title: Towards a whole-genome sequence for rye (Secale cereale L.).
abstract: We report on a whole-genome draft sequence of rye (Secale cereale L.). Rye is a diploid Triticeae species closely related to wheat and barley, and an important crop for food and feed in Central and Eastern Europe. Through whole-genome shotgun sequencing of the 7.9-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. Our reference sequence represents nearly the entire low-copy portion of the rye genome. This 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 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.
authors.affiliation: Technical University of Munich, Plant Breeding, Liesel-Beckmann-Str. 2, 85354, Freising, Germany.
authors.forename: Eva
authors.initials: E
authors.lastname: Bauer
authors.affiliation: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466, Stadt Seeland, Germany.
authors.forename: Thomas
authors.initials: T
authors.lastname: Schmutzer
authors.affiliation: Universität Hohenheim, Crop Biodiversity and Breeding Informatics, Fruwirthstr. 21, 70599, Stuttgart, Germany.
authors.forename: Ivan
authors.initials: I
authors.lastname: Barilar
authors.affiliation: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466, Stadt Seeland, Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: Mascher
authors.affiliation: Helmholtz Zentrum München, Plant Genome and Systems Biology, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany.
authors.forename: Heidrun
authors.initials: H
authors.lastname: Gundlach
authors.affiliation: Helmholtz Zentrum München, Plant Genome and Systems Biology, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany.
authors.forename: Mihaela M
authors.initials: MM
authors.lastname: Martis
authors.affiliation: Helmholtz Zentrum München, Plant Genome and Systems Biology, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany.
authors.forename: Sven O
authors.initials: SO
authors.lastname: Twardziok
authors.affiliation: Julius Kühn-Institute, Institute for Breeding Research on Agricultural Crops, Rudolf-Schick-Platz 3a, 18190, Sanitz, Germany.
authors.forename: Bernd
authors.initials: B
authors.lastname: Hackauf
authors.affiliation: KWS LOCHOW GMBH, Ferdinand-von-Lochow-Str. 5, 29303, Bergen, Germany.
authors.forename: Andres
authors.initials: A
authors.lastname: Gordillo
authors.affiliation: KWS LOCHOW GMBH, Ferdinand-von-Lochow-Str. 5, 29303, Bergen, Germany.
authors.forename: Peer
authors.initials: P
authors.lastname: Wilde
authors.affiliation: KWS LOCHOW GMBH, Ferdinand-von-Lochow-Str. 5, 29303, Bergen, Germany.
authors.forename: Malthe
authors.initials: M
authors.lastname: Schmidt
authors.affiliation: KWS LOCHOW GMBH, Ferdinand-von-Lochow-Str. 5, 29303, Bergen, Germany.
authors.forename: Viktor
authors.initials: V
authors.lastname: Korzun
authors.affiliation: Helmholtz Zentrum München, Plant Genome and Systems Biology, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany.
authors.forename: Klaus F X
authors.initials: KF
authors.lastname: Mayer
authors.affiliation: Universität Hohenheim, Crop Biodiversity and Breeding Informatics, Fruwirthstr. 21, 70599, Stuttgart, Germany.
authors.forename: Karl
authors.initials: K
authors.lastname: Schmid
authors.affiliation: Technical University of Munich, Plant Breeding, Liesel-Beckmann-Str. 2, 85354, Freising, Germany.
authors.forename: Chris-Carolin
authors.initials: CC
authors.lastname: Schön
authors.affiliation: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466, Stadt Seeland, Germany.
authors.forename: Uwe
authors.initials: U
authors.lastname: Scholz
mesh_terms: D032461:Chromosomes, Plant / Q000235:genetics*; D018744:DNA, Plant / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics; D023281:Genomics; D005838:Genotype; D012434:Secale / Q000235:genetics*; D026801:Synteny
chemical_list: D018744:DNA, Plant
keywords: Rye600k genotyping array; Secale cereale L.; de novo genome assembly; diversity; high-density genetic map; rye; rye genome zipper; selection signals; single nucleotide variants; whole-genome shotgun sequencing