Presentation bresil 2012 vpm 01
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The document discusses genetic resources of Coffea canephora: 1. C. canephora has a large natural genetic diversity originating from populations across Africa. Major genetic groups include the Guinean and Congolese pools. 2. Several countries and organizations have surveyed wild C. canephora populations, though more surveys are still needed. Maintaining genetic resources ex situ and in situ poses challenges. 3. The genetic diversity available in local areas may vary significantly depending on the genetic origins introduced historically and the degree of informal genetic mixing versus controlled breeding programs. Tracing the origins of local resources can be difficult.
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Presentation bresil 2012 vpm 01
- 1. Genetic resources (and their use) TITRE in Coffea canephora • Texte – Texte • Texte – Texte » Texte Prepared by: Dr Christophe Montagnon • Texte Cirad/Ird UMR RPB « Resistance of Plants to Bioagressors » christophe.montagnon@cirad.fr Presented by: Dr Pierre Marraccini Cirad/UMR AGAP « Amélioration Génétique et Adaptation des Plantes » marraccini@cirad.fr
- 2. Genetic resources and their use TITRE in Coffea canephora • Texte – Texte Dr Christophe Montagnon • Texte “ Dear coffee friends, – would like to thank the organization committee of this I Texte important conference for their kind invitation. I thought I could come but reasons » Texte beyond my control forced me to cancel my trip to Brazil. I deeply regret it as I know there are so many good friends of mine in this room. Among them, I would like to mention Dr Koffi N’Goran, from Côte d’Ivoire where part of my heart • Texte belongs and where I’ve learned so many things on Coffea canephora. I want to thank Pierre for having accepted to present my talk. If there is any question or doubts after presentation, please feel free to send me an email (on the slide) and I’ll be more than happy to answer ” christophe.montagnon@cirad.fr
- 3. 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
- 4. 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
- 5. 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
- 6. Ancestor of C. canephora : Progenitor of C. arabica (Lashermes et al, 1999 - Mol Gen Genet, 261:259-266) 100,000 years ago Ancestor of C. canephora Ancestor of C. eugenioides X Ancestor of C. arabica (4n) Separation Re-union C. canephora C. arabica C. eugenioides History: Timor hybrids and Catimors, Sarchimors Arabusta 5
- 7. Geographical origin and natural populations of CC C. arabica Natural distribution area = Africa • C. canephora : • from Guinea to Uganda C. canephora • From Centrafrican Republic to Angola Much larger than: • C. arabica : = Ethiopia + Southern Sudan Fragmented :Western + Central Africa + Uganda 7
- 8. 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
- 9. Genetic diversity of wild CC populations • Survey • Maintain • Describe 9
- 10. Genetic diversity of wild CC populations: Survey Year Surveyed Countries Organisms Where in field Reference collection 1975-1991 Côte d’Ivoire IRCC Côte d’Ivoire Berthaud, 1986 ORSTOM Le Pierres (Rapport) Couturon et Montagnon, 1991 (Rapport) 1975 Centrafrican Republic IRCC Centrafrican Berthaud et Guillaumet, 1978 Republic Côte d’Ivoire 1983 Cameroon IRCC Cameroon Anthony et al., 1984 ORSTOM Côte d’Ivoire 1985 Congo (Brazza) ORSTOM Congo (Brazza) De Namur et al., 1988 Côte d’Ivoire 1987 Guinée IRCC Guinée Le Pierres et al., 1990 ORSTOM Côte d’Ivoire 2005-2008 Ouganda Cirad–Uganda Ouganda Musoli et al., 2009 A lot of international efforts…But less since the 80’s… 10
- 11. 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
