Unlike his colleagues at the beginning of the 20th century, Ernest S. Salmon, a professor at Wye College outside of London, was certain that American hop varieties belonged to one distinct species and all European varieties to another. “All our books tell us that the varieties of hops cultivated over the world have all arisen from the one species, Humulus lupulus,” he wrote in 1917. “I am convinced that this is not the case.”
Salmon had taken charge of a nascent hop breeding program at Wye in 1906. Pointing to Gregor Mendel’s principles of heredity, he was certain that resin content and aroma were what Mendel called “fixed characters”—that is, they were innate to a given hop variety, rather than the region in which it was grown. His goal was to create hybrid, transatlantic hop strains that would feature the aroma profile British brewers preferred, but with the higher resin content found in American hops.
Professor W.T. Macoun, Dominion Horticulturist for Canada, provided the North American hop that Salmon needed. He collected it in the town of Morden, south of Winnipeg in Manitoba. Hops grew wild along a creek that flowed through the town. “Old residents in this town assure me that there has never been an introduction of cultivated hops in the district,” Macoun wrote. The hops were transplanted to town lots to cover unsightly places.
Salmon planted the hop, which he labeled BB1, in 1917 in the nursery at Wye, where it was pollinated by an unknown English male hop. He harvested the seeds in the fall of 1918, raised hundreds of BB1’s children in a greenhouse beginning in 1919, and planted the most promising of them in the nursery in 1922. He chose to name and release two of them after more than a decade of brewing trials.
Neither brewers nor farmers in the United Kingdom embraced those first two varieties, Brewer’s Gold and Bullion, but there was no going back. When Salmon began at Wye College, hops contained 4% alpha acids on average, and 6% at the most. Breeders have since created varieties with cones that contain more than 20% alpha acids, almost always using cultivars that lead back to Salmon’s two breeds. Relatively recently, the definition of what constitutes a pleasant hoppy flavor and aroma has also broadened to include fruity and exotic characteristics. Popular varieties such as Citra, Mosaic, Centennial, and Sorachi Ace are all, to varying degrees, offsprings of Brewer’s Gold.
Ultimately, Salmon’s assertion that hops from America are different than those from England or the Continent proved correct, the scientific consensus now being that the lineages are separated by more than a million years of evolution. More recently, chemical and molecular genetic analysis has established the higher diversity of American wild hops compared to European wild hops.
A century ago, Salmon needed luck to locate a wild hop that proved his thesis was correct. But today, hop scientists have tools to establish if a plant found growing on its own in Upstate New York or the American Southwest is native, is one that originated from across the Atlantic, or is perhaps an American wild/European hybrid. The use of next generation sequencing (NGS) in particular has begun to push hop breeding, and therefore hops, further. And it isn’t just hops. That technology will also change two other essential beer ingredients: yeast and barley.
“[Sequencing] helps us understand where different yeast strains (or hop or malt varieties) come from and how they are related; and perhaps, more importantly, it helps us breed better varieties that combine the best properties of parental varieties and strains,” says Kevin Verstrepen, a yeast geneticist at the Catholic University of Leuven and the Flanders Institute for Biotechnology.
Next generation sequencing technologies first became available in the aughts, replacing a first generation that emerged in 1977. They are much faster, more accurate, and, as a result, more cost-efficient. “Today … just one student can do all the work that was accomplished in genomics theses during the 1980s and 1990s in less than a second, at a tiny fraction of the cost,” write Rob DeSalle and Ian Tattersall in their 2019 book, “A Natural History of Beer.”
Sequencing begins with ordering the building blocks called nucleotide bases (there are four kinds) within a small piece, or strand, of DNA. The fragments are aligned based on overlapping portions to assemble the sequences of larger regions of DNA and, eventually, entire chromosomes. A genome is the sum total of an organism’s DNA. The Sanger method, developed in the 1970s by British biochemist Frederick Sanger, sequences one single DNA fragment at a time. NGS platforms are able to sequence millions of fragments simultaneously.
