Scientists from the James Hutton Institute and the University of Dundee have been part of an international research team that recently reached a milestone in unravelling the species wide genetic diversity of domesticated barley.

With the complete genome sequencing of 20 diverse genotypes, the researchers have completed the first step in decoding the genetic information of the entire species.

The upshot of this is that scientists and breeders will greatly benefit from these new findings, which have been published in the magazine, Nature.

To get all genetic information of an individual, its genome must be completely decoded and the Dundee scientists and international partners had already succeeded in doing this for one specific variety three years ago. But to understand the genetic information of the entire species, more was required and this is now a significant step closer to deciphering this so-called pan-genome.

Individual genomes sometimes differ considerably in their number of genes and in the arrangement and orientation of large parts of individual chromosomes, which carry genetic information. These structural changes in barley can present an insurmountable barrier for manipulating important plant characters in breeding.

The scientists used species-wide genetic diversity data to identify and select 20 highly diverse genotypes for complete sequencing. "Criteria for the selection included the greatest possible differences in their genetic diversity, geographical origin and biological traits such as winter or spring type, grain hull, row-type," said Professor Dr Nils Stein, head of the genomics of genetic resources research group at the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), the lead institution in the study.

Besides the observation that two barley varieties can differ substantially in their total gene content, the scientists found amazing differences in the linear order of the genetic information in the chromosomes that are termed structural variants.

Two of these attracted particular interest to the scientists. In the first, a link was established to ‘mutation breeding’ in the 1960s and has spread unnoticed through breeding to present-day varieties.

In the second, the observed variation had possibly occurred and was selected during environmental adaptation as barley production spread from its origins in the 'fertile crescent', the boomerang-shaped region of the Middle East that was home to some of the earliest human civilisations.

The genes encompassed by this region had previously been identified by the Hutton group as being critical for adaptation to northern European environments. "We never knew that this gene was part of a much bigger chromosomal rearrangement,” said the study co-author, Professor Robbie Waugh, of the JHI and the University of Dundee.

“This confirmed that major structural variants can play a decisive role in both crop evolution and breeding. The only way these could have been discovered is through the complete genome sequencing of diverse individuals," he said.

"Naturally occurring, or artificially induced inversions are evidence of a considerable dynamics in the genome organisation of this important crop species."

The new findings will have significant scientific and practical impact. “We now know for sure that in the future, structural variation will need to be accounted for in barley research and breeding,” Professor Waugh said.

However, the research still faced major challenges. “The pan-genome study is largely restricted to cultivated barleys that have gone through the massive genetic bottleneck that is a result of domestication,” commented Professor Waugh. "We still need to explore the direct ancestors of today's cultivated crop.”

Faced with growing climate and other environmental concerns, scientists in the consortium are convinced that the solutions to many of our future agricultural challenges will lie in the genomes of diverse relatives of our currently cultivated crop varieties.

* The project involved scientists from Germany, Australia, Canada, USA, China and Japan. JHI is the site of the International Barley Hub, an initiative which seeks to create a unique, integrated, open platform for the translation of barley research into economic, social, environmental and commercial impacts for the breeding, farming, malting, brewing, feed, food, health and related industries. It is supported through the Tay Cities Deal.