Re-Creating Coffea arabica

March 12, 2017

I have read the stories of possible extinction of the species Coffea arabica by about 2080 A.D. This was predicted on the basis of climatic changes associated with increasing temperatures and global warming1. Scientific efforts at saving this plant are important for the survival of innumerable small farmer families involved in growing coffee and the economic well being of over 80 developing countries involved in supplying this commodity to the consumers all over the world. From what I read, these efforts can be classified into two categories.

The first category of efforts is directed at conserving the wild coffee plants by shifting them to the higher elevations in the montane forests of Ethiopia, the homeland of Arabica coffee1,2. This is very important in the context of high value39 of these genetic resources and also the fact that only a small fraction of the complete gene pool of this species is utilized in the evolution of commercial coffee cultivars40. Recalcitrance of the seed of coffee for conservation in seed banks leaves the only option of maintaining these plants in the form of an orchard that involves not only considerable expenditure but also serious commitment and a variety of plantation management skills3,4.

The second category of efforts is directed towards re-creating Arabica coffee by interspecific hybridization of its putative progenitor species2, a commendable approach undertaken by some scientists at the World Coffee Research. I have been thinking about the proposed action that involves hybridizing C. canephora and C. eugenioides, the species that are perceived to be the progenitors9,13,14,15 involved in giving birth to C. arabica, the lone tetraploid species of the genus Coffea. It is believed that C. eugenioides is the female progenitor and C. canephora is the male progenitor in the origin of C. arabica. The proposed approach is to involve many plants of these two species in hybridization to include as much genetic diversity as possible, as the current perception is that only single plants of these two species are involved in the origin of C. arabica2. If this perception is true, how can we explain the large diversity observed in the wild C. arabica populations. The morphological diversity of the samples drawn from these wild populations is considerably large to think that all of it is derived from just two parent plants5,6,7,8. So, I would like to think that the origin of this important species involved several hybridizations and interbreeding of those hybrids, even if it was between only two species. There are other possible pathways also that could have involved in the birth of original archetypal Arabica.

The origin of C. arabica was considered to have taken place in the Pleistocene period of the Quaternary9, a time when agriculture has not yet begun. Thus, any hybridization events were spontaneous and survival of the hybrid species was solely through positive Natural Selection. Early thinking on the origin of C. arabica also suggested that C. eugenioides10,11,12,13,14,15,16,19 could be the female progenitor. However, the male progenitor was thought to be C. canephora13,14,15,19, C. congensis11,14, C. liberica10,12,19  C. dewevrei12,17,18, C. racemosa24 or C. kapakata25 by different investigators on the basis of certain characters observed in C. arabica. If these perceptions were considered to be true, we have to visualize a scenario of these species coexisting in a population that might have got separated from the centre of origin and diversity of Coffea in a remote area (probably, present equatorial Africa) and found itself in a hostile and inhospitable climate. This could have been a consequence of one of the glaciations events of Pleistocene. That probably triggered a new evolutionary trend through inter species hybridization and spontaneous tetraploidization20,21. Even in this case, assuming a single hybridization event between single plants of any two species severely restricts the diversity that a species needs to survive so many millennia of time in an environment that has been undergoing change constantly42. Our present knowledge of the family Rubiaceae and the species C. arabica indicates that the family probably originated in the Eocene period22 and C. arabica in the Pleistocene (late Pleistocene or early Holocene?)9. This means that the species has survived, at the least, 12000 years or more up to about 2.5 million years. This survival demands that the organism should carry adequate genetic diversity and plasticity to adapt to the contemporary and changing climatic conditions. Its solo existence in Ethiopian high lands and Boma Plateau, its wide adaptation in the various locations of introduction and its capability to accept genes from the related species suggest that it could be a compilospecies20,21. This means that re-creating it should involve more than two species.

Another series of thoughts on the origin of C. arabica propose that this species originated by autotetraploidy of other Coffea species. Particularly, C. eugenioides was thought to have given rise to Arabica by autotetraploidy because of the morphological resemblances of its autotetraploid13. Support for this argument was provided by the similarity of mitochondrial genomes of C. arabica and C. eugenioides23.

The species C. arabica was not known to man until a few hundred years ago26. Its discovery by man and his development of a taste for it led to all the developments that we knew and finally to the possibility of its extinction in the next 50-60 years. Even after coffee came into world trade, Arabs controlled the coffee trade until the 18th century when plant breeding was not a scientific art, meaning that all deleterious developments happened in the last one hundred years. Thus, re-creating this species requires considerable deep thinking and sincere efforts with perceptions that should not go wrong.

