A new high quality rye reference genome reveals far greater diversity in a chromosome region already used to improve disease resistance, stress tolerance and yield in wheat.
Rye shares a long evolutionary history with barley and wheat, but its development as a major crop began considerably later.
While barley and wheat were domesticated about 10,000 years ago in the Fertile Crescent of the Near East, rye initially spread as a field weed. Over time, it gradually acquired some of the characteristics of its two closely related cereals.
Around 5,000 to 6,000 years ago, rye became a cultivated species in its own right. By the Middle Ages, it had emerged as Northern Europe’s most important bread grain.
A Large and Complex Genome
Rye’s large, complex genome has long presented challenges for researchers. It is significantly larger than the human genome, and almost 90% of it consists of repetitive DNA sequences, according to a press release.
Previous reference sequences, including one produced by the IPK Leibniz Institute in 2021, represented important advances for research and breeding. However, they remained incomplete and lacked precision, containing gaps, misaligned sections, collapsed regions and incompletely mapped centromeres.
Centromeres play a fundamental role during cell division by helping ensure daughter cells receive the same genetic information and can function properly.
Researchers Build an Improved Reference Sequence
To create the improved reference sequence, the research team used state-of-the-art sequencing technologies available at IPK through funding from the federal and state governments.
The team began by sequencing long DNA molecules from the Lo7 line, an established reference genotype in rye research. Long-read sequencing allows scientists to bridge regions of the genome that are particularly difficult to decode.
Researchers then arranged the DNA fragments in the correct order across rye’s seven chromosomes. Several independent methods were used to verify the new reference sequence and confirm its high quality.
“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 the genome for further analysis and utilisation,” says the IPK researcher.
Previously Hidden Chromosome Regions Revealed
The improved sequence provides access to regions containing identical sections of DNA in direct repetition. In earlier versions, these regions were collapsed and could not be resolved correctly.
The accurate assembly of rye’s centromeres represents a particularly important breakthrough.
“These regions have been 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 characterise them,” explains Dr. Erwang Chen.
The IPK team also found that certain mobile DNA elements, known as transposons, remained active in rye centromeres until relatively recently.
“This proves that centromeres can evolve differently between closely related cereal species.”
Transposons generate genetic variation, which can contribute to differences in biological functions.
Wheat Could Benefit From Greater Rye Diversity
The findings concerning the short arm of rye chromosome 1R, known as 1RS, are of particular interest to plant breeders.
Through crossbreeding, 1RS has already been introduced into several wheat varieties, improving traits such as disease resistance, stress tolerance and yield. The segment is especially well known for carrying resistance genes against plant-pathogenic fungi, including rust and powdery mildew.
The study suggests that the 1RS segments currently used in wheat are largely identical or, at minimum, very closely related. However, comparisons among sequenced rye genotypes show that the region is considerably more diverse in rye itself.
Rye Pan-Genome Could Support Future Breeding
“This means that there is still a great deal of untapped potential in rye diversity,” emphasises Prof. Dr. Nils Stein, head of the ‘Genebank department’. “With the new standard we have achieved in rye genome sequencing, 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 sequencing many rye genomes to create what is known as a rye pan-genome. This serves as the basis for the systematic exploration of rye’s genomic diversity for research and breeding.”
A pan-genome encompasses the full collection of genes or DNA sequences found across a species. By capturing genetic variation that cannot be represented in a single reference genome, the rye pan-genome could help researchers and breeders identify valuable traits for future rye and wheat varieties.
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