Scientists first sequenced the species of yeast used by brewers and bakers in 1996, determining the order of 12,057,500 chemical subunits. This was a step toward sequencing the human genome, a project which took more than a decade and cost a reported $3 billion overall (sequencing the first human genome itself cost about $1 billion). Today, labs charge between $300 and $1,500 for the same work. Sequencing has even become cheap enough that in 2012, Illumina, a San Diego biotechnology company located not far from White Labs, sequenced 96 strains of yeast free of charge in order to test new NGS machinery.
Not long after, Troels Prahl, head of research and development at White Labs, learned a Belgian group headed by Verstrepen was also exploring the phenotypic landscape of yeast—that is, linking what was determined genetically with observable traits. Together the two teams sequenced the genomes of 157 yeast strains, most of them used by brewers. Published in 2016, “Domestication and Divergence of Saccharomyces cerevisiae Beer Yeasts” reconstructs the history of how yeast evolved over centuries, draws a family tree, and provides a map for breeding and strain development in the future.
“[Sequencing] helps us understand where different yeast strains (or hop or malt varieties) come from and how they are related; and perhaps, more importantly, it helps us breed better varieties that combine the best properties of parental varieties and strains.”
Plant genomes are most often larger than the human genome because they have many more repetitive elements. Between 2000 and 2008, scientists sequenced the genomes of only 10 plants. Discovering markers most often called SNPs (short for single-nucleotide polymorphism) first found in the human genome made it easier to draw genetic maps and to begin to associate markers with traits. Reference genomes for barley (Hordeum vulgare L.) and hops (Humulus lupulus) are included among the more than 600 plant genomes that have since been assembled.
It took 77 scientists from 10 countries 10 years to piece together the ordered sequence of the barley genome, published in 2017. Researchers quickly discovered that the gene for alpha-amylase, the enzyme that breaks down the starch in malted barley into sugar, repeats multiple times. “That really adds to our knowledge on how to improve the levels of that. With multiple copies we can choose which ones we want to increase,” Gary Hanning, director of global barley research for Anheuser-Busch InBev, said when the research was published.
The first reported identification of molecular markers in hops was in 1995. Four years later, a rather modest 224 had been discovered. Today, more than one million SNPs have been found across the thousands of hop cultivars worldwide. However, matching markers and desirable traits—whether they are for disease resistance or unique flavors—may take longer for some characteristics than others.
“We haven’t got there yet. It’s a new frontier,” says Paul Matthews, who works as a senior research scientist at Hopsteiner, an international hop trading company with breeding programs in the United States and Germany. “We’re still in proof of concept.”
Today, breeders—whether they specialize in hops, peas, or chickens—ask themselves the same question that Gregor Mendel did more than 150 years ago: “Can I predict how a trait is passed on to the next generation?” Mendel’s principles of inheritance often serve as a guide. Before Mendel’s work became widely accepted, people believed that traits occur in offspring as a result of a blend of parental characteristics. He established that the “fixed characters” Salmon referred to (now understood to be genes) could be dominant or recessive.
The process of cross-pollinating varieties to create seeds is different for barley than hops, but the steps to develop new varieties follow similar, slow paths. Breeders need to be thinking decades ahead. “You have to have a lot of aroma types ready, but you must wait for brewers to come to you with their ideas,” says Anton Lutz, the breeder at Germany Hop Research Center. “Then you can tell them, ‘I have it.’”
The following timeline at North Dakota State University is typical for barley:
Year 1: Crosses are made and agronomic characteristics of progeny are evaluated.
Year 2: Selected lines are grown and tested, including for disease-resistance and brewing qualities.
Years 3-5: Lines advance through three sets of field trials and are sent to labs for quality analysis and disease resistance. Lines that do well are sent to the American Malting Barley Association for their first pilot scale evaluation in Year 5.
