Ghost Beans

What can we learn from colour deficiency in beans?

When albinism comes to mind, it probably conjures up an image of a white animal with pink eyes, instead of a plant or even a coffee bean.  Albinism exists within the plant kingdom, however plants with this condition tend to be exceedingly rare.  Albino plants are rare because chlorophyll, the molecule primarily responsible for the green colour in plants, is also used to harvest energy from the sun, making it difficult for the plant to survive in its absence.  Nevertheless, there are many types of albinism in humans, and consequently it is not unreasonable to expect there to be more than one in plants, so what is albinism exactly? 

Albinism occurs when the metabolic pathway responsible for generating the pigment is disrupted.  Imagine a train heading to Greenville, and something happened en route preventing it from arriving.  Much like how people want to know why a train hasn’t arrived, scientists want to know why pigments aren’t formed.

While using a GPS may be the obvious choice for locating a train, in science methods comparable to using a landline are usually initially used.  Connected to the intermediate stations en route these landlines allow one to determine whether the train has been there or not, in other words you are determining the train’s progress relative to the route.  This is essentially what Mazzafera et al. did in 1988 when they analysed for the intermediate products within suspected metabolic pathways, i.e. checking whether the plant had successfully made each molecular predecessor leading to the generation of the pigment, as one would check whether the train had passed each stop. 

Scientists will often also measure the concentration of the intermediates, as elevated levels can be symptomatic of the obstruction in the pathway, not unlike how traffic increases around constrictions (such as construction sites) in the rail or road.  While Carelli and colleagues (1974) found slightly elevated levels of chlorogenic acid in cêra coffee, Mazzafera et al. (1988) did not, keeping the biological origins of green coffee’s pigmentation an unsolved mystery as the topic, dare I say "case", remains dormant.  In other words we called all the intermediate stations on the way to Greenville and when all, except one, reported back that everything was normal, we stopped looking for the train, even though it never arrived.

Naturally, the analysis for the intermediates needs to be repeated with modern technology, but what has yet to be examined are the enzymes.  Enzymes are proteins that can be thought of as the train tracks of the metabolic pathway, transporting, transforming one molecule into another until the final product, in this case a pigment, is formed.  Each enzyme originates from the expression of specific genes, just like how rail lines are built from plans, e.g. schematics and blueprints.  If genes are missing or mutated, the enzyme will either not form or no longer be able to serve their function, permanently disrupting the metabolic pathway, e.g. pigment formation in albinism.  This would be analogous to forgetting to draw in tracks in a blueprint or including a mistake in the schematics making it impossible for a train to traverse to its destination.  If such a mistake were suspected one may go and walk the tracks to verify their existence and to confirm they were properly installed, or one may initially examine the blueprints to confirm the tracks were drawn in correctly.  These actions are analogous to what scientists verify in a lab, but instead of walking the tracks we check for enzyme activity and instead of looking at the blueprints we sequence the genetic code to verify their inclusion of the needed genes, or to identify which genes are missing.  These last activities unfortunately remain outstanding for the bean’s pigment pathways, at least in part due to the technology not existing at the time these pathways were studied.  Nevertheless, cultivating this knowledge could provide invaluable utility to the commercial sector given the pigment’s enduring association with coffee quality.  The association between pigment chemistry and the chemistry behind bean quality will be covered in a separate article.

The need for the instant gratification through commercial success has left many scientific developments underappreciated and their contribution towards innovation often taken for granted.  This makes it completely unsurprising that most people will have never heard of cêra coffee’s contribution towards our understanding of C. arabica genetics and breeding, but this is about to change.

Before venturing into this subject it is important to know that Coffea arabica var. typica was introduced to Brazil around 1719 and remained the only coffee variety on the continent until around 1860 when Coffea arabica var. bourbon was introduced (Herrera and Lambot, 2017).  This has meant that new varieties, such as cêra coffee, that have naturally evolved on the continent, are genetically similar to one another.  While from one perspective narrow genetic pools are a vulnerability, e.g. in the spread of diseases,  from another they bestow new mutants with greater genetic stability.  In a more diversified gene pool genetic stability, required to be considered a cultivar, can only be achieved after six to eight generations of targeted breeding, i.e. if coffee bears fruit only after its third year we are talking about a minimum of 18 to 24 years for the development of a new cultivar – that is if you know what you are doing.  This makes the constellation of events that led to the discovery of cêra coffee fortuitous in and of itself.

At the turn of the 20th century genetics was an emerging field, meaning that the information we now recognize as fact within the scientific and (as an extension) the coffee community had to be mined from the domain based on open questions of the time.  For instance at the time cêra coffee was discovered, scientists were still establishing how many chromosomes coffee actually had, using a microscope (Krug, 1934).  Therefore to come across a visible genetic trait (phenotype), i.e. yellow beans, with which inheritance could be studied was invaluable to the community as most of the scientific techniques we now routinely use for genetics had yet to be invented.  

Carvalho and Krug (1949) carried out breeding experiments by manually fertilizing the flowers in order to control which plants -- cêra coffee or a sibling green variety -- were the parents of the resulting bean.  Conferring the gene with the albino trait with the symbol ce (yellow beans) and that of the non-mutant the designation Ce (green beans).  The outcome of these studies allowed the authors to convert several beliefs at the time into established truths.

The first was to confirm that C. arabica genetics follow Mendelian principles, see figure below, where genes always occur in pairs, one inherited from each parent.  Although genes are inherited from both parents, they were not equally expressed in the beans.  Like blue eyes in humans, ce was determined to be a recessive gene, meaning that the trait even if inherited, may not be visibly expressed in the presence of a more dominant gene, e.g. Ce.  For the trait to emerge the genes have to be inherited from both parents, i.e. the “green” gene cannot be the majority.

The dependence of bean colour on the pollen source also quenched an ongoing debate taking place in duelling journal articles at the time, around whether coffee beans were primarily composed of perisperm or endosperm.  Most people couldn’t care less, but scientists do, since, like in humans, inevitably every organ plays a distinct role within the organism, in this case seed.  So understanding fundamentals give scientists clues regarding the seed’s future behaviour, or at least allows us to make hypotheses that we can test.  While both tissues store nutrients, perisperm evolves from the flower’s ovules, containing exclusively maternal DNA, whereas the endosperm evolves from fertilized tissue, containing both maternal and paternal genetic material.  As the colour of the bean is dependent on the pollen source Carvalho and Krug's (1949) findings irrefutably established the main tissue within coffee beans as endosperm.

Coffee’s chemistry is often reflected in the cup and consequently I was keen to hunt down what cêra coffee tasted like.  Could one pick it out of a line-up in a blind taste test?  This question remains outstanding as while Carvalho and Krug (1949) do mention that including green coffee beans depreciates the value of cêra coffee; nevertheless, it remains unclear whether price was associated with the product’s cup quality or simply its novelty.  From a personal communication with someone who has tasted it, years ago, the taste resembles its green equivalent so closely that differences in cup profile are likely only discernible by professional tasters.