title: A first survey of the rye (Secale cereale) genome composition through BAC end sequencing of the short arm of chromosome 1R.
abstract: BACKGROUND
  Rye (Secale cereale L.) belongs to tribe Triticeae and is an important temperate cereal. It is one of the parents of man-made species Triticale and has been used as a source of agronomically important genes for wheat improvement. The short arm of rye chromosome 1 (1RS), in particular is rich in useful genes, and as it may increase yield, protein content and resistance to biotic and abiotic stress, it has been introgressed into wheat as the 1BL.1RS translocation. A better knowledge of the rye genome could facilitate rye improvement and increase the efficiency of utilizing rye genes in wheat breeding.
  
  
  RESULTS
  Here, we report on BAC end sequencing of 1,536 clones from two 1RS-specific BAC libraries. We obtained 2,778 (90.4%) useful sequences with a cumulative length of 2,032,538 bp and an average read length of 732 bp. These sequences represent 0.5% of 1RS arm. The GC content of the sequenced fraction of 1RS is 45.9%, and at least 84% of the 1RS arm consists of repetitive DNA. We identified transposable element junctions in BESs and developed insertion site based polymorphism markers (ISBP). Out of the 64 primer pairs tested, 17 (26.6%) were specific for 1RS. We also identified BESs carrying microsatellites suitable for development of 1RS-specific SSR markers.
  
  
  CONCLUSIONS
  This work demonstrates the utility of chromosome arm-specific BAC libraries for targeted analysis of large Triticeae genomes and provides new sequence data from the rye genome and molecular markers for the short arm of rye chromosome 1.
authors.affiliation: Laboratory of Molecular Cytogenetics and Cytometry, Institute of Experimental Botany, Olomouc, Czech Republic. bartos@ueb.cas.cz
authors.forename: Jan
authors.initials: J
authors.lastname: Bartos
authors.forename: Etienne
authors.initials: E
authors.lastname: Paux
authors.forename: Robert
authors.initials: R
authors.lastname: Kofler
authors.forename: Miroslava
authors.initials: M
authors.lastname: Havránková
authors.forename: David
authors.initials: D
authors.lastname: Kopecký
authors.forename: Pavla
authors.initials: P
authors.lastname: Suchánková
authors.forename: Jan
authors.initials: J
authors.lastname: Safár
authors.forename: Hana
authors.initials: H
authors.lastname: Simková
authors.forename: Christopher D
authors.initials: CD
authors.lastname: Town
authors.forename: Tamas
authors.initials: T
authors.lastname: Lelley
authors.forename: Catherine
authors.initials: C
authors.lastname: Feuillet
authors.forename: Jaroslav
authors.initials: J
authors.lastname: Dolezel
mesh_terms: D001483:Base Sequence; D022202:Chromosomes, Artificial, Bacterial; D032461:Chromosomes, Plant / Q000235:genetics*; D019295:Computational Biology; D018744:DNA, Plant / Q000235:genetics; D015723:Gene Library; D017343:Genes, Plant; D005819:Genetic Markers; D018745:Genome, Plant; D017404:In Situ Hybridization, Fluorescence; D008969:Molecular Sequence Data; D020161:Physical Chromosome Mapping; D012091:Repetitive Sequences, Nucleic Acid; D012434:Secale / Q000235:genetics*; D012689:Sequence Homology, Nucleic Acid
chemical_list: D018744:DNA, Plant; D005819:Genetic Markers