STEPHANIE ALCALA explores the current state of genetic diversity and how we can create climate resilient crops, as she shares some highlights from her research project investigating the genetic composition of the beloved Panamanian Geisha.
The specialty coffee industry is most vulnerable to climate change, because it relies solely on the production of Coffea arabica, a coffee species that is highly dependent on stable montane growing conditions. It is estimated that half the amount of suitable land for coffee cultivation will be lost by 2050 due to climate change. However, coffee producers are already experiencing its effects with increasing irregularity in weather patterns which include extended periods of drought, fluctuating temperatures, and calamitous rainfall. These unpredictable climatic conditions can affect yields and coffee quality. This can then lead to economic instability for producers, who are already facing tremendous hurdles, with coffee prices often falling below the cost of production. Combine these two issues with the numerous other threats producers regularly face such as pest and diseases or cost of labor and we find coffee production caught in an endless cycle of turmoil.
Luckily, there are countless individuals and organizations dedicated to solving these issues, striving to create a sustainable coffee industry. And I believe each and every one of us has the ability to also contribute towards solving these issues, enhancing coffee’s resiliency. The solution lies in deepening our understanding of these ongoing threats and engaging with the organizations dedicated to solving these issues.
A Coffee Genetics Primer
The future of our industry depends on producers having access to plant material that can withstand future climatic conditions and produce great cup quality. However, Arabica coffee has very little genetic diversity, resulting in its limited ability to genetically adapt to climate change. So how can we address this? First, we need to understand why Arabica has a narrow genetic base. Coffea arabica was the result of a single hybridization event between two coffee species Coffea canephora (which we know as Robusta) and Coffea eugenioides, and these two species have only a 1.3 percent average difference between their genes. We see a further reduction in Arabica’s genetic diversity when we look at the cultivated population of coffee. Arabica’s historical domestication has resulted in a severe genetic bottleneck, with the majority of Arabica varieties cultivated today for global consumption deriving their genetic composition from Bourbon and/or Typica. Furthermore, it has been suggested that these original plants, initially introduced from Ethiopia to Yemen, were collected from the same forest population, meaning they were from the same genetic pool. However, not all hope is lost.
During Arabica’s inception, the plant was created as an allotetraploid organism. This means the species C. arabica duplicated each of its parent’s chromosomes, doubling the size of its genome. So, while both of its parents are diploid organisms, Arabica is a polyploidorganism, possessing a genome that contains a C. eugenioides-like genome and a C. canephora-like genome. Allotetraploid organisms are very common across flowering plants, but Arabica is the only coffee species out of 125 that possesses this evolutionary trait. This raises an intriguing question: Has being a polyploid organism contributed to Arabica coffees extremely novel characteristics, such as its ability to produce complexity in the cup? Moreover, research indicates that polyploid organisms can possess long-term evolutionary adaptive capabilities, so perhaps this can translate to Arabica being genetically more capable of adapting to climate change than any other coffee species.
By focusing on the genetic possibilities that Arabica’s unique genome provides us, we can begin to shift our attention towards selective breeding. Selective breeding is when humans facilitate the sexual reproduction of two organisms in order to obtain an offspring with desirable traits. In the case of coffee, selective breeding has been used to obtain offspring with traits of drought tolerance or disease resistance. Therefore, selective breeding is essential to enhance resiliency and confidence for our producers while ensuring the longevity of our industry. There are two sources of incredible genetic diversity that can hold the key for Arabica’s success. The 124 other coffee species that exist in the wild populations and the indigenous Arabica coffee varieties that have remained in Ethiopia and surrounding regions have been developing their own mutations and genetic adaptations, separate from the existing roster of cultivars.
Today s cultivars differ tremendously in their ability to thrive in certain environments, differing in their levels of disease resistance, cupping potential, and so forth. But as we know, most of these cultivars are genetically similar due to their shared genetic base. One of the exceptions is the Gesha variety that originated from a wild Ethiopian population near the village of Gorei and eventually became established in tropical Americas as Geisha. After a long peregrination that started with an expedition by British colonial officers to collect Ethiopian plant material in 1931, it was first dispersed among African countries, then made its way to Costa Rica, and ultimately Panama. The Gesha, having experienced a recent divergence in Ethiopia, was genetically different than anything Latin America had cultivated prior to this. It was a game changer.
The rediscovery of Geisha has since led to its further dispersal across the Americas, where you can now find it being grown in regions such as Bolivia, Guatemala, and even California, all of which have derived their plant material from Hacienda La Esmeralda. This dispersal of Geisha led me to ask: How much genetic diversity lies within the Panamanian Geisha? If producers were converting their farms to primarily grow Geisha, how would this influence their farms climate resiliency? Are all Geishas genetically similar or is there genetic variation? And is that genetic variation associated with a distinct attribute or trait? As a graduate student studying genetics, I had an opportunity to investigate: How genetically diverse is the cultivated Panamanian Geisha?
