Re-Creating Coffea arabica

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

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  2. Siddle J, Venema V. 2015. Saving coffee from extinction. http://www.bbc.com/news/magazine-32736366.
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