Dear GrainGenes members,
We are happy to announce and share new rye genomic resources with the cereals community.
Our recently accepted paper in Plant Journal reports on a whole-genome draft sequence of rye (Secale cereale L.). Through whole-genome shotgun sequencing of the ~ 8 Gbp genome of the winter rye inbred line Lo7 we obtained a de novo assembly represented by 1.29 million scaffolds covering a total length of 2.8 Gbp. The reference sequence represents nearly the entire low-copy portion of the rye genome. The genome assembly was used to predict 27,784 rye gene models based on homology to sequenced grass genomes. Through resequencing of 10 rye inbred lines and one accession of the wild relative S. vavilovii, we discovered more than 90 million single nucleotide variants and short insertions/deletions in the rye genome. From these variants, we developed the high-density Rye600k Affymetrix genotyping array with 600,843 markers which enabled anchoring the sequence contigs along a high-density genetic map and establishing a synteny-based virtual gene order. Genotyping data were used to characterize the diversity of rye breeding pools and genetic resources and to obtain a genome-wide map of selection signals differentiating the divergent gene pools.
This rye whole-genome sequence closes a gap in Triticeae genome research and will be highly valuable for comparative genomics, functional studies and genome-based breeding in rye and related species. All resources such as the assembly, sequence raw data, markers on the array, rye genome zipper and high-density genetic map are publically available (see links in our paper).
This is the reference:
Bauer E, Schmutzer T, Barilar I, Mascher M, Gundlach H, Martis MM, Twardziok SO, Hackauf B, Gordillo A, Wilde P, Schmidt M, Korzun V, Mayer KFX, Schmid K, Schön C-C, Scholz U (2016) Towards a whole-genome sequence for rye (Secale cereale L.) Plant J, DOI: 10.1111/tpj.13436
With kind regards
Dr. Eva Bauer
Technische Universität München
Lehrstuhl für Pflanzenzüchtung (Plant Breeding)