

GU 144C

GU 175 V

GU 239 H

GU 255V

GU 290 HGU 341 H

ICS 1 ICS 43 ICS 95IFC 5

IMC 23IMC 39IMC 47

IMC 53

IMC 60IMC 67

IMC 76

LCT EEN 163

LCT EEN 241

MA 12

MAN 15-2MAN 15-60

MO 20

MOCORONGON38

NA 33

NA 79

P 30PA 107PA 118PA 121PA 13

PA 137PA 150PA 151

PA 175

PA 20

PA 300PA 303

PA 7PA 70PA 88

PNG 218

POUND 10

POUND 12

POUND 15

POUND 7

RB 46RB 49

RIM 41

S84

SCA 12

SCA 23

SCA 6SCA 9

SGU 50T16/613

T17/524 T44/547T60/887

T63/967

T63/971

T65/238

T65/326T79/467

T79/501

T85/799

PA 146

IMC 47 (type 2)

PA 186PA 65

PA 188

AMEL 67AMEL 10 AMEL 4

AMEL 19

AMEL 9

AMEL 130

AMEL 22AMEL 16

AMEL 67AMEL 78

AMEL 129

AMEL 43

AMEL 17

AMEL 71

AMEL 2AMEL 77

AMEL 20

AMEL 51 AMEL 118

NA 34Q10R3662B

Co

ord

. 2 (

11

.8%

)

Coord. 1 (20.2%)




Coefficient

2.00 5.25 8.50 11.75 15.00

AFF1 AFF3 AFF6

C74 OBD12 W4/65

OBD20 OBD14 OBD16 OBD10

AFF2 AFF13

AME03 AME02

AK11 AFF15

C13 AFF22

BOK14 T20/21

CF62 CTIS23

AFF20 AK01 AK02 AK03

BOK13 AK06

OBD15 BOK15

AK04 OBD24 OBD13

AFF4 AFF7 AFF8

OBD17 OBD19 OBD18 AFF11

C43 AME04 OBD21 AFF17

C68 W5/85 T7/12

AME01 C72 C64 C67

T83/5 C20 C27 C40 C75

AFF21 AFF19

OBD22 CF176 ICS60 ICS40 ICS39

ICS6 C22 C23

WEU-1 OBD23

AK10 AK09 AK07

W4/44 AMAZ10

T17/11 CTIS24 CTIS25

AK05 OBD11 OBD05

AFF5 AFF10 AFF12

AFF9 AFF14 AFF18 SCA6

AFF16 T86/80

C67 PA35

C27 W4/70 W4/37 W4/61 T65/7 AK08

2

4

5

3

1

1

2

3

4

5

6

7

8

9

10

11

12

13

14

15

16

17

18

19

20

21

22

23

24

1

2

3

4

5

6

7

8



Key Questions

Did the fingerprinting work through African Cocoa Initiative (ACI) cover the entire germplasm in breeders’ collection in each country?

No, however it has opened a gateway to understand the diversity available and presence of duplicates or mislabeled accessions/genotypes.

A set of unique or true-to-type genotypes/varieties/hybrids can be identified, shared between different countries (based on their adaptability and suitability) and maintained for long-term usage in the region through long-term conservation in the field as well as in vitro and cryo-preservation of the embryo’s.

Hybrids or varieties could be generated from this set of true-to-type genotypes.

Should there be any further fingerprinting work to be carried out?

Yes, it is mainly because the diversity present in the breeders’ collection and the seed gardens is not enough to provide solutions for cocoa improvement.



Way Forward

A new research culture is required: Research is required along the full stretch of the research and development

continuum Research on intensification, diversification, marketing efficiency, policy/institutional

environment – research across disciplines Need to develop, validate and scale up innovation packages that address:

technical-institutional-financial elements Innovation platforms that bring together public and private partners, i.e. research

priorities should not be determined by researchers alone and vice versa

Way Forward: Continue stakeholders engagements including farmers, public institutes, private

sectors, governmental agencies, NGOs and other partners Focused investment



Sustainable Increase in Cocoa Yields

Cocoayield

Environment Management

Biotic stresses

Abiotic stresses

Pests Diseases

Planting material

High quality planting material of high yielding clones is fundamental to optimum plant performance

Habitat management(GAP, NRM and post-harvest)

GEM Factor: Clean planting material and integrated management is key



Acknowledgements

USAID – Feed the Future

WCF – All public and private partners

ACI project

CRIN, Nigeria

CRIG, Ghana

CNRA, Cote d’Ivoire

IRAD, Cameroon

ITRA, Togo

Trushar Shah

Bioscience Center

LGC, UK



Thank You


true-to-type fingerprinting: implications towards cocoa

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