BMC Genomics 2009, 10:1 http://www.biomedcentral.com/1471-2164/10/1 map (Figure 2 and Table 1). We compared recombination distances between adjacent framework markers that were mapped on both the best-position map and the frame- work map and overall the female-to-male ratio for the framework map was 1.23, slightly lower than the ratio of 1.28 observed above in the best-position map. Among the Z-linked microsatellites, all six markers showed highly significant linkage between each other with LODs > 37.0. This linkage group spanned 23.8 cM in the sex-average map, 48.9 cM in the male map and 10.6 cM in female map, which corresponds to a female-to-male ratio of 0.22. The female linkage map indicates the posi- tion and approximate extent of a pseudoautosomal region (PAR) from SJ069 to beyond SJ048. In females, no recom- bination was observed between SJ083 and SJ046 and no heterozygosity was observed for these markers; therefore they must lie outside the pseudoautosomal region, sug- gesting that the pseudoautosomal boundary lies between SJ048 and SJ046. As expected, there is considerable differ- ence in male and female recombination rates for the pseu- doautosomal region of the Z-chromosome, with the male distance between SJ108 and SJ069 being 41.7 cM as com- pared to the female distance of 5.1 cM. This increased sex- specific recombination rate between the three pseudoau- tosomal loci was similar to the observations in the pseu- doautosomal regions of the mammalian sex chromosomes, for example in humans [50], ovines [51] and bovines [52]. In the sex-average map, the map density was 4.0 cM/marker among all Z-linked markers and 3.3 cM/marker among the five framework loci. Differences in recombination rate between sexes In addition to a much shorter total length of autosomal linkage maps in males than in females, the maps allowed comparison of meiotic recombination rate between sexes. The sexes show significant differences in recombination rates, both in general and for specific pairs of linked mark- ers (Wilcoxon's signed-rank test, P = 0.037; Figure 3 and Table 2). In the best-position map (Figure 1), the propor- tion of intervals in the autosomal linkage groups that demonstrated a higher recombination fraction in females was 54.3%. Among all adjacent autosomal markers the recombination fraction was 1.28 times higher in females than in the males. However, there were exceptions to this in some LGs, and in some specific intervals within LGs. For instance, LG7 and LG8 exhibited higher recombina- tion fractions in males than in females (Table 2). The number of intervals that show higher recombination frac- tions in the male map relative to the female map was less, but not negligible (Figure 3). When investigating the dis- tortions over the autosomal linkage groups, two of the nine linkage groups showed significant (P < 0.05) differ- ence in recombination rate between the sex-specific maps (Table 2). This was also observed when the overall map length was investigated for sex-specific difference. All in all, these results suggest that overall recombination is sig- nificantly suppressed in male meiosis as compared to female meiosis. Comparative mapping The BLAST searches under both settings generated the same set of significant hits at 1e-10. We found 25 homolo- gous (21.4%, 25/117) zebra finch sequences using a cross-species MEGABLAST search in NCBI's zebra finch genome database (Table 3). By BLAST searching using two methods, in total 22 mapped (20.5%, 22/107) and three unlinked loci for which a homologous sequence could be identified in chicken were assigned to a chromosomal location in the chicken genome (Table 3). The 10 Siberian jay LGs corresponded to five different autosomal and one Z chromosome in chicken. Loci from the same Siberian jay LG matched sequences on a single chicken chromo- some in the BLAST analysis (Figure 4 and Table 3), with the exception of loci SJ039, SJ101 and SJ076 on the auto- somal LGs (LG1, LG2, and LG3, respectively) that mapped to chicken chromosome Z (GgaZ), whereas the other loci on these LGs mapped to the chicken autosomes. Table 2: The Wilcoxon's signed-rank test results for recombination fraction (θ) between sexes with linkage groups Average θFb Average θMc Wilcoxon's signed-rank test (P)d Linkage groups LG1 LG2 LG3 LG4 LG5 LG6 LG7 LG8 LG9 Total autosomal LGZ Na 28 26 12 10 7 5 2 1 1 92 5 0.071 0.085 0.152 0.101 0.127 0.178 0.115 0.09 0.12 0.101 0.02 0.055 0.054 0.133 0.077 0.110 0.126 0.145 0.18 0.08 0.079 0.094 θF/θM 1.29 1.57 1.14 1.31 1.15 1.41 0.79 0.5 1.5 1.28 0.21 0.174 0.046 * 0.323 0.038 * 0.687 0.192 0.5 - - 0.037 * 0.025* a number of intervals; b average recombination fraction in females; c average recombination fractions in males; d *, significant, P < 0.05. Page 6 of 17 (page number not for citation purposes)