Barley pan-genome: scientists unravel diversity of domesticated barley

Published on 26 November 2020

An international research team including scientists from the James Hutton Institute and the University of Dundee has reached a milestone on the way to unravelling the species-wide genetic diversity of domesticated barley.

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With the complete genome sequencing of 20 diverse genotypes, the researchers completed the first step in decoding the genetic information of the entire species - the barley pan-genome. Scientists and breeders will greatly benefit from these new findings, which have today been published in the renowned magazine Nature.

In order to record all genetic information of an individual, its genome must be completely decoded. Dundee scientists and international partners already succeeded in doing this for one specific variety three years ago. But to understand the genetic information of the entire species, much more is required. The international team has now taken 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 the barley genome can present an insurmountable barrier for manipulating important plant characters in breeding.

They used species-wide genetic diversity data to identify and select twenty 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," says Prof Dr Nils Stein, head of the Genomics of Genetic Resources research group at the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), lead institution of 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 since spread unnoticed through breeding to present-day varieties. In the second, the observed variation was possibly occurred and was selected during environmental adaptation as barley production spread from its origins in the Fertile Crescent.

One 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,” says Prof Robbie Waugh, of the James Hutton Institute and the University of Dundee.

“This new observation confirms 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. 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 have created a new knowledge-base and opened up a treasure trove of new information", says Prof Dr Stein.

“We now know for sure that in the future, structural variation will need to be accounted for in barley research and breeding,” Prof Waugh adds.

Despite current progress, the research community still faces 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,” comments Prof. 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.

The James Hutton Institute’s Dundee campus 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. The project is supported through the Tay Cities Deal.

Paper: Jayakodi, Padmarasu et al. (2020), The barley pan-genome reveals the hidden legacy of mutation breeding. Nature. DOI:10.1038/s41586-020-2947-8

Story category Research