An Introduction to Coffea Genetics

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

In an era where wild coffee is in actual imminent danger, the industry is increasingly interested in keeping up with the many scientific advances in coffee. In order to follow the current news, research, and events related to the genetics of Coffea arabica, it helps to first understand some basic biological vocabulary and concepts on this complex topic. Below are some key points to get you started in this learning process. The Specialty Coffee Association of America (SCAA) will continue to follow this important topic though updates and exciting new programming at the upcoming SCAA Symposium in April 2013.

Genes Determine Everything

In nature, an organism (be it plant, animal, or fungi) and its reaction to its external environment is only possible due to its particular genetics. Genes coding for specific characteristics are located on specific locations (loci) on our chromosomes, and are made up of inherited alleles (bits of DNA on a loci that eventually may code for a trait). Each organism inherits alleles that make up a particular code from whatever method its species uses to reproduce, making each individual organism’s unique genotype. This code dictates the formation of amino acids, the building blocks of life, and exists within each cell in that organism.  These amino acids (as coded by genes) are responsible for size, shape, physiological processes, reproductive characteristics, tolerance of environmental extremes, preferred habitat, dispersal and colonizing ability, the timing of seasonal events (phenology), disease resistance, and all other traits. New mutations and mishaps in genetic coding can lead to some unique genetic differences, most of the time these are non-essential and insignificant. It is only in a rare case that an accidental mutation in DNA is a very advantageous one. In the end, each individual genetic code is responsible for the phenotype of that organism, or the observable presentation of the organism.

Genetic Diversity is Critically Important

For any species or population thereof, the diversity of genes is the key to preserving a species. Having lots of different genes among a population increases the probability that one or more individuals will have the necessary genes to adapt to and excel under challenges in the environment. The assumption is that these individuals would therefore be able to reproduce and pass on their genetic advantage to new individuals (think, survival of the fittest). A population made up of one clone (with exactly the same genetics) would be helpless to survive many threats. The wider variety of genes present, the more likely a species or population would be able to adapt to what is thrown at it. Today, there is an urgent need for adaptation to climate change or acclimation to extreme environmental and climatic events.

Unfortunately, there is no way to look around in the forest and guess how much genetic diversity lies within a particular population. Despite the fact that one may notice a large variability in the phenotypes of a plant, this does not tell the whole story of the genomic diversity. Also, if you document diversity in one population or geographic area, there is no way to extrapolate to a larger area. So, there is no way to predict what genetic diversity may lie in a particular region. It is impossible to look back into time and see what forces, including but not limited to human, environmental, and intra-species (such as an insect outbreak, or competition with another similar plant) stimuli that may or may not have given a particular genetic trait advantages. In the end, all we can do is try to catch up the scientific research on all wild C. arabica before more is lost.

C. arabica is what I like to call a ‘sensitive’ plant due to its very specific environmental requirements. It is a high altitude plant in the tropics due to its specific temperature requirements, but we know that as climate change progresses it will need to adapt to warmer regions in order to thrive in the future. This is one of the key reasons why we want to preserve all of the possible genetic variation we can within wild arabica. As of today we do not know in what variety we may find a gene for heat-tolerance (if it exists), but we know how costly it would be to accidentally lose it. In reality, this much-sought-after trait may exist in another related Coffea species; perhaps a parent or a distant relative of arabica could one day be crossed in order to create such a trait. Either way, we don’t know enough to count anything out. We know that other species can be crossed with C. arabica, but breeding in this way can take 25-30 years to create a stable new variety.

C. arabica Has Many Disadvantages in Today’s Changing World

In coffee, most traditional C. arabica cultivars and most of the coffees we drink today have been bred from a select base of a few plants transported from Ethiopia via Yemen long ago. We have heard tales of these arabica forefathers crossing the high seas and making long arduous journeys across the globe. Those tales of botanical glory may or may not have real merit, but what we do know is that most of the arabica we drink today was historically the result of either plants bred in Martinique or Réunion (once Bourbon) Islands, and these lines of coffee have been spread across the globe and inbred ever since. This sort of long-term self fertilization leads to inbreeding depression and loss of genetic diversity.

When we hear the word ‘inbreeding’, our human perspective tends to kick in and we immediately imagine our few and unfortunate examples of this within our own species. Lucky for coffee, plants have a different perspective on reproduction; most plants having both male and female organs, and can self-fertilize. Yes, inbreeding still has a negative connotation in plant science. Some traits shown to be affected by inbreeding depression include pollen quantity, amount of seed, germination rate, growth rate and competitive ability (Keller and Waller, 2002). It is not ideal for any organism. Many plants even have evolved mechanisms to prevent self-fertilization (inbreeding). However, many plants, depending on the makeup of their alleles, can self-fertilize for generations without any immediate problem. Throughout all life forms, the long-term consequence of inbreeding is that no new and possibly helpful genetic codes enter the gene pool. There is also the possibility of deleterious mutations, but we see these less in plants because in most cases the embryos will self-regulate and not grow when such problems occur at a cellular level. Over time, when plants self-fertilize they grow more homogonous, or similar.  Genetic erosion refers to the loss of particular genetics in a species due to population separation or the inability of those plants to fertilize each other. In coffee, you can imagine this is exactly what has happened. The few ‘coffee forefathers’ have been separated from the wild gene pool (in East Africa) for hundreds of years and perhaps as many generations. We already have evidence that we are losing indigenous C. arabica in the field, and have predicted that this phenomenon will only continue (Davis et al., 2012).

In nature, most of the time, a population or species will slowly adapt to external stimuli (like changing weather, pest or disease outbreaks, etc…) via natural selection of genotypes (organism with the particularly advantageous genetic code) able to best deal with that stimuli. However, that sort of shift in the genetics of a plant population requires many generations, and with coffee, this can take decades or longer. More often in arabica, population diversity will stay the same or be lowered due to self-fertilization without much cross-breeding. It is estimated that ~90% of arabica is self-fertilized. While Ethiopian collections do exist around the globe per collection expeditions in the mid 1900s, these plants have since been used to cross and create new varieties, the recent wave of these being known colloquially in the industry as the ‘F1 hybrids’.

We Can Tackle this Problem

What can we do about this lack of genetic diversity in coffee? How can we make sure not to lose more of our precious genetic resources? To address this question we have to know what we are working with. There is really no other way to understand what genetic variation may be lost but to first attempt to document that existing wild variation. In fact, that is exactly what World Coffee Research (WCR) was attempting to do on the South Sudan expedition. If you are interested in following the new results from that project, check out the new companion article to this, which will be available shortly in the SCAA Chronicle magazine. This was just the first step in a series of germplasm conservation projects in WCRs future. As WCR and other groups move forward with documenting and preserving what we have for wild genetic resources, we will have the ability to begin investigating what advantages or helpful traits these wild genotypes and phenotypes hold.

Another way we can move forward is to arm ourselves with information. The truth is, most of us are not coffee geneticists and breeders, but with knowledge of the important fundamentals of their work we can help spread the word and build momentum for this effort. If you would like to elevate your education on this topic to the next level, consider attending this year’s Symposium and Exposition, to be held in Boston April 10-11 and April 11-14, 2013, respectively. During Symposium, we will be presenting an in-depth session ‘Coffea Genetics: Unlocking the Possibilities’ in which we will be discussing arabica genetic restriction, the problems this poses to the specialty coffee industry, and projects underway to address this. At the Exposition, we will be offering a special Science Seminar on this topic within our Skill building Workshops. We hope you will join us in acknowledging this critical issue and consider joining us for these informative opportunities.