BMC Genomics 2009, 10:1 http://www.biomedcentral.com/1471-2164/10/1 Table 3: The homologous loci of microsatellites mapped in Siberian jay on the chicken and zebra finch genome assigned using BLAST analyses of the clone sequences of the microsatellites and the homologous zebra finch WGS sequences. Locus Linkage group Zebra finch Ensemble ID Chicken Ensemble ID Gga a Chicken genome start position (bp) SJ010 LG1 SJ016 LG1 SJ022 LG1 SJ025 LG1 SJ057 LG1 SJ094 LG1 SJ113 LG1 SJ020 unlinked SJ005 unlinked SJ036 LG2 SJ072 LG2 CK.1B5D LG2 SJ026 LG2 SJ054 LG2 SJ116 LG2 SJ034 unlinked SJ015 LG3 SJ032 LG7 SJ087 LG7 SJ117 LG7 SJ049 LG4 SJ009 LGZ SJ101 LG2 SJ039 LG1 SJ076 LG3 SJ050 LG1 SJ051 LG1 SJ055 LG1 SJ064 LG1 SJ112 LG1 CK.2A5A LG1 SJ029 LG4 SJ033 LG4 SJ106 LG4 SJ017 LG5 SJ041 LG9 SJ069 LGZ SJ083 LGZ gb|AC188472.1 - - gb|AC188472.1 - - - - gb|AC188184.3 - - gb|AC225878.2 gb|AC206427.2 gb|AC188186.2 gb|AC148379.2 - gb|AC188188.2 - gb|AC155211.2 - - - gb|AC213969.2 gb|AC231254.2 gb|AC188376.1 gb|AC189030.1 gb|AC189030.1 gb|AC189030.1 gb|AC206426.2 gb|AC192320.2 gb|AC188469.1 gb|AC188184.3 gb|AC188469.1 gb|AC188184.3 gb|AC192320.2 gb|AC210531.1 gb|AC188466.2 gb|AC229626.2 NW_001471554.1 Gga1_WGA51_2b NW_001471545.1 Gga1_WGA43_2b NW_001471526.1 Gga1_WGA26_2b NW_001471534.1 Gga1_WGA33_2b NW_001471554.1 Gga1_WGA51_2b NW_001471554.1 Gga1_WGA51_2b NW_001471545.1 Gga1_WGA43_2b NW_001471529.1 Gga1_WGA29_2b NW_001471513.1 Gga1_WGA14_2c NW_001471639.1 Gga2_WGA66_2b NW_001471633.1 Gga2_WGA60_2b NW_001471639.1 Gga2_WGA66_2b NW_001471639.1 Gga2_WGA66_2c NW_001471633.1 Gga2_WGA60_2c NW_001471633.1 Gga2_WGA60_2c NW_001471654.1 Gga2_WGA81_2b NW_001471673.1 Gga3_WGA106_2c NW_001471681.1 Gga4_WGA107_2b NW_001471681.1 Gga4_WGA107_2c NW_001471681.1 Gga4_WGA107_2b NW_001471710.1 Gga5_WGA136_2b NW_001488876.1 GgaZ_WGA457_2b NW_001488849.1 GgaZ_WGA430_2b NW_001488882.1 GgaZ_WGA463_2c NW_001488862.1 GgaZ_WGA443_2c - - - - - - - - - - - - - 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 3 4 4 4 5 Z Z Z Z - - - - - - - - - - - - - 9,129,918 9,256,107 2,462,620 20,407,077 7,801,901 22,042,793 8,757,200 1,098,266 2,080,202 20,469,429 32,273,874 23,539,833 21,465,630 6,229,425 22,279,892 2,075,856 3,458,567 8,679,773 4,015,500 8,679,607 9,314,084 1,412,682 1,097,987 1,315,022 825,441 - - - - - - - - - - - - - a Chicken chromosome number; b Via the clone sequences of the Siberian jay microsatellites; c Via the homologous zebra finch WGS sequences lations [28]. In fact, it is one of only a few genetic linkage maps of wild bird species to date. Apart from the revealing evidence for sex differences in recombination rates, the constructed maps represent an excellent resource from which the markers may be selected for future mapping projects in this and related species, as well as for compar- ative genomic studies of genome organisation. In what follows, we will discuss the salient features of the con- structed linkage maps in comparison to similar maps and results from earlier studies. In particular, we will pay attention to sex-specific differences in recombination rates, map coverage and some other issues deserving future attention. Genotyping in the mapping population The constructed map contains 107 microsatellites, of which 101 are autosomal, three Z-chromosome-specific and three pseudoautosomal loci (see below). The ideal set of molecular marker data for linkage mapping has no missing values, no genotyping errors and the markers seg- regate in the expected ratio for the specific type of popula- tion [53]. In practice, however, mapping data is compromised in all of these respects. However, as simu- lated and concluded in previous research [53], the effect of missing genotypes depends greatly on the sample size: the smaller the sample, the more severe the effects are likely to be. In comparison to published simulations, in Page 8 of 17 (page number not for citation purposes)