Abstract
BackgroundThe 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.ResultsEighty 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.ConclusionWe 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.
Highlights
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
In addition to the genetic and BAC contig maps that have already been used, the RH map will provide an independent source of data to assist the chicken genome sequence assembly process towards a finished quality sequence
We present here the radiation hybrid map of chicken chromosome 2, built by using markers chosen from the GGA2 genetic map and a substantial number of additional markers developed from chicken EST data
Summary
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. Chicken is a model organism in various fields of biology, such as embryology or immunology It is the only bird species for which the genome has been studied in detail and a lot is expected from its use in comparative genome analyses. This will help to detect sequences conserved between species, which should correspond to unknown exons and to regulatory or other functional regions. Such analyses will be essential for the annotation of other genomes, including that of human (page number not for citation purposes). In addition to the genetic and BAC contig maps that have already been used, the RH map will provide an independent source of data to assist the chicken genome sequence assembly process towards a finished quality sequence
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