BMC Genomics 2009, 10:1 http://www.biomedcentral.com/1471-2164/10/1 ful for identifying QTLs and genomic regions related to traits of ecological importance. Furthermore, because the maps are constructed with codominant markers, they should be transportable to other pedigrees in this species, as perhaps also to closely related species where the micro- satellites are conserved. Hence, the map will serve as a ref- erence map for genomic analyses in the Siberian jay, as well as a useful resource for comparative genomic studies in birds. Last but not least, given the access to individual level fitness data from this pedigreed population, the map might prove useful for more detailed studies in genetics of fitness and inbreeding depression in this small isolate population [42]. Methods Study species and pedigree The Siberian jay (Perisoreus infaustus) is a medium sized (body mass ca. 85–90 g) and relatively long-lived (average generation time ca. 4 years) oscine passerine bird from the Corvidae family [89,90]. It has a wide geographical distri- bution range in northern Eurasia where it occurs in the taiga forests from Fennoscandia to Siberia [40,91]. The Siberian jay has a stable socially monogamous breeding system and a prolonged brood care in which the dispersal of the young is delayed [34,37]. Hence, it lives in small territorial groups consisting of a breeding (alpha) pair, their retained offspring and/or unrelated immigrants [34,39,92]. Genetic diversity and structuring of the species has been investigated with mitochondrial DNA sequence analyses [91] and with a few available microsatellite markers [40,93]. However, its karyotype and genome structure remain undescribed. So far, 2n = 80 chromo- somes is common in the order Passeriformes (e.g. [13,88,94,95]. Likewise, as in all avian species with heteromorphic sex chromosomes, the sex-determination in the Siberian jays conforms to the ZW female-ZZ male system [96]. The material for this study comes from a Siberian jay pop- ulation breeding at Suupohja (ca. 66°18'N, 29°29'E), western Finland. Annual individual-level monitoring of the population began in 1974 and has continued ever since. More details concerning the study population and field monitoring activities can be found from [40,42,93,97]. To obtain DNA, all animals used in this study were sampled for approximately 200 μl of blood from the wing vein, or for tail feathers. Pedigrees for the population were established through direct field observa- tion in combination with molecular parentage verifica- tion using microsatellite markers [40,93,97]. The mapping population analysed here was selected from a large Siberian jay data set comprising more than 1000 individuals. Five major families consisting of 349 animals (172 males and 177 females) from the years 1975 to 2006 were identified. In the total pedigree, 169 different male and 142 different female offspring were fathered by 85 males and mothered by 95 females. The five family pedi- grees used for linkage analysis varied in depth from four to six generations and ranged in size from 72 to 97 ani- mals. These family pedigree configurations yield large numbers of pairwise relationships, which include, but are not limited to, parent-offspring, full-sibs, half-sibs, grand- parent-grandchild, great grandparent-great grandchild, avuncular, half-avuncular, and the first cousin relation- ships. The complex nature of the pedigree is mainly ascribed to two properties of the species. One is that the Siberian jays are philopatric, and some of the young remain in their natal territories up to the age of three years [98], such that the offspring occasionally enter the pedi- gree as parents in subsequent years. The other is that a few birds in one family are also involved as parental animals in another family and that several birds are present in more than one family pedigree. A more thorough descrip- tion of the structure of the mapping pedigree can be found from [40,42,93]. Microsatellite markers and genotyping Genomic DNAs were extracted from blood samples or from the tail feather shafts using the DNeasy Blood & Tis- sue Kit (Qiagen, Helsinki, Finland) following the manu- facturer's instructions as described earlier in [44]. A total of 117 polymorphic microsatellite loci were used, includ- ing nine markers previously described in [93], 92 loci in [44] and 16 developed in this study. Development of the 16 new microsatellites reported in this study was carried out as described in [44] and sequence data from the loci have been deposited with EMBL/GenBank Data Libraries (see Additional File 1). Detailed information of all these loci including their names, primer sequences, Genbank accession numbers, repeat motifs and the size range of the detected alleles is available in Additional File 1. All PCRs were multiplexed by combining 3 – 4 primer pairs in each reaction. The amplifications were performed in 10 μl reac- tions with 2 pm of each primer, 1× Quiagen multiplex mastermix, 0.5 × Q-solution, and approximately 30 ng of template DNA. The general temperature profile was 15 min at 95°C, 30 cycles of 30 sec at 94°C, 90 sec at 56°C and 60 sec at 72°C, followed by a final extension step at 72°C for 10 min. PCR products were analysed on Mega- BACE™ 1000 capillary sequencer (GE Healthcare Life Sci- ences, Little Chalfont, UK) and genotypes were determined using program Fragment Profiler version 1.2 (GE Healthcare Life Sciences, Little Chalfont, UK). In addition to the studied samples, one negative control and a reference DNA were included in all the amplifications in order to exclude the contaminant in the solutions and standardize the size of allele fragments of samples from different plates, respectively. Page 13 of 17 (page number not for citation purposes)