presentation bresil 2012 vpm 01

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Genetic resources (and their use) in Coffea canephora

Prepared by: Dr Christophe Montagnon

Cirad/Ird UMR RPB « Resistance of Plants to Bioagressors »

[email protected]

Presented by: Dr Pierre Marraccini

Cirad/UMR AGAP « Amélioration Génétique et Adaptation des Plantes »

[email protected]

TITRE

• Texte

– Texte

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Genetic resources and their use in Coffea canephora

Dr Christophe Montagnon

“ Dear coffee friends, I would like to thank the organization committee of thisimportant conference for their kind invitation. I thought I could come but reasonsbeyond my control forced me to cancel my trip to Brazil. I deeply regret it as Iknow there are so many good friends of mine in this room. Among them, I wouldlike to mention Dr Koffi N’Goran, from Côte d’Ivoire where part of my heartbelongs and where I’ve learned so many things on Coffea canephora. I want tothank Pierre for having accepted to present my talk. If there is any question ordoubts after presentation, please feel free to send me an email (on the slide) andI’ll be more than happy to answer ”

[email protected]

Background

• Importance of Coffea canephora (CC)– Growing share against Arabica (25 35 %)– Soluble industry– Biological meaning for arabica coffee

• Importance of breeding– Crucial factor for productivity and quality– Farmers shall benefit from the genetic progress

• Importance of genetic resources (GR)– What do we know about CC-GR?– Optimal use ?

2

Content of the presentation

• CC within the Coffea Genus

• CC natural / wild genetic diversity

– Natural area of distribution

– Surveys, Maintenance, Description

• Access to CC genetic resources

• Use of CC genetic resources

• Conclusions and perspectives

3

C. canephora within the big Coffea genus (Davis et al, 2011- Botanical Journal of the Linnaean Society 167 : 357-77.)

• Coffea:

– more than 100 species – Psilanthus subsumed to Coffea– Structuration in several clades (geographic)

• C. canephora :

– LG/C Clade = Lower Guinea/Congolian

– ‘Canephora alliance’ together with:• C. brevipes

• C. congensis

• …

– Easy to inter-cross with most Coffea species

Combined plastid–internal transcribed spacer (ITS) (Davis et al, 2011)

4

100,000 years ago

History: Timor hybrids and Catimors, SarchimorsArabusta

Separation

C. canephora C. arabica C. eugenioides

Ancestor of C. canephora : Progenitor of C. arabica(Lashermes et al, 1999 - Mol Gen Genet, 261:259-266)

Ancestor of C. canephora Ancestor of C. eugenioides

X

Ancestor of C. arabica (4n)

Re-union

5

Geographical origin and natural populations of CC

C. arabica

C. canephora

Natural distribution area = Africa

• C. canephora : • from Guinea to Uganda• From Centrafrican Republic to Angola

Much larger than:

• C. arabica : = Ethiopia + Southern Sudan

Fragmented :Western + Central Africa + Uganda

7

Geographical origin and natural populations of CC

• Natural population size: from few to hundreds of trees in a delimited area

• Distance between natural populations: few hundred meters to several kms

• Dissemination of pollen• Insects• Wind• Several kilometers in some occasion

• Dissemination of seeds = mostly zoochory(>100km)

• Birds• Small mammals• Apes • Elephant• Man !

8

Genetic diversity of wild CC populations

• Survey

• Maintain

• Describe

9

Genetic diversity of wild CC populations: Survey

Year Surveyed Countries Organisms Where in field

collection

Reference

1975-1991 Côte d’Ivoire IRCC

ORSTOM

Côte d’Ivoire Berthaud, 1986

Le Pierres (Rapport)

Couturon et Montagnon, 1991

(Rapport)

1975 Centrafrican Republic IRCC Centrafrican

Republic

Côte d’Ivoire

Berthaud et Guillaumet, 1978

1983 Cameroon IRCC

ORSTOM

Cameroon

Côte d’Ivoire

Anthony et al., 1984

1985 Congo (Brazza) ORSTOM Congo (Brazza)

Côte d’Ivoire

De Namur et al., 1988

1987 Guinée IRCC

ORSTOM

Guinée

Côte d’Ivoire

Le Pierres et al., 1990

2005-2008 Ouganda Cirad–Uganda Ouganda Musoli et al., 2009

A lot of international efforts…But less since the 80’s…

10

Genetic diversity of wild CC populations: Survey

• Further surveys to put on the agenda. • Funds needed• But cost of doing nothing ?

