CATIE´s Breeding strategy for selecting cacao varieties with … · The cacao crop and its associated multibillion dollar value chain are at risk due to the growing spread and impact

“CATIE´s Breeding strategy for selecting cacao varieties with durable resistance to diseases”

Dr. Wilbert Phillips-MoraCacao Breeding Program, Leader

Henry A. Wallace Main BuildingTropical Agricultural Research and Higher Education Center

CATIE, Turrialba, Costa Rica

The cacao crop and its associated

multibillion dollar value chain are at risk

due to the growing spread and impact of

diseases and the effects of climate change.

Dr.W. Phillips, Cacao Breeding Program, CATIE 7170, Turrialba, C.R.

Moniliasis

(Moniliophthora roreri)

Black pod(Phytophthora spp)

Witches´ broom(Moniliophthora perniciosa)

In tropical America, the impact of black pod, witches’ broom and frosty pod will

certainly be responsible for far greater losses.


Alto BeniBOLIVIA

JULIO 2012

Chiapas and

Tabasco, MEXICO

APRIL 2005

El SalvadorJunio, 2009


The implementation of improved

varieties would increase production

and control diseases in ways that are

more:

Effective

Long-lasting

Less-expensive

Environmentally

friendly

A cacao production

and disease control

that is social,

environmental, and

economic sustainable


However, the task is not easy because cacao

breeding is a laborious and lengthy process requiring

a combination of:

Expertise

Continuity

Biological, human and financial resources

that rarely converge.


Breeding for resistance to pathogens and pests must have top priority worldwide

(Hogenboom, 1992)

Advantages of Genetic

Resistance

Introduced gene is inherited

and permanent.

No action is needed on the

part of the grower.

Resistance does not harm the

environment.

Resistance is compatible with

other disease management

methods.

Diseases resistance genes are one of the most

important natural resources determining the survival

of the human species (Mundt, 1994)

And the survival of choco-lovers ¡


SOME DEFINITIONS


Quantitative resistance (polygenic, horizontal): resistance that is

phenotypically incomplete and is based on the additive action of many

genes.

Qualitative (monogenic, vertical resistance): the type most frequently

deployed in plant breeding, which is often ephemeral.

Durability: concerns the ease with which the pathogen can adapt to the

host´s resistance.

Durable resistance to a plant disease is the

“resistance that remains effective during its

prolonged and widespread use in an environment

favorable to the disease” (Johnson 1984)


The most widely used sources of resistance to witches’ broom are SCA 6 and SCA 12 (approx. 300 improved varieties with this background, Meinhardt 2008)

Resistance in SCA-6 is monogenic, caused by a single recessive major gene.

SCA clone resistance appeared to be durable based on observation in Trinidad over 50 years (Bartely 2001 Laker 1990),

However, Scavina-based tolerance to witches’ broom has eroded in the Brazilian Amazon, Ecuador, and Peru, due possibly to variants of the pathogen (Barley 2001, Bailey & Meinhart 2016).

Monogenic resistance to witches´ broom of clonesSCA-6 and SCA-12.


The probability of a resistance breakdown depends on the evolutionary potential of the pathogen

• Type of resistance: monogenic > polygenic

• Type of reproduction of the pathogen: sexual+asexual > sexual > asexual

• Capacity of the pathogen for dispersal: air > water > soil

• The size of the pathogen population: affected by control methods and

environmental conditions.

• The resistance deployment strategy: pyramiding, mixture of cultivars, etc


INVOLVED FACTORS

Pathogens that pose the lowest risk of breaking down resistance genes are those with strict asexual

reproduction, low potential for gene flow, small effective populations sizes, and low mutation rates

(McDonald & Linde 2002)

M. roreri(moniliasis orfrosty pod rot)

M. perniciosa(witches´ broom)

Probability of a resistance breakdownA risk assessment chart provided by the APS and adapted to cacao diseases by W. Phillips

Risk: M. perniciosa = Phytophthora spp > M. roreri

Reproduction/matting

system.

Gene/genotype flow.

Effective population

size.

