Scientists Unlock Benefits of Barley Genome

UC Riverside research team helps develop a genomics resource to improve the crop’s yield and quality

Photo shows barley spikes.

Barley is one of the world’s most important cereal crops. Photo credit: Close Lab, UC Riverside.

RIVERSIDE, Calif. — Scientists, including researchers at the University of California, Riverside, have developed a high-resolution genomic resource for barley that they say will help produce higher yields, improve pest and disease resistance, and enhance the nutritional value of the grain.

The resource gives new molecular and cellular insight into the biology of barley, one of the world’s most important and earliest domesticated cereal crops. It represents a hub for trait isolation, understanding and exploiting natural genetic diversity and investigating the unique biology and evolution of the crop.

“This resource will serve as an essential reference for genetic research and breeding and help advance gene discovery and genome-assisted crop improvement,” said Timothy Close, a professor of genetics at UC Riverside and one of the leaders of the research project.

Study results appear online today (Oct. 17) in the journal Nature.

In the research paper, the scientists provide a detailed overview of the functional portions of the barley genome, revealing the order and structure of most of its 32,000 genes. They also give a detailed analysis of where and when barley genes are switched on in different tissues and at different stages of development.

Photo shows Timothy Close and Stefano Lonardi.

Timothy Close (left) and Stefano Lonardi made significant contributions to the research project. Photo credit: UCR Strategic Communications.

The scientists also describe the location of dynamic regions of the barley genome that carry genes conferring resistance to devastating diseases, such as powdery mildew, Fusarium head blight and rusts. The result, they say, is a better understanding of the crop’s immune system and the genetic differences among barley cultivars.

Nearly twice as large as the human or maize genomes and about 12 times the size of the rice genome, the barley genome was a challenge to sequence due to its complexity and its large proportion of repetitive regions, which are difficult to piece together into a true linear order.

“The majority of the barley genome is composed of highly repetitive ‘junk’ DNA, which makes whole-genome sequencing difficult,” Close explained. “The UCR team first identified gene-rich segments of the genome, called BACs.  Then we determined the primary sequence of more than 2,000 of these BACs.”

The raw sequence data relevant to the new resource was generated in UCR’s Institute of Integrative Genome Biology core facility.

“For the purpose of determining the sequences of each BAC, we developed a novel protocol that takes advantage of recent advances in combinatorial pooling design and borrows ideas from error-correcting codes — like the ones used in CDs and DVDs,” said Stefano Lonardi, a professor of computer science and engineering at UCR, who worked closely with Close on the research.

A member of the grass family, barley is a high-fiber and high-protein grain and a widely adaptable crop. Approximately three-quarters of its global production is used for animal feed, 20 percent is malted for use in alcoholic and non-alcoholic beverages, and 5 percent as an ingredient in a range of food products.

The success of the barley genome sequencing and other grass family crops, such as wheat and rye, will allow breeders and scientists to effectively address the challenge of feeding the world’s burgeoning population under the constraints of an environment that increasingly challenges farmers and ranchers with extreme weather events.

To develop the barley genome resource, Close and Lonardi joined researchers at the University of Minnesota, USDA-Agricultural Research Service and 19 other organizations around the world. Together, the scientists make up the International Barley Sequencing Consortium (IBSC), which was founded in 2006 and is presently headed by the lead author of the Nature paper, Nils Stein at the Leibniz Institute of Plant Genetics and Crop Plant Research, Germany.

The IBSC created the high-resolution barley genome resource that places the majority of barley genes in order.  Included in the resource, too, are the sequences of nearly all genes and associated regulatory regions, which offers new direction to researchers seeking to improve barley yield and quality.

Besides Close and Lonardi, the following researchers at UCR are members of the interdisciplinary collaboration between the departments of Botany & Plant Sciences and Computer Science & Engineering that contributed to the research project: postdoctoral scholars Kavitha Madishetty, Jan T. Svensson and Prasanna Bhat; undergraduates Matthew Moscou, Josh Resnik and Matthew Alpert; Ph.D. student Denisa Duma; visiting scientists Francesca Cordero and Marco Beccuti; faculty member Gianfranco Ciardo; assistant specialist Yaqin Ma; and programmer Steve Wanamaker.

The UCR portion of the research was funded by grants to Close and Lonardi from the National Science Foundation and the USDA.

Media Contact

Tel: (951) 827-6050
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Additional Contacts

Timothy Close
Tel: (951) 827-3318

Stefano Lonardi
Tel: (951) 827-2203

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