• Priority = Gabon, Angola, RDC

• Maybe some national initiatives we are not aware of…Important to know…

11

Genetic diversity of wild CC populations Maintain• In situ :

• Genetic erosion with deforestation

• Farmers plantations = important opportunity !

• Field collection : Côte d’Ivoire / French Guyana / Private initiatives

• Genetic erosion 3 % per year

• Climatic events

• Political disrupt

• In vitro

• Costly

• Genetic erosion

• Genetic stability ?

Cryopreservation (storage at liquid nitrogen

temperature, -196°C)– Dussert et al, 1998- Seed Science Research (1998), 8 : pp 9-15)

Cost effective - Really needs to be considered (Dulloo et al, 2009- Crop Science

Vol. 49 No. 6, p. 2123-2138)

12

Genetic diversity of wild CC populations Maintain

• Maintaining genetic resources is not an easy task !!!

• Definitely to be put on the agenda

• Support currently set field collections

• Maybe with an international mandate ?

13

Genetic diversity of wild CC populations: Describe• Describing is different from Evaluating

• Describing is neutral / Evaluating gives a value (selection criteria)

• Value is subjective and can vary with time and space

• Describing is not only through molecular markers

• Environment stable morphological descriptors are useful

• Description is a serious issue, not to be neglected. Only way to make further use of genetic resources

• Description shall be stored an made available in databases: not that difficult but time consuming and has a cost

• Makes sense to implement and manage description data together with field collection curators

14

Genetic diversity of wild C. canephora populations: Describe

WHAT DO WE KNOW ?

Structuration of the genetic diversity of CC populations

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Main C. canephora genetic groups and historic location of survey

Guinean Pool

Congolese Pool

UG

Genetic structuration follows geographical pattern

16

KouillouKonilon

• An important genetic diversity

G C

Berthaud (isozymes)

G SG2SG1

Montagnon et al., (isozymes)

G CSG1 SG2 B

Dussert et al., (RFLP)

19

Genetic diversity of wild CC populations: DescribeWHAT DO WE KNOW ?

Structuration of the genetic diversity of CC populations

Large genetic diversity

One homogenous Guinean Pool + a sub-structured Congolese Pool

Strong structure

Ideal situation in plant breeding for taking advantage of heterosis ?

Depends on actual access to Genetic Resources and what Genetic Resources…

29

Actual access to Genetic Resources of CC

What kind of Genetic Resources ?

• Complex and different situations

• Important to speak the same languages

• Definitions…

30

• P0 : Wild populations or locally domesticated populations from wild populations (landraces)– Represents the local natural genetic group

– No mix with other groups

Actual access to Genetic Resources of CCFew definitions – P0, P1 and Pn

31

• P1 : Individuals originating from a cross between two different P0. – Roughly similar to a F1 as a breeder concept

– Might be a controlled or natural cross between a local and an introduced P0 in plantations or field collection

– Highly heterozygous

• Pn : Any population originating from one or several generation of any P1 intercross– Roughly similar to recombining population as a breeder concept

– Might be a controlled or natural cross between different P1 in plantations or field collection

– Genealogy hard to trace back (CC : strictly outcrossing species)

– Genetic richness depending on the genetic groups represented by P0 founders (parents of involved P1)

Guinean SG2 SG1 P0

P1

Note: virtually impossible to rebuilt separated P0 from P1 or Pn

2 founders P0

Pn

3 founders P0

Crossing controlledOr uncontrolled in plantations / field

collections

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Two main channels

– Major one= Early farmers exchanging material between countries• Exchanging P0

• As a consequence:– Different introduced cultivated P0 in the same plantation

– Introduced P0 cultivated nearby local P0

• As a result:– Intercrossing between different P0

– First generation of P1

– Local replanting with some P1 and then Pn

– Next seeds exchange with a distance farmer = P1 or Pn

– And so on…

• Original P0 are lost

• Almost no traceability : only try to deduce genetic origins from observed present genetic pattern

– Minor one = Traceable institutional exchange between countries or private initiatives

• Populations in field collections

• Maintenance across the years (or decades) ?

Actual access to Genetic Resources of CCHow they have traveled and inter-mixed?

33

P0

• Have P0 of different genetic origin been introduced in my country ?

– I do not know

– I assume so but I have no traceability. It was not under institutional control.

