World Coffee Research at Work

By Emma Sage, Coffee Science Manager, Specialty Coffee Association of America

Update on the South Sudan C. arabica Conservation Project 

Back in April of 2012, World Coffee Research led an expedition trip to South Sudan, where we hunted for and collected samples from wild C. arabica accessions. This was a multi-purpose trip, partially to train university staff and students at origin as well as assess the health and viability of the unique and exciting wild coffee growing in the long forgotten forests of South Sudan.

The long-term vision for the project is oriented around assessing the populations and perhaps one day growing native coffee in the region, or even cultivating these lines to be grown in different origin countries. To begin that long process, we collected plant samples in order to better understand the levels of genetic diversity represented in these populations. Based on this information, recommendations could be made as to the most appropriate way to conserve this invaluable genetic diversity.

Dr. Sarada Krishnan was one of the scientists who was a part of the South Sudan expedition crew and led the charge of collecting accessions for genetic analysis. She noted the location and environment of each population, recorded the status of the tree and tagged each one for later visits. She collected leaves from each tree in order to understand how they were related and how much genetic diversity exists within and between populations. Dr. Krishnan is currently the Director of Horticulture and Center for Global Initiatives at Denver Botanic Gardens ( However, it turns out that she also has a long history with coffee. Her family, including her father and uncles, owned coffee plantations in the state of Kerala, India. In graduate school she gravitated towards coffee after becoming interested in the flora of Madagascar. Some time ago, her father sold his plantation. Now, she is continuing the family tradition with her own, a recent purchase of two farms and partial ownership of another in the Jamaica Blue Mountain district, and a coffee distribution company in the United States named “Diversity Coffee”. She hopes in the future to devote twenty acres to scientific research.

She became interested in World Coffee Research (WCR) when it began to be discussed within the coffee industry, and has participated actively since. Her ties to and professional experience with international tropical agricultural development are strong, and today she is responsible for developing and leading global initiatives at the Denver Botanic Gardens.

Conservation at a Botanic Garden

You may wonder what the purpose of a Botanic Garden is, other than to please a botany-geek on a weekend stroll. In fact, botanic gardens serve many purposes within their local communities while acting as international safeguards of biodiversity. The Denver Botanic Gardens, for example, is committed to genetic conservation, supporting many programs that focus on this topic. They focus on species endemic to the Rocky Mountains and similar habitats, but also participate in global partnerships and house over 9,000 species on-site, keeping track of each of their 36,000+ plants with a unique accession tracking system (each plant with its own bar code). They also participate in a worldwide seed sharing program with other botanic gardens, which allows them to have access to many diverse and unusual plants from different regions while providing the seed from some of their locally endemic species.

The Denver Botanic Gardens also keeps a large herbarium. A herbarium is a catalogue of actual plant samples, dried, pressed in paper, labeled, and preserved for the long-term, sometimes hundreds of years. Why do we need herbariums, in the age of genetic mapping and whole genome-cracking? Initially, they were created to house the many plants that botanic gardens could not keep (due to space or incompatible growing environments) in their live collections. It turns out, there is some information you can never get from genetics. A herbarium allows researchers to keep a historic record of plant phenotypes, or to see morphology change over a historic or geographic gradient. Today, we are thankful for the existence of herbariums so we can understand historical range and phenology information, which can be very helpful when trying to understand modern problems, like climate change. These plant samples are preserved appropriately so that they potentially can also be used to gain historic genetic information. Around the world today, almost all known species are represented in herbaria, catalogued and safe for whenever we are ready to investigate them.

An Update on WCR South Sudan Research

What happened to the plant samples we collected on the WCR South Sudan expedition? We collected them to catalogue what genetic variation existed in those wild C. arabica plants. Dr. Krishnan got her samples back to the lab in Denver, isolated the genetic material of these wild coffee plants, and then she worked with a lab in Nevada to run a set of molecular markers through the DNA of these samples in order to determine how similar or different they are from each other. These ‘markers’ are really small pieces of the DNA code that have been identified by researchers to exist in coffee. The places that the markers fall on the genome allow researchers to estimate the amount of differences between individuals or populations.

When researchers learn where the markers lie and the distances between them, they can input this information into computer programs that helps them understand the data. In the computer program, they are driving the analysis. Scientists have to choose the populations, which means that they must group the plants in the best, most logical way that they can. This can be easy, if large distances separate the population, but this is not always the case. As on our South Sudanese trip, we collected plant samples from a few distinct natural areas as well as a few ‘garden style’ plots cultivated in the local villages. Dr. Krishnan found the best possible population groupings for our collections to proceed with the analysis.

After analysis of the genetic results, Dr. Krishnan, along with the other scientists involved in the project, has determined that the wild C. arabica plants we found in South Sudan had a fair amount of overall genetic diversity, comparable to the amount of diversity documented in other wild arabica populations. One particular garden of plants near a small village displayed a high amount of genetic variation, encompassing almost all of the regional diversity in a small plot. This could be indicative of what was present in the original undisturbed forests when the plants were brought to villages to be utilized locally. This is helpful information to have when the WCR team returns to South Sudan, with the possibility of establishing a field genebank to preserve the existing wild South Sudanese C. arabica germplasm. With limited land and water resources, understanding the genetic diversity of potential specimens is very important so that the maximum genetic diversity can be conserved without including redundant genotypes in a genebank. What we have to remember is that we do not yet exactly know how these plants are related to any cultivar or wild variety. This could be included in the further analysis of these samples.

On the other hand, we collected samples from a few trees cultivated near a different village that told a very different genetic story. Dr. Krishnan found them to be the most different genetically than the forest populations. This only made sense after we remembered the particular story of coffee that we had heard in that village. The woman who had originally planted them (in the 1940’s) told us a story of taking the seeds from a ‘British plantation’ of coffee. Perhaps some missionary or other British colonizer had brought a small amount of coffee with them in the past to grow in South Sudan. Perhaps someone else had brought seeds from neighboring Ethiopia. We can only compare them to plants in other areas to see where they might have originated. It will likely remain an interesting mystery.

It is the sobering truth that today the specialty coffee industry does not have a comprehensive picture of the genetic resources that might one day save our differentiated market. As this work from South Sudan continues and other germplasm collection missions are initiated by World Coffee Research, we will slowly learn more about the exact picture surrounding wild C. arabica genetics. What will be critical after wild genotypes are catalogued is moving forward to pursue phenotypes in order to reveal what, if any, advantageous traits they may possess that the industry can use for breeding. In the end, if we want more high quality, flavorful and differentiated specialty coffee, we need to grow out these wild plants to observe and taste them. The only way that we will make progress and assure a safe supply of specialty coffee is breeding coffee with future climates in mind. It turns out we are already losing wild C. arabica genotypes due to altered land-use and climate change and will likely continue to each year we do not act. What are we waiting for? Get your company involved in WCR to support this vital effort.

If you are interested in learning more about genetic diversity, and why it is so important in coffee, check our recent article in the Coffee Science section of the SCAA Digital Chronicle.

Emma Sage is the SCAA Coffee Science Manager. Before moving into the coffee industry, she completed degrees in ecology and botany, and dabbled in the wine industry. She enjoys learning all there is to know about the science of coffee (and more importantly, sharing it with you).