Improved reference genome supports the breeding of rye and wheat
“The new reference sequence represents a quantum leap for rye research and breeding”
rye is not only a hardy and high-yielding crop, but also possesses a valuable gene pool for wheat breeding. An international research team led by the IPK Leibniz Institute has significantly improved the foundations for research and breeding by publishing a high-quality reference genome sequence. For the first time, the sequence includes the complete centromeres of all seven chromosome pairs. Centromeres play a crucial role in the correct distribution of genetic information during cell division. The study’s findings have now been published in the journal *Nature Communications*.
Rye shares a close and long evolutionary history with barley and wheat. However, its history as an important crop is significantly shorter. While barley and wheat were “domesticated” 10,000 years ago in the so-called Fertile Crescent of the Near East, rye initially spread as a field weed. In the process, rye gradually adopted some characteristics of its two “big brothers and sisters,” until rye, too, became a cultivated species in its own right 5,000–6,000 years ago and emerged as the most important bread grain in Northern Europe during the Middle Ages.
However, the large and complex rye genome poses challenges for science. Not only is the genome significantly larger than the human genome, but nearly 90 percent of it consists of repetitive DNA sequences. Previous reference sequences, such as the one generated at the IPK in 2021, represented very useful and important advances for research and breeding. However, these remained incomplete and too imprecise. They contained gaps, misaligned segments, collapsed regions, and, not least, incompletely mapped centromeres. The latter are critically important during cell division to ensure that the resulting daughter cells receive the same genetic information, enabling them to function properly.
To create the now-improved reference sequence, the research team utilized the most advanced sequencing technologies available at the IPK, made possible by federal and state funding. In a first step, long DNA molecules from the Lo7 line were sequenced. This line is an established reference genotype in rye research. The long read lengths make it possible to bridge difficult-to-sequence regions of the genome more efficiently. In the next step, the DNA fragments were arranged in the correct order on the seven chromosomes. The researchers then verified the new reference sequence using several independent methods and were able to confirm the high quality of the genome sequence.
“The new reference sequence represents a quantum leap for rye research and breeding,” explains Dr. Erwang Chen, first author of the study. “It is more complete than previous versions, corrects earlier assembly errors, and provides access to regions of genetic information for further analysis and utilization,” says the IPK researcher. “In these regions, there are identical segments in direct repetition that were only present in a collapsed form in earlier versions and could not be correctly resolved.” The correct composition of the centromeres, in particular, represents a breakthrough. “These regions were particularly difficult to decipher until now. With the new sequence, we can now see how these central regions of the chromosomes are structured and which DNA elements characterize them,” explains Dr. Erwang Chen. In addition, the IPK research team was able to show that certain mobile DNA elements, known as transposons, were active in rye centromeres until recently. “This proves that centromeres can develop differently among closely related cereal species.” This is because transposons lead to variations, which in turn result in different functions.
Of particular interest for breeding are the new findings regarding the “short” arm of rye chromosome 1R, known as 1RS. This arm has already been transferred to several wheat varieties through crossbreeding and improves traits such as disease resistance, stress tolerance, and yield. Particularly well-known are resistance genes against plant-pathogenic fungi, such as rust or powdery mildew. The study shows that the 1RS segments used in wheat are all more or less identical or at least very closely related to one another. When this segment is now compared across the various decoded rye genotypes, it becomes clear that this region exhibits much greater variability in rye.
“This means that there is still a great deal of untapped potential in rye diversity,” emphasizes Prof. Dr. Nils Stein, head of the “Gene Bank” department. “With the newly achieved standard for genome sequencing in rye, we can now take the next step. As part of the “RyeHub” research project, funded by the Federal Ministry of Research, Technology, and Space (BMFTR), we have already begun decoding many rye genomes to create what is known as a rye pangenome. This serves as the basis for the systematic characterization of rye’s genomic diversity for research and breeding.” Researchers use the term “pangenome” to refer to the totality of all genes or DNA sequences of a species.
Note: This article has been translated using a computer system without human intervention. LUMITOS offers these automatic translations to present a wider range of current news. Since this article has been translated with automatic translation, it is possible that it contains errors in vocabulary, syntax or grammar. The original article in German can be found here.
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