BMC Genomics 2009, 10:1 http://www.biomedcentral.com/1471-2164/10/1 ences (see [63,73]). For example, numbers of hypotheses including sexual selection [83]), haploid selection [86], sex differences in the internal or external environment [4] and sex differences in gene expression [67] have been evoked to explain the heterochiasmy pattern in birds. In this long-term isolated population studied here, we assume that the heterochiasmy could be more or less attributed to the sexual selection and the sex differences in the internal environment. However, irrespectively of the proximate mechanisms, the significant sex differences in recombination rates in the Siberian jay have obvious prac- tical implications for future work. For instance, the lower average rate of recombination in males than in females should be advantageous for QTL-mapping of genetic traits in initial low resolution analysis [87]. Conserved synteny, but changed marker order, in a genomic comparison with the chicken The study confirms the remarkable degree of conserved synteny between passerines and chicken (see [4,6- 9,13,14]), albeit based on only a small number of compa- rable chromosomes. Surprisingly, loci SJ039, SJ076 and SJ101 on autosomal LGs were mapped to GgaZ, which was known to be homologous to Z chromosome in pas- serines [this study, [8,9,13]]. As argued in [12], this obser- vation may suggest chromosome fusions/fissions, a spurious match, or a more complex history of the loci. Future mapping studies may help to elucidate this. Locus SJ009, which was identified within the PAR region for the Siberian jay, was found to be conserved between LGZ and GgaZ. This is consistent with previous reports of cytoge- netic and genetic mapping of the Z chromosome that the PAR region was conserved between chicken and passer- ines [8,88]. However, this is not the case for the other three loci (SJ039, SJ076 and SJ101) on the autosomal LGs in Siberian jay. Thus, there are more inconsistencies than consistencies in the Z-chromosomal genomic comparison between Siberian jay and chicken in this study, which is different from previous results of Z-chromosomal synteny between the passerines and chicken [9,12,13]. Further studies to explore the potential explanations are needed in the future. The BLAST analysis located three unlinked loci, SJ005, SJ020 and SJ034 on Gga1 and Gga2. This can be explained by the fact that these three markers had few informative meioses and therefore low power in linkage analysis and/or that these loci are located in telomeric region, which may have a higher recombination rate. Indeed, as indicated in Figure 4, these three loci are located to the end of Gga1 and Gga2 in chicken (SJ005 at 2.0 Mb of Gga1, SJ020 at 1.1 Mb of Gga1; SJ034 at 2.1 Mb of Gga2). Although synteny was conserved, there were multiple cases of inter- and intra-chromosomal rearrangements. Similar patterns have also been observed in other passer- ine birds on both sex and autosomal chromosomes (see [9,14]). As a contrast to the previous studies, the extent of chromosomal rearrangements as observed in the Gga1- LG1 and Gga2-LG2 comparisons has not previously been reported. For example, in the comparative mapping anal- ysis between the zebra finch and the chicken, only a few instances of inversions and translocations were found for chromosome 1 [8]. Of the total 22 homologous loci between chicken and Siberian jay found here, 12 loci (12/ 22, 55%) were involved in inter- or intra-chromosomal rearrangement, while a lesser proportion of the rearrange- ments were observed in the chicken/collared flycatcher (26/159, 16.4%) [7] and chicken/great reed warbler (7/ 44, 15.9%) comparisons [13]. There are several possible explanations for the different rates of genome evolution, e.g. the species-specific differences in rate of mutations and/or genome evolution could have contributed to the more or less genetic similarity of different passerines to the chicken; also, it has been suggested that population structuring in species with otherwise large population sizes facilitate chromosomal rearrangements. However, the scenario outlined here should be considered with cau- tion because (i) a small number of comparable chromo- somes (n = 6) was identified here between the Siberian jay and the chicken; (ii) most of the chromosomal rearrange- ments are only from three chromosomes (chromosomes 1, 2 and Z). Thus, further extensive comparative mapping of genomes and genetic linkage maps of the chicken, zebra finch, great reed warbler and Siberian jay with more and denser genome coverage should provide a more detailed picture of marker order rearrangement between passerines and chicken during avian evolution. Also, more sequence data to make the genome comparison between the chicken and the zebra finch, whose genomes are only currently sequenced in birds, is worthwhile. At any rate, the important message from our comparative analyses is that a high level of observed synteny does not necessarily mean conserved marker order. If the internal rearrangements tend to occur frequently across the genome, then map information derived from one species will not be readily transferable to another. Conclusion A salient feature of genetic linkage maps is that they improve with use. The described linkage maps of Siberian jay genome presented here, based on a large number of informative meioses, will serve as a basis for a future high- resolution map. In particular, the framework map should enable the rapid construction of the next generation of higher-density linkage maps. From the evolutionary infer- ence point-of-view, the linkage maps constructed here have potential to contribute to our understanding of pat- terns of genome evolution in birds, and that of passerines in particular. In addition, despite the need for increased density of markers, the maps will be also potentially use- Page 12 of 17 (page number not for citation purposes)