Chromosome-scale genome assembly provides insights into rye biology, evolution, and agronomic potential

We present a chromosome-scale annotated assembly of the rye (Secale cereale L. inbred line 9Lo79) genome, which we use to explore Triticeae genomic evolution, and rye9s superior disease and stress tolerance. The rye genome shares chromosome-level organization with other Triticeae cereals, but exhibits unique retrotransposon dynamics and structural features. Crop improvement in rye, as well as in wheat and triticale, will profit from investigations of rye gene families implicated in pathogen resistance, low temperature tolerance, and fertility control systems for hybrid breeding. We show that rye introgressions in wheat breeding panels can be characterised in high-throughput to predict the yield effects and trade-offs of rye chromatin.