BMC Genomics Research article A first-generation microsatellite-based genetic linkage map of the Siberian jay (Perisoreus infaustus): insights into avian genome evolution Sonja Jaari, Meng-Hua Li* and Juha Merilä BioMed Central Open Access Address: Ecological Genetics Research Unit, Department of Biological and Environmental Sciences, PO Box 65, FIN-00014 University of Helsinki, Finland Email: Sonja Jaari - sonja.jaari@helsinki.fi; Meng-Hua Li* - menghua.li@helsinki.fi; Juha Merilä - juha.merila@helsinki.fi * Corresponding author Published: 3 January 2009 BMC Genomics 2009, 10:1 doi:10.1186/1471-2164-10-1 This article is available from: http://www.biomedcentral.com/1471-2164/10/1 Received: 16 July 2008 Accepted: 3 January 2009 © 2009 Jaari et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Genomic resources for the majority of free-living vertebrates of ecological and evolutionary importance are scarce. Therefore, linkage maps with high-density genome coverage are needed for progress in genomics of wild species. The Siberian jay (Perisoreus infaustus; Corvidae) is a passerine bird which has been subject to lots of research in the areas of ecology and evolutionary biology. Knowledge of its genome structure and organization is required to advance our understanding of the genetic basis of ecologically important traits in this species, as well as to provide insights into avian genome evolution. Results: We describe the first genetic linkage map of Siberian jay constructed using 117 microsatellites and a mapping pedigree of 349 animals representing five families from a natural population breeding in western Finland from the years 1975 to 2006. Markers were resolved into nine autosomal and a Z-chromosome-specific linkage group, 10 markers remaining unlinked. The best-position map with the most likely positions of all significantly linked loci had a total sex-average size of 862.8 cM, with an average interval distance of 9.69 cM. The female map covered 988.4 cM, whereas the male map covered only 774 cM. The Z-chromosome linkage group comprised six markers, three pseudoautosomal and three sex-specific loci, and spanned 10.6 cM in females and 48.9 cM in males. Eighty-one of the mapped loci could be ordered on a framework map with odds of >1000:1 covering a total size of 809.6 cM in females and 694.2 cM in males. Significant sex specific distortions towards reduced male recombination rates were revealed in the entire best-position map as well as within two autosomal linkage groups. Comparative mapping between Siberian jay and chicken anchored 22 homologous loci on 6 different linkage groups corresponding to chicken chromosomes Gga1, 2, 3, 4, 5, and Z. Quite a few cases of intra-chromosomal rearrangements within the autosomes and three cases of inter-chromosomal rearrangement between the Siberian jay autosomal linkage groups (LG1, LG2 and LG3) and the chicken sex chromosome GgaZ were observed, suggesting a conserved synteny, but changes in marker order, within autosomes during about 100 million years of avian evolution. Conclusion: The constructed linkage map represents a valuable resource for intraspecific genomics of Siberian jay, as well as for avian comparative genomic studies. Apart from providing novel insights into sex-specific recombination rates and patterns, the described maps – from a previously genomically uncharacterized superfamily (Corvidae) of passerine birds – provide new insights into avian genome evolution. In combination with high-resolution data on quantitative trait variability from the study population, they also provide a foundation for QTL-mapping studies. Page 1 of 17 (page number not for citation purposes)