Phytophthoraspp

(black pod rot)

Suelo Agua Aire

PROGRESSES AT CATIE TO DEVELOP VARIETIES WITH DURABLE RESISTANCE TO M. roreri

1. Level and distribution of genetic diversity.

2. Type of reproduction of the pathogen: sexual+asexual , sexual or asexual?

3. Type of resistance: monogenic or polygenic?

4. Identification of resistant genotypes

5. Accumulation of resistant genes against M. roreri

6. The resistance deployment strategy: pyramiding, mixture of cultivars, etc.


1. LEVEL AND DISTRIBUTION OF THE GENETIC DIVERSITY OF

M. roreri

1

2

5

4

36

8

28

9

7 10

11

12

13

14

15

Colombia

16

17

18

19

22

2120

2324

25

Perú

Venezuela

Honduras

Nicaragua

Costa Rica

Panamá

Ecuador

27

26

HO NDURAS: Department of Gracias a

Dios (1)

NICARAGUA: Región Atlántico Norte

(2), Departments of Río San Juan (3) and

Matagalpa (4)

CO STA RICA: Provinces of Alajuela

(5), Heredia (6), Limón (7), Cartago (8),

Puntarenas (9)

PANAMA: Province of Colón (10)

CO LO MBIA: Departments of Antioquia

(11), Caldas (12), Norte de Santander

(13), Santander (14), Huila (15)

VENEZUELA: States of Mérida (16),

Zulia (17), Táchira (18)

ECUADO R: Provinces of Esmeraldas

(19), Pichincha (20), Los Ríos (21),

Guayas (22), Manabí (23), Napo (24),

Imbabura (25), Carchi (26)

PERU: Departments of San Martín (27),

Huánuco (28)

E42 E11 C7 Co14

Co8E17 E10 C5

C3 Co5 E9E37

Co2Co17C29E27

w

p

COLLECTION OF SAMPLES

OF M. roreri in tropical

America

120 isolates

8 countries

28 cacao regions


MOLECULAR STUDIES

94 isolates were analysed using 3

techniques

AFLP (Amplified Fragment Length polymorphism)

ISSR (Inter Simple Sequence Repeat)

ITS sequence analyses


Genetic diversity of M. roreri

in Colombia, Ecuador and

Central America


5

3

5

5

1. Co-Central

2. Co-East

3. Bolívar

4. Gileri

5. Co-West

3

33

4

3

5

5

5

5

5

5

2

wp

Five major genetic groups of M.

roreri were identified.

Two groups are widely dispersed :

Bolivar: Easter Colombia,

Peripheric Ecuador, Venezuela and

Peru

Co-West: Western Colombia,

Central Ecuador and Central

America.

The remaining groups are endemic to

Colombia (Co-East Co-Central

o Ecuador (Gileri ).

Biogeography of M. roreri

1

1

5

3

2

4

Santander, Colombia.

Virulence of 7 isolates of M. roreri

Co1 Zulia, Norte de Santander

Co5 Río Negro, Santander

Co14 San Vicente de Chucurí, Santader

Co16 El Carmen de Chucurí, Santander

Co8 San Jerónimo, Antioquia

Co-13 Carepa, Antioquia

Co10 Palestina, Caldas

5 cacao clones: CAP-34, ICS-1,

ICS-95, SCC-61, TSH-565

PHYTOPATHOLOGICAL STUDY


The virulence of the isolates

showed statistical differences.

Five isolates were highly

aggressive and two less severe

(Co-1 and Co-5).

However, under appropriate

conditions, all isolates are

capable of inflicting

considerable levels of damage.

Clone (ICS-95) displayed a

significant level of resistance

against all isolates, opens the

possibility to select genotypes

with a durable resistance.

RESULTS


2. TYPE OF REPRODUCTION OFM. roreri

Reproduction in M. roreri is predominantly

asexual.

Very few strands of evidence supporting

recombination were found.

Only two genotypes from Ecuador (E20,

E32) showed some bands typically present

in other genetic group so they could

represent hybrids between two groups.

Point mutations were evident and possibly

constitutes the main source of genetic

differentiation.

Sexual reproduction



88 (RNASeq)-derived SNPs

172 M. roreri isolates

Tipe of reproduction: Absence of

heterozygosity for the 88 SNP markers

indicates reproduction in M. roreri is

clonal and likely due to a homothalic life

style.

Origin: the Upper Magdalena Valley of

Colombia showed the highest levels of

genetic diversity

3. TYPE OF RESISTANCE AGAINST M. roreri

Monogenic or polygenic ??

A

quantitative

response.

Immunity

was not

observed.

Artificial inoculations of moniliasis. CATIE, Turrialba 1984


Reaction of resistant clones is very

stable.

