What are split inversions

On the way to the barley pan genome

24.11.2020

Three years after the characterization of the first barley genome, an international team led by scientists from the IPK has now come a considerable step closer to deciphering the so-called pan genome of barley. The results have now been published in the science magazine Nature. How the researchers proceeded, what the new findings mean for breeding and what challenges are still waiting for the researchers, explains Prof. Dr. Interview with Nils Stein, Head of the Genomics Working Group on Genetic Resources.

Prof. Dr. Nils Stein Photo: IPK / Andreas Bähring

 

  • You are now one big step closer to decoding the barley pan genome. What exactly is the pan genome about?

The concept of the pan genome describes the phenomenon that, contrary to original assumptions from times before genome sequencing, different individuals of a species do not share exactly the same amount of genetic information. Rather, all individuals have a large common body of shared genetic information (genes), the so-called “core genome”. In addition, there is a "variable genome", in the composition of which individual representatives of a species can differ to a greater or lesser extent. This contains, for example, genes that have been selected by adapting to certain environmental conditions. Only the pan genome, which becomes visible by comparing the genomes of numerous plants, ultimately shows the complete genome information of a species as well as the existing genetic diversity that is characteristic of this species, in our case barley. Put simply, it is a matter of differentiating the genetic information into precise intersections and subsets.

  • How can the pan genome be characterized in the case of barley? And why is decryption so important?

In order to describe the pan genome of barley, one needs complete genome sequences for genetically very diverse barley genotypes. We estimate that at least 50-100 complete genome sequences are required to describe the genetic information of the barley crop, including all variants, in an approximately comprehensive manner. This is very time-consuming when you consider that the complete decoding of the genome of a barley was considered impossible for a long time. This is due to the fact that the barley genome has an 80-90 percent share of sequence units of different lengths, some of which can be repeated hundreds or thousands of times. This posed almost insoluble problems for bioinformatics for a long time when putting together the sequence snippets obtained as part of a genome sequencing project. The first complete decoding of a barley genome was only possible in 2017. In order to understand the genetic information of the entire barley species, it is now necessary to decipher the pan genome.

  • How did you proceed exactly?
The starting point for the investigation was the roughly 22,000 barley seed samples from the federal headquarters Ex situ-Genebank at the IPK. Their genomes were pre-characterized by means of punctual DNA sequencing. On the basis of the genetic diversity information obtained in this way, 20 genotypes were initially selected from this large group. Genotypes that differ genetically as much as possible from one another.
  • What criteria was used for the selection?
The most important characteristic in the selection was in fact the greatest possible genetic difference between the candidates. This usually overlapped with a very large variety or distance of their respective geographical origin. In addition, we made sure that typical main characteristics for barley such as winter or summer type, naked or covered seediness, two- or multi-row ear shapes were represented in the list of genotypes.
  • What surprised you in particular?
The individual genomes sometimes differ considerably in the number of their genes and in the arrangement and orientation of large sections of individual chromosomes, i.e. the carriers of genetic information. This is important to know because these “structural” changes in the genome can represent an insurmountable hurdle when combining important properties in cross-breeding.
  • What other findings did the investigation provide?
We found amazing differences in the linear arrangement of genetic information in the chromosomes - so-called genome structure differences. Two of these structural variations, so-called inversions, i.e. opposing arrangements of genetic information in two genomes, were particularly interesting. In one case, a reference to the mutation breeding of the 1960s could be established for the structural change, as a result of which the change has spread unnoticed through breeding into today's varieties. In the second case, the observed genome structure variation is related to the environmental adaptation during the historical, northwestern expansion of barley cultivation to Central and Northern Europe. The description of such inversions in barley is new.
  • Why are these inversions so important?
They can play a decisive role in the breeding process because they prevent recombination, i.e. make the breeding new combination of desired traits impossible. But not only that: These naturally occurring or artificially triggered inversions are evidence of a considerable dynamic in the genome organization of this second most important culture species in Europe.
  • How can breeding benefit from these new findings?
We have created a new database and opened up a new wealth of information for breeding. Molecular markers could now be used to specifically take structural genome differences into account in barley breeding.
  • Ultimately, it's all about preparing barley for the challenges posed by climate change, isn't it?
Yes that's true. The problem is as follows: The barley that we know today has been bred specifically for the highest possible yield under stable, Central European environmental conditions. That worked very well for a long time. One consequence of modern plant breeding, however, is basically a decrease in the genetic diversity of the cultivated varieties. And that is exactly what is catching up with us today in times of climate change. Environmental conditions are no longer as stable as usual. New environmental phenomena, such as extreme heat during flowering, drought, or even precipitation with very large amounts of water in the shortest possible time, occur more frequently and at shorter intervals, which has already been reflected in significantly lower yields in recent years. Breeding is based on the use and recombination of the existing genetic diversity. Here offer the plant genetic resources from the federal headquarters Ex situ-Genbank at the IPK created a reservoir to search for properties that we urgently need today. It's about a genetic rejuvenation for our barley.
  • What challenges are still ahead of you?
Despite the first successful step in describing the barley pan genome, we have not yet captured the full diversity of barley. To do this, we have to completely sequence and decode other genotypes. In this next step, we also want to include wild barley, the direct ancestor of today's cultivated barley, and take a closer look at it. Wild barley is an important, but so far hardly used, component of the entire gene pool available to modern plant breeding. And I am absolutely certain that we are discovering diversity that can be of considerable value for future barley breeding and research.