- 12. 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 Cryopreservation (storage at liquid nitrogen temperature, -196°C)– Dussert et al, 1998- Seed Science • In vitro Research (1998), 8 : pp 9-15) • Costly Cost effective - Really needs to be • Genetic erosion considered (Dulloo et al, 2009- Crop Science Vol. 49 No. 6, p. 2123-2138) • Genetic stability ? 12
- 13. 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
- 14. 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
- 15. Genetic diversity of wild C. canephora populations: Describe WHAT DO WE KNOW ? Structuration of the genetic diversity of CC populations 15
- 16. Congolese Pool Guinean Pool UG Kouillou Konilon Genetic structuration follows geographical pattern Main C. canephora genetic groups and historic location of survey 16
- 17. • An important genetic diversity Berthaud (isozymes) G C Montagnon et al., (isozymes) G SG1 SG2 Dussert et al., (RFLP) G SG1 SG2 B C 19
- 18. Genetic diversity of wild CC populations: Describe WHAT 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
- 19. Actual access to Genetic Resources of CC What kind of Genetic Resources ? • Complex and different situations • Important to speak the same languages • Definitions… 30
- 20. Actual access to Genetic Resources of CC Few definitions – P0, P1 and Pn • P0 : Wild populations or locally domesticated populations from wild populations (landraces) – Represents the local natural genetic group – No mix with other groups • 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) 31
- 21. Guinean SG2 SG1 P0 P1 Crossing controlled Or uncontrolled in plantations / field collections Pn 2 founders P0 3 founders P0 Note: virtually impossible to rebuilt separated P0 from P1 or Pn 32
- 22. Actual access to Genetic Resources of CC How they have traveled and inter-mixed? 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) ? 33
- 23. Actual access to Genetic Resources of CC What is my local genetic availability? P0 • Have P0 of different genetic origin been introduced in my country ? – I do not know Most cases – 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 Brazil – Yes P0 from different genetic origins and they are well maintained in field collections Côte d’Ivoire: very complete French Guyana: quite complete Nestlé CCC: supposedly complete 34
- 24. Actual access to Genetic Resources of CC What is my local genetic availability? 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. Brazil, Vietnam (?) • 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… Côte d’Ivoire + former Main Breeding Centers (Indonesia, Madagascar, Uganda …) • I do not know Most cases 35
- 25. Actual access to Genetic Resources of CC What is my local genetic availability? 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
- 26. Actual access to Genetic Resources of CC What is my local genetic availability? Some contrasted situations… 37
- 27. Actual access to Genetic Resources of CC What is my local genetic availability? Some contrasted situations… 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
- 28. Actual access to Genetic Resources of CC What is my local genetic availability? Some contrasted situations… Brazil • Well referenced field collections • Mostly one origin (SG1) • Well referenced breeding programs • Most part of cultivated material is the selected varieties 38
- 29. Actual access to Genetic Resources of CC What is my local genetic availability? Some contrasted situations… 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
- 30. Actual access to Genetic Resources of CC What is my local genetic availability? Some contrasted situations… Ecuador • Well referenced but small field collections • Well referenced breeding programs • 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 = 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