Out in the Field
In the summer of 2016, I found myself in the Chiriquí Province of Panama, traversing the farms of Hacienda La Esmeralda with Fernando Callo, one of the greatest field technicians out there. The farm’s lots are fragmented and dispersed across the Chiriquí Province, all perched above the beautiful agricultural town of Boquete. This has resulted in Hacienda La Esmeralda having a network of lots, each possessing its own unique environmental conditions. Fernando, a Bolivian and recent graduate of the Tropical Agricultural Research and Higher Education Center (CATIE), began showing me around, explaining to me how each farm harbored Geisha s plants with distinct but recurring morphological variations. He also explained that some of these morphological variants produced differences in their cup quality.
These morphological distinctions included green- and bronze-tipped leaves, where young leaves display either bronze- or green-colored leaves but as they mature, the leaves all turn green in color. Other variations included plants with significant differences in internodal distances, leaf size and shape, and branch structure, as well as plants that were overall shorter in stature and produced higher yields. Fernando explained that the shorter-statured plants along with the plants of different leaf color all produced coffee with differences in cup quality. With no published studies investigating the genetic diversity associated with these morphological variations found within the variety Geisha, I set out to determine if these differences were associated with genetic variation or were simply due to phenotypic plasticity. If the differences in morphology were due to phenotypic plasticity, that would mean the samples shared the same genetic composition, and the morphological differences were a result of plant’s responding (adapting) to changes in the environment.
The plants selected for the study spanned five lots and aimed to encompass the range of morphological differences exhibited by Geisha. With Catuai being the only other variety grown in abundance, samples of this variety were also collected, which would later be used as comparative proxies in the genetic analysis.
In order to examine whether differences existed among the sampled plants, a Double -Digest Restriction-site Associated DNA (ddRAD) library preparation approach was used to detect single nucleotide polymorphisms (SNPs). Detecting a SNP would indicate that, at a specific location within the genome of one of our samples, a single nucleotide differed from another sample. Advances in technology such as DNA sequencing have created amazing opportunities to explore the genetic underpinnings of organisms such as coffee that were inconceivable just years ago. To determine whether or not morphological differences were associated with genetic variation, we would expect to see plants of the same morphological types share the same SNPs.
The Search for Genetic Diversity
So, what were the findings? According to the genetic analysis, it was determined that there was no clear genetic correlation between bronze-tipped and green-tipped leaves. However, this is apparently due to a single dominant gene being responsible for young bronze-tipped leaves, while individuals possessing double recessive alleles produce young green-tipped leaves which explains why our analysis based on assessing SNPs across reduced-representation libraries of each samples genome was unable to determine a distinct correlation based on a single gene.
Furthermore, our analyses indicated no clear genetic correlation between the different morphological types of Geisha. However, even though there was no direct correlation, the results did indicate quite a bit of genetic variation among the Geisha samples. Lastly, when we examined the genetic variation across all of our samples, there was a clear genetic distinction between the Catuai samples and the Geisha samples, which was expected due to Catuai being an offspring of Caturra and Mundo Nuevo, making it a descendant of both Typica and Bourbon. However, there was an exception: One of the shorter-statured Geisha individuals exhibited closer genetic relatedness to the Catuai samples than it did to the Geisha group. Although there were two different samples of the shorter-statured Geisha included in the analysis, the second sample showed more genetic relatedness to the Geisha samples. This suggests that perhaps a specific gene is driving this morphological trait. Being able to study coffee genetics has provided me with a deeper appreciation for this fascinating plant and of how an entire industry depends on the cultivation and value chain of a single species.
For me, the main takeaway from my research is this: This Ethiopian variety was successfully able to cultivate in Latin America – giving it not only a unique genetic makeup, but also a fascinating (wicked!) cupping profile. So not only should we divert resources to create new varieties, but also share genetically diverse varieties from Ethiopia and neighboring regions with other countries around the world. We are living in a unique time where we are faced with these complex issues, but also have access to incredible technology that can help us solve these threats. I do believe our industry will continue to improve upon itself, but that requires continuously challenging the status quo and remaining open to innovation. I would like to see us shift our focus and resources back to what our entire industry depends upon for its existence: plant material that is capable of producing high-quality coffee.
STEPHANIE ALCALA is a recipient of the SCA LEAD Scholarship. She holds a bachelor’s degree in Environmental Science from Whittier College and a master’s degree in Ecology and Evolutionary Biology from the University of Michigan, both of which inform her work as Sustainability Supervisor at Coffee Manufactory.
 There is a lot of controversy over the spelling of this variety. In this piece, I use Geisha to indicate the Panamanian cultivar (I collected my samples in Panama, where the name Geisha is used and is directly associated with Panama) and Gesha to refer to the Ethiopian variety, although perhaps this is still not quite right. According to historical documents, the plant material that was collected in Ethiopia and ultimately made its way to Panama was actually collected near the village of Gorei (also called Bardo or Borde) on the northeastern edge of Geisha Mountain. Maybe we should actually be calling this variety Gorei!
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