– Yes but it was mostly only one single genetic origin P0

– Yes P0 from different genetic origins and they are well maintained in field collections

Actual access to Genetic Resources of CCWhat is my local genetic availability?

Côte d’Ivoire: very completeFrench Guyana: quite completeNestlé CCC: supposedly complete

Brazil

Most cases

34

P1 and Pn

• I have or have had in the past a strong and well referenced breeding scheme and/or introduction strategy so that I can trace back my crosses from original P0 . Plantations are mostly planted with my selected varieties.

• Same but my varieties were not massively adopted, so that cultivated material is quite different from what I can offer from my breeding programs.– Either because informal introduction channels

– Or because seeds are re-used without control

– Or both…

• I do not know


Brazil, Vietnam (?)

Côte d’Ivoire + former Main Breeding Centers

(Indonesia, Madagascar, Uganda…)

Most cases

35

In few words…

• Available genetic resources:

– Under control in research stations

– In situ in national coffee plantations (often neglected)

• Knowledge about genetic resources

- Mostly quite weak if not absent

- --> Needs a deep genotyping analysis to know what is the warehouse !!!


36


Some contrasted situations…

37

Côte d’Ivoire

• Well referenced and complete field collections

• All genetic origins but no wild Ugandan (UW)

• Well referenced breeding programs with P1 varieties from Guinean and Congolese P0

• Most part of cultivated material represents Pn mostly originating from Guinean, SG2 and SG1 original P0 (Montagnon et al, 1993 Café Cacao Thé, 37 (2) : 115-119)



37

Brazil

• Well referenced field collections

• Mostly one origin (SG1)

• Well referenced breeding programs

• Most part of cultivated material is the selected varieties



38

Mexico

• Well referenced but small field collections

• Well referenced breeding programs (Romex)

• No published available information on the corresponding genetic diversity

• Most part of cultivated material is not composed of selected varieties

• Preliminary study on cultivated material = One homogeneous Pn involving mainly SG2 and some SG1 alleles not that far from a SG2 P0. Apparently no Guinean alleles. (Montagnon, unpublished data).



39

Ecuador





• Preliminary study on cultivated material = two P0 SG1 and SG2. Apparently no Guinean alleles. (Leroy & Loor, unpublished data).

• Hypothesis: Contrasted ecosystems - Selection of SG1 and SG2 types in dry and humid areas, respectively.



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B

SG2

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Genetic diversity within C. canephora genotypes from Ecuador

Genotypes from Ecuador are in pink

To be published, Cirad – Iniapcollaboration – T. Leroy & G. Rey Loor

Ecuador





• Preliminary study on cultivated material = two P0 SG1 and SG2. Apparently no Guinean alleles. (Leroy & Loor, unpublished data).

• Hypothesis: Contrasted ecosystems - Selection of SG1 and SG2 types in dry and humid areas, respectively.



40

Closing the Genetic Diversity and Resources description

Opening the optimal use of Available Genetic Resources

42

Few words on breeding theories

• The Graal of any breeder is Genetic Diversity

• Let’s consider two contrasted situations:

• Breeder have access to distinct P0 Populations

• Breeder have only access to Pn populations

43

Guinean SG2 SG1 P0

Pn

3 founders P0

• Allelic diversity is comparable in both situations

• In genetically distinct groups (discontinuity)

• In a continumwhere all trees bear a mosaic of the genetic diversity

44

Guinean SG2 SG1 P0

“Available P0” situation

Heterosis = hybrid vigor : offspring is superior to both parents

Parents shall be:- Genetically distant- complementary traits

Belongs to different heterotic groups

Are CC P0 heterotic groups ?

Guinean and congolese groups are heterotic (Leroy et al, 1993. Euphytica 67:113-25.)

eg: G x SG1 or G x SG2

Congolese groups btw themselves: low heterosis for SG1 x SG2 (in Côte d’Ivoire conditions) to be tested for other groups combinations

45

0

20

40

60

80

100

120

140

160

A A x B B

Yield

Heterosis: AxB is better than either A or B

Guinean SG2 SG1 P0

“Available P0” situation

Heterosis = hybrid vigor : offspring is superior to both parents

Parents shall be:- Genetically distant- complementary traits

Belongs to different heterotic groups

Are CC P0 heterotic groups ?