- 31. Genetic diversity within C. canephora genotypes from Ecuador SG2 Ecuador Ecuador Ecuador Ecuador Ecuador Ecuador Ecuador Ecuador Ecuador ineac7 Ecuador Ecuador Ecuadorineac7 Ecuador Ecuador Ecuador inc Ecuador libengue ineac7ineac2 Ecuador K_MM Ecuador ineac2 ineac7Ecuador Ecuador Ecuador Ecuador Ecuador ineac7Ecuador EcuadorEcuador kalangala Ecuador 80 Ecuador Ecuador Ecuador Ecuador nganda erecterect Ecuador Ecuador erect erect erect Ecuador erect erect 81 Ecuador Ecuador Ecuador Ecuador Ecuador Ecuador erect Ecuador bresilEcuador nganda kalangala erect kalangala nganda erect 86 Ecuador ineac7 Ecuador Ecuador K_MM K_MMK_MM K_NK cdivers kalangala libengue bresil nemaya Ecuador kalangala Ecuador Ecuador Ecuador erect Ecuador K_NK kalangala erect K_NK kalangala ngandanganda Ecuador 91 nganda EcuadorEcuador Ecuador Ecuador erect Ecuador kalangalaEcuador98 100 Ecuador erectEcuador ineac2 EcuadorEcuador erect K_MMK_MM K_NK nganda erectineac2erect Ecuador8280Ecuador Ecuador nganda kalangala erectnganda Ecuador ineac7 nganda Ecuador ineac2 luki K_NK K_Kab K_Kab K_MM K_MM K_NK K_NKK_MM kalangala 100 K_NK K_MM K_NK K_MM K_NK K_NK K_NK K_NK K_NK K_NK K_NK K_Kab K_MM erect Ecuador K_NK nganda ineac2 erect nganda nganda bresil nganda kalangala Ecuador ineac2 ineac2 Ecuador 100 Ecuador bresil nemaya Ecuador luki Guilavotazou conilons conilons conilons conilons SG1 K_Kab K_NK kalangala nganda kalangala nganda nganda erect 97 93 erect ineac2 Ecuador conilons Ecuador Ecuadorconilons conilons Ecuador niaouliconilons K_Kab K_MM I_19K_MMK_MM K_NK K_Nka K_Kab Ecuador kalangala nganda100 89 91 80 Ecuadorconilons Ecuador conilons Ecuador conilons conilons conilons conilons K_Kab K_Kab K_Kab K_Kab K_Kab 91 90 Ecuador niaouli Ecuador I_new K_MM I_newK_NK I_15K_Kab I_15 91 Ecuador Ecuador Ecuador conilons conilons Ecuador Ecuador niaouli I_15 I_15 I_15 I_15 I_new I_new I_15 I_15 I_15I_15I_19 I_15I_15I_14 K_Kab I_15 I_15 niaouli conilons niaouliniaouli conilons Ecuador Ecuador Ecuador I_14 I_19 I_14 I_15 I_15 I_15 90 100 niaouli conilons niaouli niaouli I_11 K_NK 100 nganda I_14I_15 K_MMI_18 I_11 I_14 I_14 I_11I_14 K_MMI_14 I_14 I_14 I_newI_15I_15 I_18 I_19 I_14 K_NKK_MM K_NKK_NK K_Kab K_NKK_NKK_NK I_15 K_NK K_NK luki K_KabI_15 K_NK K_NK K_MM I_15K_MM K_MM K_NK K_NK K_NK K_NK K_MM K_NK I_15 lukilukiluki luki luki luki luki luki luki K_NK I_14 I_11 K_MM I_new I_15 luki luki luki luki K_MM kalangala K_NK lukiluki luki luki luki K_Kzi K_MM K_MM K_MM nganda I_new K_Kzi K_Kzi K_Kzi K_MM K_MMK_MM I_19 K_MM K_MM K_MM I_27 luki luki luki luki luki luki luki luki K_MM K_MM K_MMK_MM K_Kab I_18 89 K_MM kalangala kalangala 89 kalangalaK_MM kalangala nganda nganda kalangalaerect kalangala kalangala I_11 nganda nganda nganda nganda libengue nganda nganda nganda kalangala kalangala erect kalangala kalangala kalangala nganda nganda ngandaerect libengue nganda libengue libengue libengue libengue libengue pelezi libengue 99 libengue libengue libengue libengue libengue libenguelibengue libengue 100 nana nana libengue libengue libengue libengue 98 nananana nana libengue nana libengue 91 nana nana nana nana nana nana nana nana nana 85 81 nana nana nananana 93 nana nana nana nana nana nanaineac2 nana nana nana nana B 84 nananana nana nana nana nana ineac2 nana nananana nana nana nana 100nana nana nananana nana nana nana nana nananana nana nana nana 91 nana 90nana nana nana nana nana nana nana nana nana nana inc nana nana nananana nana nana nana nana nana C nana 86 97 90 Genotypes from 100 fourougbankoro 91 100 Ecuador are in pink 92 96 82 ira2 90 ira2ira2Maclaudi 96 pine fourougbankoro Gamé 100 fourougbankoro Gamé pine ira1 ira2 ira2 Maclaudi Maclaudi fourougbankoro Gamé mouniandougou mouniandougou pine pinepine