Green Coffee Genetics

 When was the first genome of coffee sequenced? 

HN- In 2009, a canephora plan was first sequenced, and subsequently in 2017 an arabica Gesha was sequenced and then in 2018, a Bourbon was sequenced.  

Our listeners might know what genome sequencing is or why it would be important, could you go into detail about why it is?  

HN- A genome sequence is kind of like a big map where the location of the genes inside of an organism lives. It is really important for breeders to understand where the genes are located that control whether a plant is tall or short, for instance. If you want to target a specific trait in a plant, you will want to know where it lives.    

Today, we will focus on arabica, how many chromosomes does it have? And is the species genetically diverse? How does this help or hurt the sustainability of coffee? 

HN- There are about 138 species in the family, within which canephora, arabica, and robusta are varieties. Arabica is a tetraploid which means it carries 4 copies of the 11 chromosomes that are typical in this family, it has 44 chromosomes. Because of this, it is hard to interbreed arabica with other species. Arabica is more sensitive to heat diseases and pests, but it has higher cup quality. One might want to combine traits from arabica with other species.  

It is estimated that arabica came into existence 10,000 years ago via a random cross between eugenioides and canephora. It has come into existence relatively recently, so it hasn’t had as much time to diversify. The way humans have interacted with it has also caused a smaller genetic pool. Arabica originated in highlands forests in Ethiopia and made its way to Yemen for commercial production and from there was taken on colonial trade routes. It was taken to Europe and tropical colonial outposts and every time it moved someone took a handful of seeds from the population and with this, humans created a genetic bottleneck of genetic diversity as it spread throughout the world. Long-term this has implications for the sustainability of coffee. The more genetic diversity the bigger your toolkit is [to protect the plant, increase quality etc]. It has wonderful traits, but the future of coffee is at risk, due to climate change, pests, and diseases. Arabica has been declining in its dominance, robusta has begun to take over.  

In the short term, we can breed high Arabica performers to yield great results but in the long term will present a challenge and we need to understand that bringing more genetic diversity to the species is important.  

One way this is done is with the Timor Hybrid, probably the most famous example of an interspecific hybrid that we have. It’s a cross between arabica and robusta, but it’s tetraploid so it’s an arabica variety, which is really awesome because as I mentioned before, it’s really wonderful for breeders to be able to exploit. 

What is the difference between simply a tree on a farm, versus a variety? 

HN- To be a variety, a plant must have been developed for certain characteristics and then stabilized so it is distinct and uniform. There is a sort of legal definition of what variety is. [It is] the difference between farmers saving heirloom seeds versus going to a nursery and buying a specific variety. Because it is this specific variety you know you will be getting something that has a particular flavor, it will be a certain height etc because there are quality steps during seed production that guarantee this. Historically, this has been missing from coffee, this quality control step.  

A lot of farmers have populations of trees rather than a stabilized variety being plotted on the land. You might have a field of trees from a selection, but they haven’t been stabilized into a distinct, uniform, replicable variety. 

In other cases, people took original plant populations, did field trials, and said “That particular plant looks amazing, we’re going to take the offspring of that and plant it” and by the time you get out to the sixth or seventh generation of selecting, you’ve got a very uniform plant that will, generation after generation be true to type. You won’t get variation in the field. If you take the seeds and plant them, they’ll look just like the mother plant. That’s a fixed variety. 

What is the difference between breeding and genetically modifying plants? 

HN- Genetic modification is a process or an approach that can be followed in the service of breeding but doesn’t have to be. Breeding is the creation of new genetic material varieties. Genetic modification is one way to do that and the other way, the main way is through farmer selection which is a very informal type of breeding. Most boutique varieties are simply just farmer selections that are picked out because they have been looking for a specific type of traits.  

Farmers are basically helping plants have plant sex. They are making intentional choices about which plants they want to cross or which trees they want to select. They encourage natural selection of the processes by encouraging the traits that they want.  But otherwise, they are not intervening. Gene editing is another option in which is working with an existing plant, and they are removing snippets of genetics. They aren’t adding genetic material in, just editing it out, known often by people as CRISPR. Genetic modification is taking genetic material from other species and putting it into another. 

In coffee, there have been some experiences of genetic editing and modification. As far as we know there is no coffee that is commercially grown that is a result of genetic modification or editing, 

What is the difference between cultivar and variety? 

HN – On the breeding side they can be used interchangeably. A cultivar is when humans create varieties. Varieties are defined, fixed, homogenized, and stable generation after generation. 

CK – That confirms my suspicions that I’ve been using more botanical terms than breeder terms because I often default to “cultivar” when I talk about trees in a field on a farm being raised commercially. 

HN – One of the reasons WCR uses “variety” is because there’s something called “plant variety protection” that is the primary type of intellectual property protection for plant varieties or cultivars. That whole system uses “variety” as the primary term, it’s also by default the term breeders also use.  

What about, these varieties like we see in Colombia – Chiroso, Wush Wush, and even Pink Bourbon – is there any chance for a farmer to obtain proprietary rights on discovering a new variety?  

HN-There could be. If a farmer has selected and stabilized it after many generations, you can apply for plant variety protection. That’s one of the requirements, the seed must grow up to look like its mother and it takes generations of selection to achieve that. 

But you can’t just find a plant on your farm and get plant variety protection if it hasn’t been stabilized. Coffee is not very formalized in that way, you don’t have to have legal ownership of a thing to create value for a product. 

