The Genome Structure of Rye (Secale cereal L.) and its Multiple Parents

Rye (Secale cereal L.), a member of the Triticeae tribe, is an important hybrid crop in Central and Eastern Europe. To unlock the genomic inventory and evolution of rye, we combined chromosome sorting, a high resolution genetic map comprising more than 3,000 SNP markers, next generation sequencing and systematic exploitation of synteny to sequenced model grass genomes.

A virtual gene order for each of the seven individual rye chromosomes was obtained using 1x-fold coverage 454 sequencing of sorted rye chromosomes and subsequent integration using the “GenomeZipper” approach. As a result, a linear gene order map of 22,426 non-redundant gene loci of the rye genome has been obtained.

The related grass genomes of barley, Brachypodium, rice, and sorghum share large conserved chromosome segments (syntenic blocks) and provide a suitable reference for the study of rye chromosome evolution. Compared to barley the rye genome exhibits multiple chromosomal rearrangements and an evolutionary model involving five consecutive translocations can be proposed for the rye genome. Comparison of the degree of syntenic conservation, the sequence homology and synonymous substitution rate against related grass genomes demonstrate pronounced distortions among different segments. In line with phylogenetic observations we hypothesize that the modern genome of Secale cereale is a mosaic of segments from several ancestral genomes rather than the result of a series of intragenomic rearrangements. We speculate that the observed genomic mosaic involved a series of polyploidisation or introgression events that might have been eased by the outbreeding lifestyle of rye.