BMC Genomics 2009, 10:1 http://www.biomedcentral.com/1471-2164/10/1 Results Characteristics of polymorphic microsatellites Of the 117 microsatellites scored, six loci (SJ009, SJ046, SJ048, SJ069, SJ083 and SJ108) were assigned to the Z- chromosome by observation of complete cosegregation with sex and the observation of heterozygosity in some males but none of the females in the pedigrees. None of the markers examined appeared to be situated in W-chro- mosome since all the markers had alleles in the males. The number of informative meioses varied from 33 (SJ047) to 474 (CKL5) with an average of 284.63 informative mei- oses per locus. More details about levels of genetic varia- bility (HO, HE and PIC) are shown in Additional File 1. Genetic linkage maps An overview of the linkage data is given in Figures 1, 2 and Table 1 depicting the best-position and framework link- age maps and their characteristics. Of the 117 microsatel- lites, 107 loci (91%) were assembled into 9 autosomal linkage groups (LG1 – LG9) and one Z-chromosome link- age group (LGZ), and the other 10 polymorphic microsat- ellites (SJ002, SJ003, SJ005, SJ020, SJ030, SJ034, SJ118, MJG1, PER1 and LTML8) appeared to be unlinked to any other marker by two-point analysis with LOD scores < 3.0. Of the ten unmapped markers, six had less than 60 informative meioses while four had more than 200 informative meioses. Of the nine autosomal LGs, seven comprised of six or more loci and the remaining three LGs each contained two or three loci, with an average of ca. 11 microsatellites per LG. For the sex-average autosomal LGs in the best-position map (Figure 1), the meiotic lengths, evaluated as the distance between the outermost markers on each LG, ranged from 10.6 cM (LG09) to 185.6 cM (LG01) spanning in total 862.8 cM of the Siberian jay genome. The average marker interval was 9.69 cM calcu- lated as the arithmetic mean of the map distances between adjacent markers (Table 1). On the maps, 35.9% (33/92) of the intervals between markers varied from 0 to 5 cM, 31.5% (29/92) ranged from 5 to 10 cM, and 20.7% (19/ 92) from 10 to 20 cM, and 12% (11/92) were > 20 cM. Sex-specific autosomal maps were also constructed (Fig- ure 1). The sum of the length of all autosomal LGs was 774.0 cM in males and 988.4 cM in females, with an aver- age intermarker spacing of 8.6 cM and 12.1 cM, respec- tively. The male map comprises LGs ranging in length from 7.7 cM to 171.1 cM while the female map contains LGs with a length from 9.2 cM to 229.2 cM (Table 1). Out of the nine pairs of male and female LGs, seven were larger in the female map and two were larger in the male map. In total, the autosomal LGs were smaller in males as com- pared to females with a female-to-male map ratio of 1.28. The sex-average map was intermediate in length between sex-specific maps, and 1.12 times longer than the male map. Framework markers, which could be ordered with LOD score of 3.0 or greater (indicating odds of 1000:1), are indicated in bold fonts in the best-position map (Figure 1). Of the total 107 mapped markers, 81 loci were signif- icantly ordered in the framework map and most (16/24) of the remaining loci could be placed with significant sup- port in either of two alternative intervals. When only the framework markers were considered, the total size of autosomal linkage groups was 692.1 cM in the sex-average map, 649.4 cM in the male map, and 799 cM in the female Table 1: Characteristics of the best-position and framework maps for Siberian jay LG Best-position map (cM) No. of loci Sex average LG1 29 LG2 27 LG3 13 LG4 11 LG5 8 LG6 6 LG7 3 LG8 2 LG9 2 LGAb 101 LGZ 6 185.6 181.5 182.6 98.2 85.2 78.2 26.4 14.5 10.6 862.8 23.8 213.6 229.2 197.9 110 92.9 98.9 24.3 9.2 12.4 988.4 10.6 168.3 141.3 171.1 86.7 82.1 65.4 32.3 19.1 7.7 774 48.9 Average inter- marker distancea 6.87 6.72 16.6 9.82 12.17 15.64 13.2 15.5 10.6 9.69 4.76 1.27 1.62 1.16 1.27 1.13 1.51 0.75 0.48 1.61 1.28 0.22 Female-specific linkage groups Male-specific linkage groups a The average inter-marker distance is based on the sex-average map b total autosomal linkage groups Framework map (cM) Ratio of / No. of loci Sex maps average 20 21 10 9 7 3 2 2 2 76 5 167.0 141.3 170.2 76.0 83.9 14.4 14.2 14.5 10.6 692.1 22.1 Average inter- marker distancea 182.8 212.1 175.5 88.3 93.4 15.5 9.8 9.2 12.4 799 10.6 156.7 8.35 116.8 6.73 171.3 17.02 63.8 8.44 78.4 11.99 13.2 4.80 22.4 7.10 19.1 7.25 7.7 5.30 649.4 9.11 44.8 4.42 Ratio of / maps 1.17 1.82 1.02 1.38 1.19 1.17 0.44 0.48 1.61 1.23 0.24 Page 3 of 17 (page number not for citation purposes)