Reaction of intermediate and susceptible

clones is affected by weather conditions

0

5

10

15

20

25

30

35

40

45

50

55

60

65

70

75

80

85

90

95

100C

AT

IE-R

6

CA

TIE

-R4

CA

TIE

-R5

CA

TIE

-R2

CA

TIE

-R1

UF

-273

T1

GU

133

-N

CA

TIE

-R3

CA

TIE

-R7

PA

-169

UF

-712

EE

T-1

83

ICS

-95

T1

PM

CT

-58

ICS

-43

SG

U-8

4

AR

F-4

AR

F-6

UF

-273

T2

CC

-240

CC

-137

AR

F-1

4

Árb

ol-

81

IMC

-60

CC

N-5

1 T

2

PM

CT

-82

A-1

73

(RE

TR

O)

AR

F-2

2

AR

F-3

7

P-2

3

SIC

-1

A5

-R2 (

T3)

A-1

74

(RE

TR

O)

CC

-252

EE

T-5

9

A-1

47

(RE

TR

O)

BE

-8

CC

-42

CC

-27

AR

F-1

0

ICS

44

SC

A-6

PO

UN

D-7

CA

TIE

-10

00

SC

A-1

2

RB

-41

L6 field trial (14 años)

Clon

(%)

Incidence of moniliasis


Stable reaction of highly resistant clones but very

variable for intermediate and susceptible clones.

Time (years)

Incid

en

ce

of

mo

nil

iasis

(%)

Pound-7 and SCA-6

(Susceptibles)

CATIE-R6

(Highly resistant.)

L6Dr.W. Phillips, Cacao Breeding Program, CATIE 7170, Turrialba, C.R.

Cervantes-Martinez, C.; Brown, J.S.; Schnell, R.J.; Phillips-Mora, W.; Takrama, J.F.; Motamayor, JC. 2006. Combining ability for disease resistance, yield, and horticultural traits of cacao (Theobroma cacao L.) clones. Journal of the American Society for Horticultural Science 131(2):231-241

25 crosses between “resistant x resistant” or

“resistant x high yielding” clones were

studied during 9 years.

Objective: Estimate general and specific

combining ability of the parental clones for

resistance to frosty pod and black pod

diseases.

Resistance to moniliasis showed

predominantly an additive gene action.

Population: 256 F1 progeny from the cross

”Pound-7 × UF 273” established at CATIE.

A linkage map with 10 linkage groups (LGs) was

generated using 180 markers.

The map was used to locate putative quantitative

trait loci (QTL) for resistance to frosty pod and

black pod rots.

Five QTLs for frosty pod resistance were found

with very solid support. UF 273 appeared to be

the source of resistance.

Brown S; Phillips-Mora W; Power E; Krol C; Cervantes-Martinez C; Motamayor JC, and Schnell R. 2007. Mapping QTLs for resistance to Frosty Pod and Black Pod Diseases and Horticultural Traits in Theobroma cacao L. Crop Science 47:1851-1858.

Brown S; Phillips-Mora W; Power E; Krol C; Cervantes-Martinez C; Motamayor JC, and Schnell R. 2007. Mapping QTLs for resistance to Frosty Pod and Black Pod Diseases and Horticultural Traits in Theobroma cacao L. Crop Science 47:1851-1858.

1

1

3

2

POUND-7 x UF-273

256 F1 progeny, 180 MARKERS

Marker Assisted selection

4. IDENTIFICATION OF RESISTANT GENOTYPES AGAINST P. palmivora

and M. roreri

Broad genetic diversity

Appropriate artificial inoculation

techniques

INTERNATIONAL CACAO COLLECTION AT CATIE (IC3)one of the two universal depositories of cacao

Duplicated in two contrasting sites1260 genotypes from all over the world

The genebank provides the basis for a permanent program to identify disease

resistant genotypes, used as the cornerstone of the local improvement program.

Black pod

(Phytophthora palmivora)

Moniliasis

(Moniliophthora roreri)

Phillips M., W. 1986. Evaluación de la resistencia de cultivares de cacao (Theobroma cacao L.) a Moniliophthora roreri Cif. Par. IN Conf.

Internacional de Investigación en cacao. 1987. Santo Domingo, República Dominicana.

Phillips-Mora, W; Castillo, J; Krauss, U; Rodríguez, E and Wilkinson, M.J. 2005. Evaluation of cacao (Theobroma cacao) clones against seven

Colombian isolates of Moniliophthora roreri from four pathogen genetic groups. Plant Pathology 54 (3): 483-490.