Considering the climate of Quaternary that is also called the Ice Age27, large areas of the earth were covered by glaciers in the Pleistocene, the first epoch of the Quaternary. These ice sheets started melting with increasing temperatures towards the later part of that epoch and the glaciation events were linked to the origin of Arabica coffee during this period9. Considering its wild existence in the upper montane forests of Ethiopia, a plausible assumption is that the nascent allotetraploid was adapted to a climate that was the colder even at that time. Thus, if we wish to re-create Arabica from the same progenitor species, we should also have a similar climate for its adaptation. This scenario appears to be a very difficult one to create. Over the several millennia of Quaternary, some of the other species of Coffea were found to be adaptable in much harsher climates. Some of these species were found to be crossable with C. arabica and were used in its improvement and some were thought to be involved in its origin as already mentioned. There is also considerable understanding of the crossability relationships among the species of Coffea15,16. There were reports of spontaneous hybridization between species giving birth to Arabicoids with introgressed genes28,43 from some of these species and even a case of allopolyploidy16. All these natural hybrids and the allopolyploid were used in improving Arabica for disease and pest resistance29,30,44. An important point is that all of them were created in the contemporary climate of the recent past and all of them closely resemble Arabica in their morphology. Thus, thoughts on re-creating Arabica may have to be re-oriented to include the many species of the diploid gene pool that manifest considerable resistance to the many adversaries of Arabica coffee in the current climate. This leads to the creation of a gene pyramid34 that helps the new arrival to resist the adversaries for a considerably long time.

Why should we include the other species that were known to produce beans that give a poor quality beverage? What are the genetic implications for quality and adaptation?

In the context of these questions, I would like to address the matter of adaptation first. The events of Pleistocene that led to the first appearance of C. arabica and its survival until now would have included resistance to the contemporary pests and diseases in all likelihood as this determines the fitness to survive41. That resistance has seen the species through the so many centuries that it has been existing before its discovery by man and his manipulations to produce it on a commercial basis. The pests and diseases that infest the various varieties of Arabica coffee, now-a-days is attributed to the lower genetic diversity in the gene pool of cultivated Arabica initially35 and this observation got extended to the wild forms also ain a recent study of the germplasm collections maintained in Costa Rica as mentioned in an internet story2. One limitation of this germplasm study could be that the explorers who collected these materials depended primarily on the morphological characters and the genetic diversity of collections may be very low in the modern context of molecular biology. Sampling of the early collections also would have been random. Thus, this could be a profound reflection of the Founder effect. Also, it is possible that the disease and pest organisms evolved into forms that can overcome the innate resistance of original Arabicas. Some of the modern hybrids carrying the introgressed genes from diploid species are manifesting resistance to some of the disease and pest adversaries and promise to be of value in cultivation31,35,43. Considering these facts, it may be pragmatic to think of re-creating C. arabica by involving different diploid species carrying resistance to nematodes, leaf miners, stem borers and the diseases like leaf rust, berry disease and bacterial blight. A basic concept for creating novel allotetraploid germplasm to be used in Arabica coffee breeding was posted on this blog sometime earlier. In the present scenario of pest and disease infestation32,33, re-creating C. arabica from such diverse allotetraploids makes better sense than the suggested path of hybridizing C. canephora and C. eugenioides.

The question of coffee quality has been debated hotly for many decades. The intrinsic elements that condition the taste and flavour of the consumed beverage are described as fair average quality and can be realized in most of the coffee produced anywhere in the world. Our concern in the context of possible extinction of the coffee plant should be in preserving the coffee plants that can produce beans with this basic quality standard. The early period coffee tasters were of the belief that the best quality is realized from the Arabica coffee plants whose breeding history does not involve any diploid species36,37. But then, dealing with adversaries like coffee leaf rust, coffee berry disease and stem borers and leaf miners made it necessary to involve the diploid species like C. canephora, C. liberica, C. racemosa  and others in evolving Arabica coffee varieties. Beverage quality of these varieties was considered inferior to that of pure Arabicas for a considerable time. However, literature of the more recent times indicates that some of these hybrids are not simply good but better in quality over the conventional Arabica in beverage quality38. All these facts suggest that basic beverage quality does not suffer because of introducing genes from other Coffea species into C. arabica. On the other hand, it seems to improve. A natural allotetraploid derived by spontaneous doubling of chromosomes in a hybrid of C. liberica and C. eugenioides also produced beverage of good quality indicating tetraploidy may be at the root of Arabica’s quality. Genetic basis of such beverage quality characters was well explained in literature26. These aspects have to be seriously considered when we propose to re-create Arabica.

On the whole, re-creating Arabica coffee is important but requires to internalize many aspects as narrated above to evolve a new species (shall we call it C. arabica?) that can effectively replace the old C. arabica and survive for, at least, another 15000 years.