For example, if you’re a farmer and you buy Gesha seeds, it’s possible you’re getting offspring that’s traceable to the reference sample at CATIE, it’s possible you’re getting a sample that’s traceable back to one of the other selections from that same region in Ethiopia, and it’s also possible you’re getting something completely unrelated that just looked similar to Gesha. It’s also possible you’re getting something totally fraudulent because Gesha is worth so much! 

On the one hand, that’s problematic for a farmer who thinks they’re getting something capable of very high cup quality and it’s not. On the other hand, if it’s not a direct descendent of the CATIE reference sample but it still tastes good and you’re able to market it and make a good living from it, do we care? 

There’s one other thing about Gesha that’s so important. Those original seeds were sent to a gene bank in the 1950s and they just sat there for thirty years until there was a specialty market that a new opportunity opened up and there was a place for that plant. It really matters how we protect and preserve what diversity we do have because we don’t know what the future holds. 

CK– Another interesting story that cultivars can tell is the challenges in developing new varieties. One of the examples that demonstrates that is the story of Ruiru 11 and Batian in Kenya. Ruiru is such a complex cultivar. They have a mother and father plants that are their own hybrids. The father plant is an enormous mash of every genetic material they could get their hands on, SL 28, local Bourbon, K7, Sudan Rume, and the mother plant is a stature Catimor. Itself is a hybrid of a couple of different Catimors.  

And then they had to hand pollinate these father plants to the mother plant to get the seeds. This takes so much time to do all of this and they finally get this relatively stable population into the fields and the specialty coffee cuppers all reject it and hate it because it doesn’t taste the way they want it to. Everyone has to go back into the lab and reverse engineer this thing again to create, essentially, Batian. They take it apart and put it back together. And Batian’s a much tastier variety, in my opinion, but the timeframe that this took was probably about 30 years.  

And the primary reason it was created was to increase resistance and yields but they did pay close attention to integrating varieties that were supposed to be tasty like Sudan Rume, and this just didn’t hit when it was released.  

HN- This is a great point, and it goes back to the demand signal. The breeding process is a product development process. If you are a roaster developing a new blend, you are developing to a spec to some degree. When it comes to breeding those who are most often making those decisions are breeders that work in national coffee research institutions, and they are either publicly funded or through the government.  

Their primary responsibility is to the farmer in their country. They are breeding to what farmers are making demands for.  Especially in countries where coffee exports are a significant amount of the economy, they want to make sure that there is a market that they are selling into. But their job is not to go talk to a coffee buyer. So, there is a disconnect there. And then there is the other problem of the timeline. In the 90s when Ruiru was developed, there wasn’t a specialty market in the same way there is now. And even if it hit the market in 91, it will take 10-15 years at least for farmers to pick it up at scale.  

Over the course of the time period between when it was released and when it became available commercially is a mix-match that is hard to solve. The other way to solve the problem is to connect breeders to buyers, and in some ways, this is why the world coffee research center exists. You should breed for all of your end users but first and foremost for farmers and then buyers.   

CK-I look at the story of Ruiru as a guy who loves bright, vibrant Kenyan coffees, and I see it as kind of a failure. But at scale, varieties like Castillo, like Ruiru, that were rejected by picky tasters are still kind of successes when you pull back to the big picture because they did what they set out to do. They improved yields, which is good for farmer profits in most cases, and they improved resistance. So, how much does buyer interest matter?  

HN- If you look at farmer demand in Kenya right now, it is still primarily for Ruiru. Even though Batian performs better in the cup, it is agronomically very similar in performance to Ruiru. But, farmer preference is still primarily for Ruiru. There could be a lot of reasons it is this way, like the lack of marketing around Batian.  There are a lot of reasons why farmer demand might be different than what you think it should be. From the perspective of farmers, it is not a failure at all. Ruiru has the highest demand to this day, the Kenyan Coffee Research Institute cannot keep up with the demand for this variety.  

Within this concept of quality, what does quality mean? Is there some objective meaning of quality or is it audience dependent? From a farmer’s perspective, what quality means is they are not going to lose 30% of their production due to CBD (coffee berry disease), maybe they’ll have 10% better yields in a better year and I will still be able to sell it to someone. If quality premiums are so high that they offset those yield issues, then great. But if the cup quality demand signal is not high enough to offset those agronomic performance issues, then it’s not worth it. 

You don’t breed for the fun of it. You breed to serve the needs of your end users. 

Can you describe how the WCR Arabica and Robusta Coffee Varieties Poster came about and what you hope people will gain from it? 

HN- This year we updated our variety catalog and added Robusta. We worked with our web development team to create a visual with a science feel, to reflect that it’s complied knowledge from breeding programs and that it’s credible. And they did such a great job, and because it aligned with the work we did for the catalog, it came together very nicely. 

Very similar to the flavor wheel, the end goal is just to appreciate the profusion of what we do have and the work that has been done, and it’s a nice visual record of all the work we have left to do. 

Royal’s cultivar project was recently released too. Can you talk about what it’s about and what inspired the project? 

CK- It’s funny because they coincided so closely, neither of us was in contact with each other until after they were released! 

One of the things that I wanted to convey was a sense of narrative, of place and time, that’s often lacking from the conversation around where we get the types of coffee we celebrate. Of course, the WCR Variety Catalogue forms a big informational bank underpinning the intel that I was using to trace history and geography. 

It evolved into one big timeline, the History and Geography of Arabica Cultivars, and a second series of maps that tells stories that hadn’t been clearly visualized before about the origins of arabica, and the distribution of varieties like Typica and Bourbon that form the historical context behind the research. 

For the full conversation check out the episode here 

Download WCR’s new poster here.  

Download Royal’s new cultivars poster here