Guinean and congolese groups are heterotic (Leroy et al, 1993. Euphytica)

eg: G x SG1 or G x SG2

Congolese groups btw themselves: low heterosis for SG1 x SG2 (in Côte d’Ivoire conditions) to be tested for other groups combinations

45

Guinean SG2

“Available P0” situation – Strategy (Côte d’Ivoire)

X = Homogeneous G x SG2 hybrid (= P1) progeny

• Isolated seed garden with both G and SG2 parents

• All seeds are the G x SG2 hybrid (due

to CC being strictly outcrossing)

• Easy and cost effective to mass produce

• Seed material easy to transport and manage in large or small farmer nurseries

60Yield (100 basis) 100 140

Possible long term strategy: Reciprocal Recurrent Selection

46

“Available Pn” situation

• No heterotic groups Hybrids are not better than the best parent

• Possible cloning of outstanding trees (possible vegetative multiplication of CC)

• Rapidly fixing genetic progress (out of thousands of trees in plantations for instance)

• Possible long term strategy through classical recurrent selection

• Mass production • Horticultural: cutting gardens • In vitro somatic embryogenesis: Vitro-plants

• Cuttings or Vitro-plants: • not that easy to mass produce (as compared to seeds) • not that easy to transport and manage by farmers

47

So… Seeds or clones ???• Not that clear cut, not exclusive strategies

• Clones in seed strategy: Might think of cloning best trees within “P1” progenies BUT Cost and time consuming for questionable genetic progress (Montagnon, 2000)

• Seeds in clonal strategy: Might think of intercrossing best Pn clones for an improved Pn population

• I (Christophe) tend to believe:

• If you have access to P0, then go for intergroup crosses and seed strategy

• If you have access only to Pn, then rapidly fix genetic progress through clones while introducing P0 populations

• If you have access to both:• Put more weight on P0 / seed strategy on the long term

• Put more weight on Pn strategies (at least in the short term) if you have a specific constraint you want to address: specific quality, CWD resistance…easier to fix through cloning. 48

Except for certain specificsituations, I choose Access to P0

and intergroup seed strategy.

Conclusions / PerspectivesWhat was not part of the presentation

• Marker Assisted Selection:

• genetic diversity is needed

• Important results (Leroy et al., 2011- TGG)

• Not really the scope of this very presentation

• My opinion: prepare for it but a lot of genetic progress can still be achieved through classical breeding

• Selected varieties:

• Scope of the presentation more on pre-competitive Genetic Resources

• Great available varieties:

• Côte d’Ivoire (Hybrids)

• Uganda (clones with tolerance to CWD)

• Brazil of course

• Mexico (Romex)

• ….

• What about their actual use ?

• Very low impact / most present cultivated CC coffees are not selected varieties (but Brazil/Vietnam)

• Question of professionalization of the coffee seed sector

49

Conclusions / PerspectivesTake home message

• CC genetic diversity of CC

• So rich, So useful….while….So unequal the access to

• So many lost opportunities of genetic progress for the farmers

• So little knowledge about local availability: Genotype and further genotype !!!

• No comprehensive breeding strategy if no optimal use of Genetic Diversity

50

Trends in coffee production

Three countries account for general increase in yield, especially VN (2 t gc / Ha)All others, on average, are at 1961 levels of productivity

Evolution of Yield (Hg green coffee / Ha) since 1961: Brazil, Colombia, Vietnam vs. others (FAO)

0

5000

10000

15000

20000

25000

1961 1963 1965 1967 1969 1971 1973 1975 1977 1979 1981 1983 1985 1987 1989 1991 1993 1995 1997 1999 2001 2003 2005 2007

Brazil Colombia vietnam Others

Benchmarking Maize….

First hybrids

Conclusions / PerspectivesTake home message

• CC genetic diversity of CC

• So rich, So useful….while….So unequal the access to

• So many lost opportunities of genetic progress for the farmers

• So little knowledge about local availability: Genotype and further genotype !!!

• No comprehensive breeding strategy if no optimal use of Genetic Diversity

50

• Important players hosting Genetic Diversity:

• Côte d’Ivoire (CNRA)

• French Guyana (Cirad)

• Nestlé CCC

• All countries located in the natural area of dispersion

• Crucial to be able to share / enrich Genetic Resources :• International forum with Internationally recognized Pilot in the plane /

Coordinator

• Fair agreement and acknowledgement those who preserved Genetic Ressources

• International norms / Phytosanitary issues

• REACTIVATE surveys: First Priority = Angola, Gabon, RDC

Thanks for your attention

[email protected]

presentation bresil 2012 vpm 01

Education