Supporting papers:

SCREENING OF DISEASE REACTION USING ARTIFICIAL INOCULATION METHODS DEVELOPED AT CATIE


650 CLONES FROM THE CATIE´s

GENEBANK SCREENED

TOLERANT CLONES TO MONILIASIS

o ACT-211

o AMAZ-3-2

o AMELONADO-15(6)

o ARF (2, 5, 6, 33, 37)

o BE-8

o CC-240

o CHUA0-120

o CL-19/10

o Criollo (8, 14, 43, 66)

o EET (75, 129, 401, 407)

o EQX-69

o GC-29

o GU (123-N, 125-N, 147-N, 171-N, 254-A)

o HY-2714184

o ICS (10, 75, 95)

o IMC (27, 54, 55, 60)

o Laranja

o México-(10, 12A1, 14A1)

o ML-102

o NA-756

o Nacional-1

o Nacional-2

o P-23

o PA (44, 67, 169, 303)

o Playa Alta-2

o PMCT (12, 15, 16, 44, 46, 48, 51, 53, 82)

o Santa Clara-3

o SC-24

o SGU-84

o UF (273 T1, 613, 712).


Motamayor JC, Lachenaud P, da Silva e Mota JW, Loor R, Kuhn DN, et al. 2008. Geographic and Genetic Population

Differentiation of the Amazonian Chocolate Tree (Theobroma cacao L). PLoS ONE 3(10): e3311.

doi:10.1371/journal.pone. 0003311

Resistance genes to moniliasis were found in 7 genetic groups

Criollo (8, 14, etc)

Chuao-120

GU (123N, 125N, etc)

Nacional (1, 2, etc)

Amaz-3-2, IMC

(27, 54, etc)

PA (44, 169, etc)

NA-756

Amelonado-15(6)

5. ACCUMULATION OF RESISTANT GENES AGAINST M. roreri

Selection of high

yielding, good

quality and disease

resistant varieties for

farmer use

Recurrent selection

schemes to

accumulate

favorable genes in

single individuals


L4

T3

L5L22

Families trials1995-1998

Best trees

CROSSES

Among the best

clones

L14

L19

L17

CATIE´s GENEBANK

Six clones released for

farmers use in 2007

CROSSES

Resistant x Resistant clones

Resistant x High yielding clones

Best trees

L23

Figure 1. Chronology of the establishment of breeding trials at CATIE

2nd Release of clones

2017

T6

L6

CROSSES

Among the best local and

international clones

L25 L27

Clonal trials1998, 2004


Clonal trials2012-2013


RECURRENT SELECTION

STRATEGY

Accumulation of disease resistant genes

Heterosis in L6 (avg 15 years)

15 year Avg Yield(kg/ha/year)

15%

4%

37% 39%

49%

85% 86%

15 year Avg Incidence

(%)


Moniliasis incidence in L6 (Avg last 10 years of data)

INTERNATIONAL CONTROLS

CATIE CLONES

Inci

den

ce(%

)

4%

15%12%

4%

37% 39%

49%

85% 86%

4%15%12%

85% 86%


6. THE RESISTANT

DEPLOYMENT STRATEGY

CLONES RELEASED BY CATIE FOR FARMER

USE IN CENTRAL AMERICA AND MEXICO

CATIE´s clones are

present in 11 contries

United States


Varieties accumulating resistant genes (“pyramids”).

Mixtures of cultivars with different disease reaction.

DEPLOYMENT STRATEGIES AT CATIE



Talamanca, Costa RicaEstablecimiento de minijardines clonales en

áreas remotas

SIXAOLA, COSTA RICA

(Foto Oscar Brenes, MAG)

Biology of M. roreri

Identification of sources of resistance to frosty pod and black pod with different genetic and geographical origins.

Accumulation of resistance genes against moniliasis in single individuals for durable resistance.

Generation of clones with double resistance: moniliasis and black pod.

Generation of clones combining high yielding, precocity, disease tolerance and good quality profiles.

Release of superior clones that are available to more than 10,000 farming families in Central America and Mexico .

Achivements

at CATIE


Documents

CATIE´s Breeding strategy for selecting cacao varieties with … · The cacao crop and its associated multibillion dollar value chain are at risk due to the growing spread and impact