References

  1. Davis AP, Gole TW, Baena S, Moat J. 2012. The impact of climate change on indigenous Arabica coffee (Coffea arabica): Predicting future trends and identifying priorities. PLoS ONE 7(11): e 47981. Doi:10.1371/journal.pone.0047981.
  2. Siddle J, Venema V. 2015. Saving coffee from extinction. http://www.bbc.com/news/magazine-32736366.
  3. Engelman F, Dulloo ME, Astorga C, Dussert S, Anthony F. 2007. Conserving coffee genetic resources. Bioversity International, Rome.
  4. Aga E. 2005. Molecular genetic diversity study of forest coffee tree (Coffea arabica) populations in Ethiopia: Implications for conservation and breeding. Ph.D. Thesis. Swedish University of Agricultural Sciences, Alnarp, Sweden.
  5. Gessese MK, Bellachew B, Jarso M. 2015. Multivariate analysis of phenotypic diversity in the South Ethiopian coffee (Coffea arabica) for quantitative traits. Adv. Crop Sci. Tech S1: 003. doi. 10.4172/2329-8863.S1-003.
  6. Balami S. 2007. Genetic diversity analysis of the wild Coffea arabica populations from Harenna forest, Bale mountains of Ethiopia, using inter simple sequence repeats (ISSR) marker. M.Sc. Thesis. Addis Ababa University, Addis Ababa, Ethiopia.
  7. Montagnon C, Bouharmont P. 1996. Multivariate analysis of phenotypic diversity of Coffea arabica. Genetic Resources and Crop Evolution 43: 221-227.
  8. David P, Santos SMB, Sergio DL, Leandro DG, Filipe PPL, Luiz V, Sera T. 2008. Phenotypic analysis of Coffea arabica accessions from Ethiopia: Contribution to the understanding of Coffea arabica https://agritrop.cirad.fr/545939/1/document_545939.pdf.
  9. Lashermes P, Combes MC, Robert J, Trouslot P, D’Hont A, Anthony F, Charrier A. 1999. Molecular characterization and origin of the Coffea arabica genome. Mol Gen Genet 261: 259-266.
  10. Ram AS, Sreenivasan MS. 1981. A chemotaxonomic study of Coffea arabica In Genetics, Plant Breeding and Horticulture (PLACROSYM IV)(Ed. Vishveshwara S) pp. 368-374. Indian Society for Plantation Crops, Kasaragod, India.
  11. Raina SN, Mukai Y, Yamamoto M. 1998. In situ hybridization identifies the diploid progenitor species of Coffea arabica (Rubiaceae). Theor Appl Genet 97:1204-1209.
  12. Narasimhaswamy RL.1962. Some thoughts on the origin of Coffea arabica Coffee 4(12):1-5.
  13. Thomas AA. 1944. The wild coffees of Uganda. Genetics 40: 563-
  14. Cramer PJS. 1957. Review of literature on coffee research in Indonesia. Miscellaneous Publication # 15. IICA, Turrialba.
  15. Carvalho A, Monaco LC. 1967. Genetic relationships of selected Coffea Ciencia e Cultura 19(1): 161-165.
  16. Narasimhaswamy RL, Vishveshwara S. 1961. Report on hybrids between some diploid species of Coffea. Indian Coffee 25: 104-109.
  17. Fernie LM. 1966. Impression on coffee in Ethiopia. Kenya Coffee 31: 115-121.
  18. Mendes AJT. 1949. Observaçoes citologicas em Coffea. XII: Uma nova forma tetraploide. Bragantia 9: 25-34.
  19. Sybenga J. 1961. Genetics and cytology of coffee: A literature review. Bibl. Genet. XIX: 217-316.
  20. Ram AS. 2004. Coffea arabica L – A compilospecies: Implications for Breeding. Proc. XX International Colloquium on Coffee Science, pp. 740-746. Association Scientifique Internationale du Cafe, Paris, France.
  21. Ram AS. 2008. Speciation of Coffea arabica: Implications for genetic improvement. J Plantation Crops 36: 79-85.
  22. 2017. Rubiaceae. https://en.wikipedia.org/wiki/Rubiaceae.
