163 86 112 210 34 77 97 SxM 113 HxO MxB 359 106 107 VFeignunrdeia3gram showing marker overlap Venn diagram showing marker overlap. A four-way Venn diagram illustrates all unique, two-way, three-way and four-way sets of shared markers. The mapping populations are abbreviated as in the text: MxB = Morex × Barke, OWB = Oregon Wolfe Barley, SxM = Steptoe × Morex, HxO = Haruna Nijo × OHU602. SxM map of Kleinhofs and Graner [11] are included in Table S1 (Additional File 3). Overall, cross-referencing the 2943 SNP-only map to previous maps provides an impor- tant bridge between additional resources including a physical map now being coupled to the 2943 SNP-only map and QTLs, simple trait determinants and deletion sites that already have been mapped in prior work. Szűcs et al. [10] included 1472 of the SNPs developed in the present work in addition to SSRs, AFLPs and DArT mark- ers, making the resulting OWB map an excellent new point of cross-reference for barley markers. Synteny Each barley SNP source sequence was compared to the rice (Oryza sativa) version 5 and version 6 gene models [13] using BLASTX, and the top hit was taken as the most similar rice gene. These rice best hit coordinates were used as the basis of alignments of each of the seven barley chro- mosomes with the twelve rice chromosomes. Figure 5 is a screen shot from HarvEST:Barley [14] showing a detailed alignment of barley chromosome 5H with rice chromo- somes. From this and each of the other six barley-rice alignments the marker density is sufficient to clearly reveal major elements of barley-rice synteny, consistent in general with prior publications on Triticeae-rice synteny (for example [15,16]. The short arm of barley 5H is syn- tenic with rice 12 L. The long arm of barley 5H is syntenic with an interspersion of rice 12S and 11S genes followed by rice 9S, then rice 9 L, then rice 3 L. The position of the BMC Genomics 2009, 10:582 http://www.biomedcentral.com/1471-2164/10/582 OWB 404 243 597 235 centromere in each barley chromosome was determined using flow-sorted chromosome arms in work that will be described in detail elsewhere (Prasanna Bhat et al. in prep- aration). Of the seven barley chromosomes, 5H has the most complex barley-rice synteny relationship, being the only barley chromosome composed of major syntenous blocks from more than two ancestors of rice chromo- somes. An illustration of barley-rice synteny for all seven barley chromosomes is provided in Figure 6. The simplest relationships are essentially total synteny between barley 3H versus rice 1 (3HS = 1S, 3HL = 1L) and barley 6H ver- sus rice 2 (6HS = 2S, 6HL = 2L). The four remaining barley chromosomes each are composed of ancestors of two rice chromosomes, in each case having one ancestral chromo- some nested within the pericentric region, flanked by seg- ments of the other syntenic chromosome. Detailed views of synteny similar to Figure 5, but with zoom-in and active links to external databases, are available for all seven chro- mosomes through the Windows version of HarvEST:Bar- ley [14]. An interesting consequence of the evolutionary history of barley chromosomes is that the number of expressed genes in the pericentric regions is highly variable, ranging from relatively few in the cases of barley 3H and 6H to very many in the most extreme case of barley 7H. The rel- ative genetic map density of expressed genes has major implications for plant breeding efforts. If, for example, a trait maps to an ancestral telomeric region within the peri- centric region of barley 7H then it will be much less likely that the gene controlling that trait can be separated from neighbouring genes by recombination than, for example, a gene located in the ancestral centromeric region of rice chromosome 9, which is located in a more recombina- tionally active region on barley chromosome 5H. For example there have been several as yet unsuccessful attempts to map-base clone Mlg, a powdery mildew resist- ance gene located in the gene-dense pericentric region of 4H (Matthew Moscou, unpublished data). Similarly, the level of difficulty in map-based cloning efforts will also depend on the gene density in regions of low recombina- tion. Due to high gene density in ancestral telomeric regions which are now nested within barley chromo- somes, the pericentric regions of five barley chromosomes (1H, 2H, 4H, 5H and 7H) have high gene density. The version 6 rice genome sequence coordinates, includ- ing chromosome, arm and base pair position, are included in Table S4 (Additional File 14), along with the chromosome and arm position from version 5. The 2943 genetically mapped barley SNPs were derived from 2786 source sequences, of which 2703 have a rice BLASTX match of at least 7 × e-5. A total of 36 of these had a best BLASTX against a gene positioned to different rice chro- mosomes when comparing ortholog locations in rice ver- Page 6 of 13 (page number not for citation purposes)