BMC Genomics 2009, 10:1 http://www.biomedcentral.com/1471-2164/10/1 FFeigmuarlee v3s. male recombination fraction for 97 pairs of adjacent markers from the 10 linkage groups in the Siberian jay Female vs. male recombination fraction for 97 pairs of adjacent markers from the 10 linkage groups in the Siberian jay. Likewise, most loci on the same chicken chromosome matched sequences on a single Siberian jay LG, with the exceptions of three unlinked loci (SJ005, SJ020 and SJ034) and loci SJ009, SJ039, SJ101 and SJ076 on GgaZ that mapped to four different LGs, LGZ and LG1, LG2, and LG3, respectively. The relative order of the markers mapped to the Siberian jay LGs was compared with the same loci on chicken chro- mosomes in Figure 4. The chicken-Siberian jay compari- son indicated that the order of loci was strikingly different between the chicken macrochromosomes Gga1, Gga2 and Siberian jay LG1, LG2 in the best-position map, respec- tively. Although some loci shared the same relative order in the two species, large rearrangements of the chromo- some would have been necessary to give rise to the differ- ent orders found here. The cases of inter- and intra- chromosomal rearrangements were involved mostly in the framework loci and represented a large proportion of Gga-LG1 that spanned around a 120-cM Siberian jay/20- Mb chicken interval. The three unlinked loci, SJ005, SJ020, and SJ034, were located at the distal ends of two chicken macrochromosomes, Gga1 and Gga2. Discussion This study constitutes the first mapping effort of the Sibe- rian jay genome, and is among the first ones to present a preliminary linkage map for any entirely natural verte- brate species from the wild (reviewed in [28]). The linkage map was composed using 107 polymorphic microsatellite loci typed on ca. 350 animals, making it one of the most detailed linkage maps available for natural animal popu- Page 7 of 17 (page number not for citation purposes)