  23. Berthou F, Trouslot P, Hamon S, Vedel F, Quetier F. 1980. Analyse en electrophorese du polymorphisme biochemique des caféiers: variation enzymatique dans dix-huit populations sauvages; variation de l’ADN mitochondrial dans les especes canephora, C. eugenioides et C. arabica. Café Cacao Thé 24: 313-326.
  24. Medina DM. 1963. Microsporogenese em um hibrido triploide de Coffea racemosa x Coffea arabica L. Bragantia 22: 299-318.
  25. Monaco LC, Medina DM. 1965. Hibridacoes entre Coffea arabica e Coffea kapakata. Analise citologica de um hibride triploide. Bragantia 24: 191-201.
  26. Ram AS. 2005. Quality improvement in Arabica coffee: Relevance of Ethiopian germplasm. J. Coffee Res. 33(1&2): 15-33.
  27. Live Science. 2017. Quaternary period: Climate, animals and other facts. http://www.livescience.com/43151-quaternary-period.html.
  28. Bettencourt AJ. 1973. Consideracoes gerais sobre o Hibrido do Timor. Circular # 23, Instituto Agronomico, Campinas, Brazil.
  29. Eskes AB. 1989. Resistance. In: AC Kushalappa and AB Eskes (Eds.) Coffee Rust: Epidemiology, Resistance and Management. pp. 171-291. CRC Press, Boca Raton.
  30. Ram AS, Ganesh D, Reddy AGS, Srinivasan CS. 2004. Ligenioides – A source of new genes for Arabica coffee breeding. Proc. PLACROSYM XX. J. Plantn. Crops. 32 (Suppl.): 5-11.
  31. Ram AS. 2005. Breeding coffee for leaf rust resistance: The Indian experience. Indian Coffee 69(4): 10-13.
  32. Ram AS. 2015. Plant breeding: Importance for coffee industry in India. J. Dev. Social Change 11(4): 91-96.
  33. Avelino J, Cristancho M, Georgiou S, Imbach P, Aguilar L, Bornemann G, Laderach P, Anzueto F, Hruska AJ, Morales C. 2015. The coffee rust crisis in Colombia and Central America (2008-2013): impacts, plausible causes and proposed solutions. Food Sec. 7: 303-321.
  34. Ram AS. 2001. Breeding for rust resistance in coffee: The gene pyramid model. J. Plantn. Crops. 29(1): 10-15.
  35. Lashermes P, Andrzejewski S, Bertrand B, Combes MC, Dussert S, Graziosi G, Trouslot P, Anthony F. 2000. Molecular analysis of introgressive breeding in coffee (Coffea arabica). Theor. Appl. Genet. 100: 139-146.
  36. Van der Vossen HAM. 2008. Disease resistance and cup quality in Arabica coffee: The persistent myths in the coffee trade versus scientific evidence. In: XXII International Scientific Colloquium on Coffee. pp. 1351-1360. ASIC, Paris.
  37. The cup quality of disease resistant cultivars of Arabica coffee (Coffea arabica). Exptl. Agric. 45: 323-332.
  38. Sobreira FM, Oliveira ACB, Pereira AA, Sakyiama NS. 2015. Potential of Hibrido de Timor germplasm and its derived progenies for coffee quality improvement. Aus. J. Crop Sci. 9(4): 289-295.
  39. Hein L, Gatzweiler F. 2006. The economic value of coffee (Coffea arabica) genetic resources. J. Ecolecon. 60: 176-185.
  40. Anthony F, Bertrand B, Astorga C, Lashermes P. 2007. Characterization and assessment of Coffea arabica genetic resources conserved in the CATIE field genebank. In: Conserving coffee genetic resources (Eds. Engelman F, Dulloo ME, Astorga C, Dussert S, Anthony F), pp.35-58. Bioversity International, Rome.
  41. Coevolution. http://www2.nau.edu/~gaud/bio300w/coveol.htm.
  42. Stebbins GL. 1971.Processes of Organic Evolution. Prentice Hall (India) Ltd., New Delhi.
  43. Rodrigues Jr. CJ, Bettencourt AJ, Rijo L. 1975. Races of the pathogen and resistance to coffee rust. Annu. Rev. Phytopathology 13: 49-70.
  44. Ram AS. 2013. Coffee Breeding. LAP Publishers, Saarbrücken, Germany.

