Assignment of fourteen microsatellite markers to the chicken linkage map

A large mapping population, with 874 F2 individuals, was generated by reciprocally intercrossing 2 chicken lines. A genetic map of 2,426.6 cM comprising 25 linkage groups was established based on 145 microsatellite markers. Chromosome locations were assigned for 14 previously unmapped markers. The marker ADL0132 was previously mapped to chromosome 9; however, here close linkage to the MCW0091 marker on chromosome 4 was found. With this exception, the derived linkage map was in excellent agreement with the chicken consensus map. A comparison with the chicken genome assembly (http://genome.ucsc.edu; February 2004) suggested a few minor errors in the assembly. A PCR-RFLP test was used to genotype a single nucleotide polymorphism in the melanocortin receptor 3 (MC3R) gene in the intercross, and pyrosequencing was used to map the genes for Hemopoetic Cell Kinase (HCK) and Bone Morphogenic Protein 7 (BMP7). The HCK and BMP7 genes on linkage group E32 showed significant linkage to MC3R on the distal end of linkage group E47W24, consequently joining the 2 linkage groups. A comparison between the linkage data in the current study and the physical location of markers as revealed in the chicken genome sequence assembly (February 2004) showed a 3-fold higher recombination rate on microchromosomes than on macrochromosomes.