BMC Genomics 2009, 10:1 http://www.biomedcentral.com/1471-2164/10/1 which the results were found to be quite robust with 150 individuals and 10% of missing values, our data had much less missing values (4.5%) and a larger sample size (349 individuals). Hence, the potential biases in our map due to missing values are unlikely to be severe. Map construction and genome coverage The resulting linkage map of 107 microsatellites spans a total sex-average length of 886.6 cM, with 10 LGs. The number of markers within the data that showed signifi- cant linkage (LOD > 3.0) with at least one other marker was very high (107/117, 91.5%), a phenomenon observed also in a linkage mapping study of the great reed warbler [53]. Of the 10 unlinked markers (LOD < 3.0), four demonstrate sufficiently informative meiosis, sug- gesting that these four unlinked markers were most likely located on unique chromosomes or chromosome arms. The haploid number of ca. 40 chromosomes is typical for passerine birds (e.g. 7 macro-, 32 micro-, and a pair of sex- chromosomes in the zebra finch genome [54]) and the chicken genome is composed of 39 haploid chromo- somes (8 macro and 30 micro, and a pair of sex chromo- somes [54]). Thus, the presence of small groups and unlinked markers indicates that appreciable gaps of at least 29 additional linkage groups should be filled to con- solidate the Siberian jay map. The discrepancy between the number of LGs and the haploid number of chromo- somes has been commonly reported when constructing linkage maps in avian species (see [4]). These results could be explained in terms of the non-random distribution of microsatellites in the avian genome, where microchromo- somes – typically scarce of microsatellites [55] – consti- tute a large proportion (ca. 80%) of the total number of chromosomes. Considering the avian order Passeriformes, the current sex-pooled map of the Siberian jay at 887 cM is larger than recent maps in the great reed warbler (155 – 237 cM [4]; 707 – 858 cM [6]), but smaller than those in the collared flycatcher (1787 cM [7]) and the zebra finch (1068 cM [8]). The maximum genome coverage of the markers described in this study was estimated to be 1187 cM (887 + 200 + 100 cM) (see[56,57]), covering about a third of the Siberian jay genome of ~3800 cM, if estimated by assuming a similar genome size as in chicken [54]. It is clear that some of the microchromosomes are poorly rep- resented, or not represented at all, in the current map. This poorer coverage of the microchromosomes, as well as of the Z-chromosome, is in good agreement with the obser- vations in chicken [56], Japanese quail [58], duck [3], and great reed warbler [4,6]. However, it was argued in [8] that for the whole-genome map of the zebra finch using 876 SNPs the shorter length of linkage map relative to that of the chicken is ascribed to its unusually lower recombina- tion rates. Similarly, lower recombination rates and smaller length of linkage map were also revealed in the collared flycatchers based on 147 gene markers and 64 microsatellites [7]. Since it has been suggested that passer- ines generally have lower recombination rates than the chicken [8], the small map sizes here may also be partly due to reduced recombination rates in the Siberian jays. Nevertheless, the first-generation linkage map will undoubtedly evolve as more markers are added, with some additional linkage groups forming and some pairs of now described linkage groups coalescing into a single group. As linkage maps continue to develop, future work on the genetic map will increase the genome coverage by adding more novel genetic markers, for example, 1000's of SNP loci and additional markers will improve the resolving power of the map. A more saturated map should give more information about the genome size, exact kary- otype number and chromosomal rearrangement of Sibe- rian jay. The constructed framework map was comprised only of loci with unambiguous positions relative to each other. As shown in Table 2, only a slight expansion of the frame- work map size was detected when the non-framework markers were included in the analysis. Non-significant (P > 0.05) difference in the interval distances between frame- work markers was found in the sex-specific maps when non-framework markers were included or not, which can be due to the fact that most (19/26) of the non-framework loci still can be placed with significant (LOD = 2; odds of 100:1) support in either of two alternative intervals at LOD = 3 (odds of 1000:1). However, on the sex-average maps, a significant (P < 0.05) difference in distances between framework markers was revealed when including or excluding the non-framework markers from the analy- sis. This is probably due to the overall effect of the recom- bination heterogeneity between the sexes on estimates of sex-average map distances between framework and non- framework markers [49]. Thus, our results indicate that the framework maps can serve as the backbone of the best- position maps with a high level of confidence. Moreover, the framework map should also therefore provide a robust basis with which to apply to other pedigrees and for comparing genomic rearrangements with closely related species. Z-chromosome By assigning six genetic markers to the Z-chromosome on the basis of Mendelian inheritance and additional two- point analysis tests, we found that the recombination rates in the Z-chromosome linkage group differed sub- stantially among the sexes. In particular the ratio of recombination fraction in females (θF) and males (θM), θF/θM, in the LGZ (θF/θM < 1) contrasted markedly with those in seven of the nine autosomal linkage groups (θF/ θM > 1). These results conform to the Z-chromosome link- Page 10 of 17 (page number not for citation purposes)