Pre-emptive Breeding – The case for Coffee

September 7, 2013

High value of coffee in international trade and domestic economies of the many producing countries is well known. It is also well known that most of world’s coffee is produced in the poor and under-developed countries. This is a beverage being consumed across the world for almost four centuries and most of the consumption is in the affluent western countries. Possibly, it is on account of these facts that very little effort is directed towards the pre-emptive breeding of this important crop plant to achieve resistance against various adversaries.

If we take a look at the history of the various diseases and pests of coffee, it becomes clear that these various adversaries became prominent in different crisis times. Like all other internationally traded commodities, coffee has also been passing through ‘boom and bust’ cycles, leading to financial crises in the lives of farmers producing this crop. When the price of coffee is very low in the markets, its direct impact is on the maintenance of coffee plantations that get neglected. This leads to the more severe occurrence of diseases, of which coffee leaf rust is the most prominent. Leaf rust is a defoliating disease that predisposes the coffee plant to many other adversaries that take advantage of the situation. Defoliation leads to debilitation of the plant as its photosynthetic and other biosynthetic processes carried out by leaves get compromised opening an advantageous situation for the adversaries. Evolution of new races of coffee leaf rust that can defeat the resistance achieved by incorporating newer genes is known to be considerably rapid.

All this is true in the context of Arabica coffee that is susceptible to the pests and diseases. We have known resistance to a variety of adversaries like nematodes, insects and diseases in the various species of the diploid gene pool of coffee. Diploid species like Robusta and Liberica were utilized in a modest way towards improving leaf rust resistance of the coffee plant and Arabica – Robusta hybrids are also known to possess some resistance to the nematodes. Also, it is known that several diploid species cross well with the lone tetraploid Arabica to yield moderately fertile hybrids. Also, it is known that diploid species of coffee naturally cross to give rise to natural interspecific hybrids. These innate potencies of the coffee plants should be exploited to transfer the requisite resistance to the species of choice to create germplasm that can be used in long term breeding exercises to evolve coffee plants resistant to the various adversaries.

This is a long term exercise in breeding that also demands special skills in cytogenetics and chromosome manipulation to achieve positive and stable results that benefit the coffee farmers over long periods of time. Conceptual background for this effort comes from the fact that diploid species of coffee naturally and freely cross among themselves and also with Arabica to yield fertile or moderately fertile hybrids. As explained in the concept paper posted a few days earlier, scientists at different coffee research stations in Africa as well as other countries where some species are available in the gene banks should create diploid-diploid and diploid-tetraploid interspecific hybrids that should be handled appropriately to evolve tetraploid Arabicoids that constitute novel germplasm for breeding Arabica coffee in the future, against a variety of adversaries like newer diseases, nematodes and possibly abiotic factors arising out of climate change.


Concept Paper for Project on Novel Coffee Germplasm

August 18, 2013

Coffee is the largest exported agricultural product of Tanzania and contributes about US$115 million to their foreign exchange earnings and supports the livelihoods of about 400,000 small farmer families and many more in the processing and trading sectors26. Thus the importance of coffee for Tanzanian economy cannot be overemphasized. A similar situation can be expected in the context of the many coffee producing countries of Africa.

 

Coffea arabica the lone tetraploid (2n=4x=44) species of the genus Coffea was considered to have been derived from two diploid species of the same genus by spontaneous hybridization and doubling of chromosomes in the interspecific hybrid. Many researchers agree and sought evidence to prove this hypothesis. Presently, it is accepted by scientists that C. eugenioides could be the possible evolutionary female progenitor of C. arabica, having contributed one set of 22 chromosomes (2n=2x=22) and its cytoplasm. The other set of chromosomes appear to have been contributed by C. canephora (Robusta) or C. congensis or even by C. liberica, the species that were proposed to be the possible evolutionary male progenitor of C. arabica1-12. There is evidence that C. arabica could be a species that has inherited genes from other diploid species like C. racemosa13 or even C. stenophylla and C. excelsa (unpublished data). However, all schools agree that C. eugenioides is the putative female progenitor. This implies that most of the Arabicas carry the cytoplasm of C. eugenioides, but possibly the genes of several species, a situation akin to the nature of ‘compilospecies’14,19. This also calls for the understanding that simple breeding techniques would not lead to dependable results in resolving the complex problems of susceptibility to diseases like leaf rust, CBD, stem borer and leaf miner, the major biotic adversaries of coffee claiming over 50-60% of production cost. Observed resistance to most of these adversaries in the diploid species of Coffea and the compilospecies nature of C. arabica21,22 indicate that breeding involving interspecific hybridization is the only way to achieve resistance in C. arabica. In this context, some unique germplasm generated in the Indian coffee breeding programme, such as Devamachy (Natural hybrid of Robusta and Arabica), Robarbica (Artificial hybrid of Robusta and Arabica), Racemusta (Artificial hybrid of C. racemosa x C. canephora) and Ligenioides (Amphiploid from the artificial hybrid of C. liberica x C. eugenioides) hybrids have proven to be of value24,25. These germplasm were created as part of a long term exercise in coffee breeding in India and the initial efforts took place in the 1930s. Present proposal is with the idea of creating such germplasm in Tanzania and possibly other African countries where some of the 100 known species of Coffea are native.

Tanzania is home for 16 diploid species of Coffea. Some of the species are C. racemosa, C. sessiliflora, C. kimbozensis, C. eugenioides, C. zanguebariae, C. fadenii, C. charrieriana and C. anthonyi. These species constitute the secondary gene pool carrying important traits for the improvement of C. arabica. As C. arabica is tetraploid, and these species are diploid, it becomes necessary that these species be hybridized and diploidized to render the hybrids tetraploid and be able to cross with C. arabica and transfer the genes of interest to that species.

In the genus Coffea, the reproductive isolation barriers are incomplete and allow the intercrossing of diploid species. In fact, interspecific hybrids appear spontaneously when two or more species are growing together in any location. During the current project, it is proposed to collect as many Tanzanian diploid species of Coffea as possible through seeds and establish a germplasm bank at the University of Dodoma and possibly Tanzania Coffee Research Institute to eventually generate hybrids from all possible combinations of these species. As Coffea species are perennial plants, their initial establishment is expected to take, at least, 3-4 years and the generation of hybrids can be done in the subsequent period of another 4-5 years. Thus, the proposed project takes about 10 years to realize the proposed products. However, genetic, cytological, biochemical and molecular characterization of these species can be carried out in the course of establishing the germplasm bank itself and the study of hybrids commences after their being generated.

