Development of a gene-based radiation hybrid map of chicken Chromosome 7 and comparison to human and mouse Mireille Morisson, Carine Jiguet–Jiglaire, Sophie Leroux, Thomas Faraut, Suzanne Bardes, Katia Feve, Carine Genet*, Fre ´de ´ rique Pitel, Denis Milan, Alain Vignal Laboratoire de Ge ´ne ´tique Cellulaire, INRA, Chemin de Borde Rouge, 31326 Castanet–Tolosan, France Received: 28 January 2004 / Accepted: 19 April 2004 Abstract To validate the ChickRH6 whole-genome radiation hybrid (WGRH) panel, we constructed a map of chicken Chromosome 7 based on 19 microsatellite markers from the genetic map and 76 ESTs (ex- pressed sequence tags), whose efficient targeted de- velopment was made possible by using the ICCARE software. This high-density radiation hybrid (RH) map of a chicken macrochromosome gives us indi- cations on characteristics of ChickRH6. The poten- tial resolution of the panel is 325 kb and the practical resolution of our framework map is 1.3 Mb. Based on these results, a complete framework map of the chicken genome would comprise 1000 markers. The marker order is in good agreement with the genetic map and comparison with the human and mouse sequence maps revealed a number of internal rear- rangements. Chicken has a long history as a model organism in various fields of biology, including gene structure with the discovery of introns (Breathnach et al. 1977), immunology with the work on B cell matu- ration (Glick 1994), and oncology with studies on tumorigenic properties of viruses (Calnek 1992). It is still a unique tool for testing gene function by dis- ruption in the DT40 cell line and for research in embryo development (Brown et al. 2003). Moreover, because of interest in the chicken as a major agri- cultural species, genetic maps and other genomics tools were developed in recent years. Data from multispecies comparative sequence analyses have highlighted the interest in using the chicken genome sequence for detecting multispecies conserved se- quences, either conserved regulatory elements or exons. Indeed, only 2% of coding sequence is missed in human–chicken sequence alignments compared with 31.4% when comparing human and fish (Fugu rubripes or Tetraodon nigroviridis) (Thomas et al. 2003). Taken together, all these considerations have led to the decision to produce a whole-genome draft sequence of this unique avian species. As compo- nents of the whole-genome assembly, bacterial arti- ficial chromosome (BAC)-based physical maps have been assembled (Ren et al. 2003), but to date, only 361 out of the 2331 BAC contigs produced were linked to the genetic map and have thus a precise chromosomal assignment. An additional problem in assembling the chicken genome will arise from its structure, composed of 8 pairs of macrochromo- somes and the Z and W gonosomes, easily recog- nized using standard cytogenetic techniques (Ladjali–Mohammedi et al. 1999), and 30 pairs of microchromosomes, merely visible as dots on metaphase preparations and therefore difficult to recognize (Auer et al. 1987). Indeed, although much has been done on the assignment by FISH (fluores- cent in situ hybridization) of linkage groups to chromosomes, 7 microchromosomes still have to be assigned to linkage groups (Masabanda et al. 2004). To help in the process of BAC contig and genome sequence assembly, radiation hybrid (RH) maps, usually of intermediate resolution between the ge- netic and BAC fingerprint maps, can be developed *Present address: Diffe ´ renciation Cellulaire et croissance, EN- SAM–INRA, 2 Place Pierre Viala—34060 Montpellier cedex 1, France Correspondence to: M. Morisson; E-mail: mmorisso@toulouse. inra.fr 732 DOI: 10.1007/s00335-004-3003-y  Volume 15, 732–739 (2004)  Ó Springer Science+Business Media, Inc. 2004