BMC Genomics 2009, 10:1 http://www.biomedcentral.com/1471-2164/10/1 Background Under various completed or ongoing projects, rapid progress has been attained in the generation of genomic resources for model organisms and domestic animals of medical, economic, or agricultural importance (e.g. [1- 3]). However, genomic resources for the majority of free- living vertebrates of ecological and evolutionary impor- tance are still scarce. For instance, in wild birds, develop- ment of genomic resources are still in their infancy, and only few initial efforts in linkage mapping [4-8], estima- tion of the extent of linkage disequilibrium [9,10], and syntenic comparison between related species [7,8,11-14] ] have been conducted. Hence, very limited information on the genome structure of wild bird species is available for further synthesis, as well as to study and characterize molecular underpinnings of phenotypic traits. Since wild passerine birds are important 'model' organisms in ecol- ogy and evolutionary biology, and in studies of life history evolution (e.g. [15]), behaviour (e.g. [16,17]) and evolu- tionary quantitative genetics in particular (e.g. [18-20]), knowledge of their genome structure and organization is vital to advance our understanding of the genetic basis of ecologically important traits [21]. Genetic maps constitute essential and powerful organiza- tional tools for genomic research [22]. Among the most important applications of genetic maps in genomic anal- yses is in that they provide a platform to support studies utilizing or aiming to apply candidate gene approaches [21,23], QTL mapping [24], comparative genomics [25], and genome annotation [26]. However, construction of genetic linkage maps for non-model organisms is compli- cated by several factors [27,28]. One of the major obsta- cles for the construction of linkage maps in passerine birds (but see [4]) is the scarcity of informative genetic markers. Among a variety of molecular makers previously employed in linkage mapping in different organisms, microsatellite markers have often proven most useful due to their hypervariability, fast evolutionary rates, codomi- nance, wide distribution throughout the genomes, and the relative ease with which they can be developed and genotyped using the polymerase chain reaction (PCR; e.g. [29]). While genetic maps exist in one form or another for various species, it is worth noticing that the studies are so far generally limited to domestic animals or natural pop- ulations of wild species that can easily be bred in captivity, or where sufficiently large litter sizes are being produced in natural settings and are accessible to sampling to allow the establishment of the pedigree necessary for linkage analysis [9]. Unfortunately, the characteristics that make populations practical for linkage mapping [9] are found only among a small fraction of species studied by ecolo- gist and evolutionary biologists. Linkage maps have now been constructed in four populations of non-model ani- mals for which long-term individual-based datasets are available (see also: [8]), and where natural long-term ped- igrees (rather than experimental breeding programmes) have been used to follow the co-segregation of marker alleles [28]. Two of these mapping populations are in ungulate species (soay sheep, Ovis aries [24]; red deer, Cer- vus elaphus [27]) and two are in passerine birds (great reed warbler, Acrocephalus arundinaceus [4,6,13]; collared fly- catcher, Ficedula albicollis [5,9,11]). The Siberian jay (Perisoreus infaustus) is a passerine bird which has been subject to considerable ecological and evolutionary research during the past decades. Studies in its breeding biology [30-33], mating system [34,35], for- aging behaviour [36], reproductive success [37], parental care and dispersal pattern [38,39], family structure [40], phenotypic plasticity [41] and levels of inbreeding [42] have been conducted. Thus, these previous studies form an appropriate setting in an initiative to explore the inte- gration of genomics with the domain of ecology and evo- lutionary biology [43], provided that at least some basic knowledge of the species' genome can be obtained. With an access to detailed pedigrees of a Siberian jay popula- tion monitored over 30 years [40,42], as well as access to a novel set of polymorphic microsatellites developed for this species [44], construction of a linkage map is now realistic. In an evolutionary context, the chicken genome sequence [45] released recently facilitates genomic studies in other bird species by comparative genomic approaches [13,25]. Moreover, given the early divergence of avian lin- eages between passeriforms and galliforms (≈ 100 million years ago; [46]) and the high level of phylogenetic diver- gence between jays belonging to the Corvidae family and the other passerines for which linkage maps have been published (e.g. [47,48]), a linkage map of the Siberian jay may provide new insights into avian genome evolution, and thereby also to the extensive morphological, life his- torical and behavioural diversification within the order Passeriformes (see [47]). The aim of this study was to develop a first-generation genetic linkage map for a wild population of Siberian jays on the basis of 117 microsatellites, including a novel set of 108 markers. To this end, a framework map was con- structed to identify markers whose local relative orders were statistically well supported with an unambiguous location in the map. Since heterochiasmy has been observed in previous studies of many species (e.g. zebrafish [49]; and great reed warbler [4]), sex-specific variation in the recombination rate and the genetic map distance were also investigated. Furthermore, to provide a comparative perspective to address the evolution of genome organisation the extent of synteny and locus order conservation between Siberian jay and chicken was evaluated by a BLAST analysis against the chicken genome sequence. Page 2 of 17 (page number not for citation purposes)