A situation of considerable relevance is that of Maize. During 1960s, cytoplasmic male sterile (CMS) lines were extensively used in USA to produce hybrid seed that helped in doubling the corn production. However, during early 1970s, all these hybrids fell susceptible to southern corn blight (caused by Helminthosporium maydis). It was found that a particular CMS line from Texas was involved in the derivation of all the hybrids rendering the cytoplasm of all the hybrids uniform. Later, this cytoplasm was named as T-cytoplasm. This exerted the selection pressure on the pathogen and resulted in the evolution of a single race (race-T) that could cause devastation of the entire lot of hybrids20. We have an analogous situation, in that most of the Arabica coffees carry the cytoplasm of C. eugenioides. According to the available information, the earliest appearance of CBD was also on C. eugenioides17. Later, it has spread to most Arabicas. This is further supported by the fact that CBD resistance is found only in the interspecific hybrids like Hibrido de Timor (HDT). Rume Sudan Arabica that possesses resistance was also shown to be distinct from pure Arabicas and closer to some lines of HDT by DNA fingerprinting studies13. Maize hybrid seed production in USA could be continued using diverse CMS lines other than Texas and a similar exercise of Arabica coffee breeding involving the cytoplasm of other species is most likely to lead to positive results. In the proposed project, tetraploid genotypes carrying diverse cytoplasmic endowments of the diploid different species will be combines with a tetraploid nucleus that can transfer genes to C. arabica will be created and will prove to be of great value in breeding this important crop plant.

On account of the value of C. arabica to the economy of all African coffee producing countries and the value of these species to the breeding of this important cash crop, the project is justified. C. arabica is susceptible to diseases like coffee berry disease (CBD), coffee leaf rust (CLR) and pests like coffee berry borer (CBB) and stem borer and innate genetic resistance to these adversaries is resident in the diploid species proposed to be collected. At present, over 50% of production cost is towards the control of these adversaries and resistant plants are expected to reduce the cost of production considerably.

Apart from the utilization of this germplasm in African countries, it can also be shared with other coffee producing countries, on mutually agreed terms to derive IPR benefits for the Institutions and to the countries of origin23.

References

 