Years 6-7: Lines are evaluated in field trials in up to 10 locations. The best are submitted to the American Malting Barley Association (AMBA) for plant scale testing in Year 7.
Years 8-10: Plant scale testing continues, with more field trials. Based on acceptance by AMBA members, a line is given a varietal name and released to farmers.
Kevin P. Smith at the University of Minnesota explains that finding new genetic markers may not just speed up this laborious process, but could also expand the amount of change possible within a particular time frame. For instance, his lab could use a genetic sample taken after Year 2 to predict the malt extract of a potential variety. “We would have had to wait until Year 4 or 5 before [measuring it],” he says. In addition, testing a sample for markers costs $20, compared to $200 to fully analyze a barley sample.
Hop breeding is also just as slow. John Henning, USDA research geneticist in Oregon, made the cross in 2000 that resulted in a hop variety he named Triumph; it wasn’t released to farmers until nearly two decades later, in 2019.
Generally, the USDA suggests would-be breeders follow this timeline:
Year 0: Make crosses.
Year 1: Seedlings are grown in the greenhouse and selected for powdery mildew resistance.
Years 2-4: Plants are assessed in the field, evaluated and harvested, then chemically analyzed.
Years 5-8: Selections are grown on multi-hill plots. Evaluation continues and complete data is collected. Samples are sent to breweries for pilot brews. Breweries select favorites.
Years 9-onwards: Selections are grown in commercial farm plots. Hops are tested at multiple breweries. Brewers accept or reject the hop.
As with barley, finding genetic markers for desirable traits in hops may shorten the breeding process, and increase the numbers of hop plants that can be evaluated. However, unlike barley, hops introduce some added genetic complexities.
Important research funded by Hopsteiner has shed light on why and when hops may not follow Mendel’s principles. To put it simply, hops do not always reproduce as would be expected. Doing research at Florida State University, Katherine Easterling, who has since joined Matthews’ Hopsteiner team, observed that during sexual reproduction, chromosomes that should have been paired in twos with donut-like shapes were linked together in long chains and rings instead.
“Today … just one student can do all the work that was accomplished in genomics theses during the 1980s and 1990s in less than a second, at a tiny fraction of the cost.”
“This observation means that there is a sequence similarity that extends beyond the parental chromosome pairs,” she says. “Although some plants and animals have been reported to demonstrate that type of chromosomal behavior, it’s considered very abnormal, and the offspring from such strange behavior can be less viable or show unexpected traits.” Jargon aside, that means that, no matter which desirable characteristics they might exhibit, certain hop varieties may still not be suitable for breeding.
“Yes, that is a problem,” says Matthews. “Some genotypes are more normal. Some are crazy. Not every variety is the same. Using technology we can look for hops a little more normal. This could change breeding forever.”
As for yeast, breeders can produce new strains in a matter of days instead of years, but they present a different challenge. When reproducing sexually, yeast adhere to Mendel’s laws. However, charting the evolution of beer yeasts revealed that 40% of strains are inclined not to reproduce sexually, and others have dramatically reduced fertility. Most often they divide through asexual budding. In Verstrepen’s lab, “We have really optimized the conditions so that strains that have very poor sexual cycles can still be persuaded to breed; it is all about tweaking the environment.”
Using a robot, the lab may generate hundreds of new strains a day. “We can create millions of crosses, but measuring which are the best ones takes time and effort. And, breeding is a numbers game. Of course, we have gotten very good at selecting the right parents to start the breeding; but even with the best parents, making more crosses increases the chances of finding one super yeast,” Verstrepen says.
For some properties, like fermentation speed, scientists use “micro-droplets”: tiny drops of wort that are barely larger than a yeast cell. “Each droplet gets one yeast cell, and we monitor how quickly that cell can consume the sugars. That way, we can test thousands of yeasts instead of hundreds when we do it using the normal lab equipment,” Verstrepen notes.
