Courtesy of UCR Close Laboratory

After 10 years of research, 77 scientists from across the world, including two UC Riverside professors, published a reference genome assembly for barley in Nature science journal on Thursday, April 27.   

With the genome of barley now sequenced, scientists are able to gain a better understanding of similar grains, such as rice, wheat, rye and oats since they now know the order of barley’s chromosomes. There is also the possibility that with a better understanding of the barley, breweries can make better beers and distilleries can make better single malt scotches. When barley is malted, it gives the beer its color and body and it also plays an important role in the fermentation process. The only ingredients in single malt scotch is water and the malted barley.

Barley is also used in other food products that do not involve alcohol, some examples being various breakfast cereals and flour.

In order to perform the study, the researchers began by shotgun sequencing, a form of sequencing used for long strands of DNA, the bacterial artificial chromosomes (BAC), which is used when there are long strands of DNA, due to the barley’s genome being nearly twice as long as the human genome and around 80 percent of the sequences that make up the genome being repetitive.

During the second step, the researchers used the BACs to put the genome into the correct sequence. It was during this step that the researchers discovered overlapping between adjacent clones which was then validated in order to construct scaffolds made of merged assemblies of individual BACs. Finally, the researchers utilized the three-dimensional proximity information to order and orient the BAC-based scaffolds. By the end of the study the barley genome consisted of 6,357 scaffolds that were made from the merged assemblies of individual BACs.

Professor and Associate Chair of Computer Science and Engineering Stefano Lonardi, who was in charge of helping assemble each BAC and verifying the results, described the process as reassembling a book that has been torn apart. The BACs represent a single chapter and all of the tools used by the researchers, the scaffolds and three-dimensional proximity information, are meant to help put each chapter back into place in the book.

“Instead of trying to assemble this huge, massive book, we assemble sections of it,” Lonardi explained, “Each fragment could overlap with millions of other fragments and if you focus on one chapter at a time, the assembly becomes easier.”

Lonardi mentioned that in 2012, he, along with his colleagues, published, in Nature science journal, their findings on the sequencing of barley. However, Lonardi explained, “It was a very poor quality assembly. The reason is because, again, the genome is so complicated.”  

Since then, better technology has been created for genomic sequencing, making the newly published study, according to Lonardi, “much, much better quality.”

With the knowledge of the barley genome sequence, there is now the potential to alter the grain in order to improve the plant. “Once you know the genomes … you can figure out the function of the gene … I’m not talking about genetic engineering. I’m talking about how you cross two different types of barley to make it better.”

By improving the grain, scientists could then increase the yield, as well as increase the quality of the grain.

UCR Professor of Genetics and Geneticists Timothy Close, who was the lead geneticist for the UCR branch of the research, explained that the German Leibniz Institute of Plant Genetics and Cultivated Plant Research (IPK) took the lead on the research, although, information was shared electronically between the different groups in Scotland, China, other parts of the United States and other countries.

Close, when talking about the potential for advances in technology to further complete the research, said, “There are newer, better ones (techniques) that will take care of spots that are, now, still a bit unclear … to really understand the species there’s a lot more to it than just sequencing and marking up one genome which is principally what this paper was. This paper goes beyond just one genome, but it goes most deeply into just one isolate of barley.”

In addition to Close and Lonardi, other co-authors include project scientist Maria Munoz-Amtriain, Department of Botany and Plant Sciences programmer Steve Wanamaker and recent computer science Ph.D. recipient Rachid Ounit.