  1. Carvalho, A., Monaco, L.C. 1967. Genetic relationships of selected Coffea species. Ciencia e Cultura 19: 151-165.
  2. Narasimhaswamy, R.L., Vishveshwara, S. 1961. Report on hybrids between some diploid species of Coffea L. Indian Coffee 25:104-109.
  3. Narasimhaswamy, R.L., Vishveshwara, S. 1967. Progress report on hybrids between diploid species of Coffea L. Turrialba 17:11-17.
  4. Charrier, A. 1978. La structure genetique des cafeiers spontanes de la region Malagache (Mascarocoffea). Memoires ORSTOM (87), Paris.
  5. Ram, A.S., Sreenivasan, M.S. 1981. A chemotaxonomic study of Coffea arabica L. In: Genetics, Plant Breeding and Horticulture (Proc. PLACROSYM IV, Ed. S. Vishvehshwara) pp. 368-374. Indian Society for Plantation Crops, Kasaragod, India.
  6. Berthou, F., Mathieu, C., Vedel, F. 1983. Chloroplast and mitochondrial DNA variation as indicator of phylogenetic relationships in the genus Coffea L. Theor. Appl. Genet. 65: 77-84.
  7. Orozco-Castillo, C., Chalmers, K.J., Powell, W., Waugh, R. 1996. RAPD and organelle specific PCR re-affirms taxonomic relationships within the genus Coffea. Plant Cell Reports 15: 337-341.
  8. Cros, J., Combes, M.C., Trouslot, P., Anthony, F., Hamon, S., Charrier, A., Lashermes, P. 1998. Phylogenetic analysis of chloroplast DNA variation in Coffea L. Mol. Phylog. Evol. 9: 109-117.
  9. Lashermes, P., Combes, M.C., Trouslot, P., Anthony, F., Charrier, A. 1996. Molecular analysis of the origin and genetic diversity of Coffea arabica L.: Implications for coffee improvement. In: Proc. Eucarpia Conference 1996, Montpellier. pp. 23-29
  10. Lashermes, P.,Combes, M.C., Cros,J., Trouslot, P., Anthony, F., Charrier, A.1995. Origin and genetic diversity of Coffea arabica L. based on DNA molecular markers. In : XVI  International Scientific Colloquim on Coffee. pp.528-536.ASIC,Paris.
  11. Lashermes, P., Combes, M.C., Trouslot, P., Charrier, A. 1997. Phylogenetic relationships of coffee-tree species (Coffea L.) as inferred from ITS sequences of nuclear ribosomal DNA. Theor. Appl. Genet. 94: 947-955.
  12. Lashermes, P., Combes, M.C., Robert, J., Trouslot, P., D’Hont, A., Anthony, F., Charrier, A. 1999. Molecular characterization and origin of the Coffea arabica L. genome. Mol. Gen. Genet. 261:259-266.
  13. Ram A.S., Sreenath, H.L. 2000. Genetic fingerprinting of coffee genotypes with varying resistance to rust. In: Recent Advances in Plantation Crops Research (Eds. N. Muraleedharan, R. Rajkumar) pp.57-62. Allied Publishers Pvt. Ltd., New Delhi.
  14. Harlan, J.R., De Wet, J.M.J. 1963. The compilospecies concept. Evolution 17:497-501.
  15. Srinivasan, C.S., Ramachandran, M. 1997. Selection 5B – S.2931 (S.333 / Devamachy hybrid) – An old arabica hybrid rediscovered with promising features. Indian Coffee (11):4-6.
  16. Sreenivasan, M.S., 1987. Cyto-Embryological Studies of Robusta-Arabica Coffee Hybrids. Ph.D. Thesis, University of Mysore, Mysore.
  17. Mogk, M. 1975. Investigations on the origin of leaf rust and coffee berry disease in the provinces of western Kenya. Mimeo Report. Coffee Research Foundation, Ruiru, Kenya.
  18. Fazuoli, L.C., Perez, M.M., Guerreiro-Filho, O., Medina-Filho, H.P., Silvarolla, M.B. 2000. Breeding and biotechnology of Coffee. In: Coffee Biotechnology and Quality (Eds. T. Sera, C.R. Soccol, A. Pandey, S. Roussos) pp. 27-46, Kluwer Academic, Dordrecht.
  19. Ram, A.S., Ganesh, D., Sreenath, H.L., Srinivasan, C.S. 2002. Genetic fingerprinting of coffee hybrids: Ligenioides x Hibrido de Timor hybrids. J. Plantation Crops 30: 18-21.
  20. Levins III, C.S. 1990. The Texas cytoplasm of Maize: Cytoplasmic male sterility and disease susceptibility. Science 250: 942-947.
  21. Ram, A.S. 2004. Coffea arabica L. A compilospecies: Implications for breeding. Proc. XX International Conference on Coffee Science, pp. 740-746. ASIC, Paris.
  22. Ram, A.S., Indira, M. 2000. Intellectual property rights: Are they important for Indian coffee research? In: Workshop on WTO Agreement on Agriculture: Implications on Coffee Industry. Coffee Board, Bangalore.
  23. Ram, A.S. 1998. Coffee materials evolved in India. Indian Coffee 62(6): 5-6.
  24. Ram, A.S., Sabir, R.K., Mythrasree, S.R., Seetharama, H.G., Rao, R.V. 2008. White Stem Borer Resistance in Coffee: Perspectives on Breeding, Management and Consumption. In: Proc. XXII International Conference on Coffee Science, pp. 1323-1335. ASIC, Paris.
  25. Ram, A.S. 2008. Speciation of Coffea arabica L.: Implications for Genetic Improvement. Journal of Plantation Crops 36: 79-85.
  26. Baffes, J. 2003. Tanzania’s Coffee Sector: Constraints and Challenges in a Global Environment. The World Bank Africa Region Working Paper #56. http://www.worldbank.org/afr/wps/index.htm

Coffea arabica is a compilospecies

August 17, 2013

There are two schools of thought regarding the origin and evolution of Coffea arabica L. the world’s most important non-alcoholic stimulant beverage. The first or conventional school of thought based their inference on the evidence raised from observations on morphological, cytological, biochemical and reproductive biological features. The school proposes that C. arabica evolved by spontaneous hybridization of C. eugenioides with C. canephora, C. congensis or C. liberica and doubling of the chromosomes in the natural hybrid. An interesting offshoot of this thought is the belief that C. arabica is a segmental allotetraploid. The second or technological school of thought hypothesizes that natural hybridization of C. eugenioides or a sub-species by an unreduced gamete of C. canephora and spontaneous stabilization of chromosome number in the progeny of triploid hybrid resulted in the evolution of C. arabica on the basis of evidence from molecular marker studies. Evidence from some of the marker studies also suggests that C. arabica may be sharing considerable genomic homologies with C. racemosa and C. congensis. Molecular cytogenetic evidence also supports that C. eugenioides and C. congensis are the probable evolutionary parents of C. arabica. The distribution of C. arabica outside the area of distribution of all diploid species was attributed to the events of Pleistocene glaciation. Both schools agree that C. eugenioides or a sub-species of it is the most probable female progenitor of C. arabica. While they differ in the matter of male progenitor, in that, a species of the canephoroid group or liberio-excelsoides group is considered to be the likely male progenitor of C. arabica. Considering the genetical evidence from plant breeding studies, the disease resistance genes of C. liberica and C. canephora are inherited by C. arabica. All these available evidence points to the possible compilospecies nature of C. arabica. This has strong implications for the breeding practices, as inheritance patterns in compilospecies are considerably different from those observed in diploids and allopolyploids. These aspects are discussed and a possible breeding model with integration of vegetative selection to maintain traits of interest in the commercially exploited arabicoid derived materials is suggested. Utilization of unique tetraploid hybrids of interspecific origin like Ligenioides, Racemusta and Robarbica are proposed for use in breeding for resistance to coffee berry disease, insects and nematodes on the basis of their cytoplasmic genetic endowments.