Shortly before the results of the yeast sequencing project were published, White Labs founder Chris White made it clear how important the research is.
“Without unlocking the genetic information we are still thinking like the 1860s,” he told an audience of homebrewers in Baltimore. He showed a slide with Saccharomyces cerevisiae—Ale yeast—“top fermenting” on one side, and Saccharomyces pastorianus—Lager yeast—“bottom fermenting” on the other. “I’m glad you’re coming to this talk because we are kind of on the brink. This is the old way of talking about this. There is going to be a new way in the next few years.”
Discussing why modern commercial tomatoes aren’t as tasty as heirloom varieties, Bob Holmes, author of “Flavor: The Science of Our Most Neglected Sense,” puts the blame on breeding practices. “We know that breeders of many crops have focused for decades on traits like disease resistance; yield; appearance; uniform size; and ease of packing, shipping, and processing … Their focus hasn’t been on flavor,” he writes.
Now armed with a map of the barley genome, breeders don’t have to focus on one trait at the possible expense of another. “Nothing has been done to breed flavor out,” says Scott Heisel, technical director at the American Malting Barley Association.
In the past, conventional wisdom held that malt flavor is created during malting. Breeders focused on agronomic traits and attributes, such as extract and amount of proteins. But recent experiments at Oregon State University now suggests variety also influences flavor. “We started this project with a question: Are there are novel flavors in barley that carry through malting and brewing and into beer? This is a revolutionary idea in the brewing world. We found that the answer is yes,” Pat Hayes said when the results of the OSU study were published.
“We started this project with a question: Are there are novel flavors in barley that carry through malting and brewing and into beer? This is a revolutionary idea in the brewing world. We found that the answer is yes.”
Barley World, Hayes’ research group, crossbred Golden Promise, a British barley strain, with a variety bred at OSU, Full Pint. Beers were brewed, then tasted by trained panelists, with the original varieties and also hundreds of their offspring.
“The progeny are showing all possible combinations of those traits,” Hayes said. “And, since we had been doing DNA fingerprinting on these progeny, we can assign certain regions of the barley genome as being responsible for these flavors. We also found that there were some differences based on where the barley was grown, but the genetic effect was larger than the environment.”
Where the barley is grown is important, obviously, to craft maltsters and brewers committed to making local beer with locally grown grain. Nonetheless, the discovery of molecular markers has made “flavor” a larger part of the conversation, and one that will likely inform future breeding efforts. “We’ve really just started to think about how we can tackle flavor,” says Kevin Smith in Minnesota. “Are there certain things we can quantify?”
Next generation sequencing facilitates such change, but it also helps assure the future of the crops that are used to make beer. Breeders are already using markers to select for disease resistance. If they can find similar markers related to yield, they may create varieties of barley and hops that are more environmentally sustainable.
Four years ago, Hopsteiner began sending teams to the American Southwest and the countries of Georgia and Kazakhstan to collect wild hops. Crop scientists around the world are working to preserve genetic diversity that could help crops survive climate change, and those at Hopsteiner have found varieties in the Southwest that are more drought-resistant. It turns out those hops may also have unique flavors. Sequencing should help breeders identify markers for multiple traits.
Hop oil contains hundreds—potentially up to 1,000—compounds that contribute to aroma and flavor, some of which, like linalool and geraniol, are prominent in certain trendy, New World aroma varieties. Hopsteiner has now identified markers for some of those compounds. That could speed up the breeding process by two or three years, Matthews says. “You will see that in the near future. I can promise you that. I just can’t tell you when.”
Despite these advances, not everything has changed for the breeders of beer’s key ingredients—at least not yet. Many still make crosses much as Salmon did more than 100 years ago. “Absolutely the same,” says Peter Darby, who took over the breeding program at Wye College in 1981. “Choosing the mother and father: all the creativity is in that stage.”
Words by Stan HieronymusIllustrations by Ben Chalapek Language