guincultiv ira1 pelezi guincultiv Maclaudi pelezi ira2 pinepine mouniandougou pine mouniandougou pine mouniandougou pine guincultiv mouniandougou mouniandougou pelezi fourougbankoro fourougbankoro ira2 ira2 fourougbankoro pine guincultiv ira1 pelezifourougbankoro guincultiv pine guincultivpelezi fourougbankoroMaclaudi guincultivguincultiv ira2 92 pelezi guincultiv fourougbankoro mouniandougou pine mouniandougou mouniandougou ira1 mouniandougou fourougbankoro ira1 pelezi mouniandougou mouniandougou pine fourougbankoro mouniandougou pelezi mouniandougouira2 guincultivira2 pelezi pine fourougbankoro ira2 ira2 mouniandougou guincultivpelezi guincultiv mouniandougou mouniandougou pine mouniandougou mouniandougou mouniandougou ira1 mouniandougou mouniandougou fourougbankoro pelezi pelezi pelezi pelezi pelezi pelezi ira2 ira2 ira2 fourougbankoro pelezi mouniandougou pine pelezipelezi pineinc mouniandougou fourougbankoro fourougbankoro pelezi guincultiv fourougbankoro pelezi pelezi mouniandougou ira1 pelezipelezi pine pine fourougbankoro guincultivpine pelezi pelezi pelezi guincultiv sabregue pine pelezi pine pine ira1 pine pine To be published, Cirad – Iniap GUINEAN collaboration – T. Leroy & G. Rey Loor
- 32. Actual access to Genetic Resources of CC What is my local genetic availability? Some contrasted situations… Ecuador • Well referenced but small field collections • Well referenced breeding programs • 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 = 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
- 33. Closing the Genetic Diversity and Resources description Opening the optimal use of Available Genetic Resources 42
- 34. 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
- 35. Guinean SG2 SG1 P0 • Allelic diversity is comparable in both situations • In genetically distinct groups (discontinuity) • In a continum where all trees bear a mosaic of the Pn genetic diversity 3 founders P0 44
- 36. “Available P0” situation Guinean SG2 SG1 P0 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
- 37. Yield 160 140 120 100 80 60 40 20 0 A AxB B Heterosis: AxB is better than either A or B
- 38. “Available P0” situation Guinean SG2 SG1 P0 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
- 39. “Available P0” situation – Strategy (Côte d’Ivoire) Guinean SG2 X = Homogeneous G x SG2 hybrid (= P1) progeny Yield (100 basis) 60 100 140 Possible long term strategy: Reciprocal Recurrent Selection • 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 46
- 40. “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
- 41. 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) Except for certain specific • Seeds in clonal strategy: Might think of intercrossing best Pn clones for an improved Pn population situations, I choose Access to P0 • I (Christophe) tend to believe: • and intergroup seed strategy. If you have access to P , then go for intergroup crosses and seed 0 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
- 42. Conclusions / Perspectives What 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
- 43. Conclusions / Perspectives Take 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
- 44. Trends in coffee production Evolution of Yield (Hg green coffee / Ha) since 1961: Brazil, Colombia, Vietnam vs. others (FAO) 25000 20000 15000 10000 5000 0 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 Three countries account for general increase in yield, especially VN (2 t gc / Ha) All others, on average, are at 1961 levels of productivity
- 45. Benchmarking Maize…. First hybrids
- 46. Conclusions / Perspectives Take 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 • 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 50
- 47. Thanks for your attention christophe.montagnon@cirad.fr