This is the summary of a paper presented at the XX International Conference on Coffee Science, ASIC, pp. 740-746. (Bangalore, 11-15 October, 2004) and has implications for future breeding efforts and the large role that African countries can play.


New Assignment

March 1, 2012

I have taken up a new assignment as Associate Professor of Genetics at the University of Dodoma in Tanzania. I hope to put my research background to utility in developing models for coffee improvement using the genetic resources available in this country.
Coffee is very important as a large foreign exchange earner for Tanzania and Tanzania is home to 16 of the over 100 known species of Coffea that can be used to improve Arabica coffee through developing interspecific hybrids to transfer genes that condition resistance many biotic adversaries.


Gene Pyramiding for CLR Resistance

January 24, 2010

J. Plantation Crops. 29: 10-15 (2001).

Breeding for rust resistance in coffee: The gene pyramid model

In the international trade of commodities, coffee occupies a place of pride, next to petroleum, in trade volume and money value. For India, coffee exports earn about Rs.15 billion annually. Many third world economies depend on the earning from this important crop. Leaf rust caused by Hemileia vastatrix is a disease of economic significance on Arabica coffee. About 32 races of this pathogen are known. Almost all coffee research institutions in the world are engaged in breeding rust resistant strains of Coffea arabica. There are nine known genes (symbolized SH1 – SH9), which condition race specific resistance of the host plant. Many combinations of these genes were already known to have been overcome by races of the rust fungus. Hibrido de Timor (HDT) is the singular genotype that remained resistant to all known races. It has a unique genotype (SH6,7,8,9) which is the probable cause of this manifestation. Gene pyramiding is conceived to be able to impart long lasting resistance to this classic disease, and a model combining all known and unknown resistance genes is presented in this paper. Involving a variety of interspecific hybrids manifesting resistance conditioned by the elements of vertical resistance, and wild arabicas with horizontal resistance, and dwarf/semi-dwarf genotypes conditioned by dominant genes, is proposed to derive a resistant plant population carrying the necessary genetic diversity and uniform plant type. Integrating vegetative multiplication in the breeding scheme makes this commercially viable by way of eliminating segregation for plant type as well as resistance.


Biochemical Markers for CLR Resistance

January 15, 2010

Proc. 15th Plantation Crops Symposium PLACROSYM XV (2002). pp. 6-13.

Biochemical Markers for Rust Resistance in Coffee

AS Ram, NP Geetha, KN Amruthesh, KR Kini,D. Ganesh
CS Srinivasa, HS Shetty

Coffee is a great commodity of international trade, sustaining the economies of over eighty developing countries that produce this crop. Commercial coffee is produced from mainly two species of the genus Coffea L. viz. C. arabica L. and C. canephora Pierre. Leaf rust is a devastating disease of coffee causing economically significant crop losses of C. arabica. Thus, achieving rust resistance is one of the major objectives of almost all Arabica coffee breeding programmes of the world. Present study was undertaken with the objective of finding biochemical markers that facilitate the identification of rust resistant plants at an early stage of development (e.g. nursery stage). The enzymes phenylalanine ammonia-lyase (PAL), lipoxygenase (LOX), peroxidase (PO) and chitinase are known for their involvement in plant defense against pathogens. Present study evaluated the constitutive level of activity of these enzymes in progeny populations derived from the cross Ligenioides (natural allo-tetraploid derived from an artificial hybrid of Coffea liberica x C. eugenioides) and Hibrido de Timor (HDT, a spontaneous tetraploid interspecific hybrid of C. arabica and C. canephora) that was manifesting high rust resistance. The study was conducted on Ligenioides, HDT, their F1, F2 and BC progenies. Results indicated that PAL and LOX are good indicators of rust resistance at the constitutive level of activity and can be effectively utilized for the identification of resistant plants. This is a first report of biochemical markers with diagnostic value and utility in coffee breeding. Implications of the utilization of biochemical markers in resistance breeding and propagation and distribution of resistant material for commercial exploitation are discussed.