title: Construction of a radiation hybrid map of chicken chromosome 2 and alignment to the chicken draft sequence.
abstract: BACKGROUND
  The ChickRH6 whole chicken genome radiation hybrid (RH) panel recently produced has already been used to build radiation hybrid maps for several chromosomes, generating comparative maps with the human and mouse genomes and suggesting improvements to the chicken draft sequence assembly. Here we present the construction of a RH map of chicken chromosome 2. Markers from the genetic map were used for alignment to the existing GGA2 (Gallus gallus chromosome 2) linkage group and EST were used to provide valuable comparative mapping information. Finally, all markers from the RH map were localised on the chicken draft sequence assembly to check for eventual discordances.
  
  
  RESULTS
  Eighty eight microsatellite markers, 10 genes and 219 EST were selected from the genetic map or on the basis of available comparative mapping information. Out of these 317 markers, 270 gave reliable amplifications on the radiation hybrid panel and 198 were effectively assigned to GGA2. The final RH map is 2794 cR6000 long and is composed of 86 framework markers distributed in 5 groups. Conservation of synteny was found between GGA2 and eight human chromosomes, with segments of conserved gene order of varying lengths.
  
  
  CONCLUSIONS
  We obtained a radiation hybrid map of chicken chromosome 2. Comparison to the human genome indicated that most of the 8 groups of conserved synteny studied underwent internal rearrangements. The alignment of our RH map to the first draft of the chicken genome sequence assembly revealed a good agreement between both sets of data, indicative of a low error rate.
authors.affiliation: Laboratoire de Génétique Cellulaire, INRA, Castanet-Tolosan, 31326, France. sleroux@toulouse.inra.fr
authors.forename: Sophie
authors.initials: S
authors.lastname: Leroux
authors.forename: Mélanie
authors.initials: M
authors.lastname: Dottax
authors.forename: Suzanne
authors.initials: S
authors.lastname: Bardes
authors.forename: Florence
authors.initials: F
authors.lastname: Vignoles
authors.forename: Katia
authors.initials: K
authors.lastname: Fève
authors.forename: Frédérique
authors.initials: F
authors.lastname: Pitel
authors.forename: Mireille
authors.initials: M
authors.lastname: Morisson
authors.forename: Alain
authors.initials: A
authors.lastname: Vignal
mesh_terms: D000818:Animals; D002645:Chickens; D002874:Chromosome Mapping; D019295:Computational Biology / Q000379:methods; D017124:Conserved Sequence; D017931:DNA Primers / Q000737:chemistry; D020224:Expressed Sequence Tags; D008040:Genetic Linkage; D005819:Genetic Markers; D005821:Genetic Techniques; D016678:Genome; D006801:Humans; D018895:Microsatellite Repeats; D008957:Models, Genetic; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction; D021101:Radiation Hybrid Mapping / Q000379:methods*; D015203:Reproducibility of Results; D013045:Species Specificity
chemical_list: D017931:DNA Primers; D005819:Genetic Markers