BMC Genomics 2009, 10:582 http://www.biomedcentral.com/1471-2164/10/582 BFaigrluerye-ri5ce synteny in detail for 5H Barley-rice synteny in detail for 5H. HarvEST screen- shot showing barley-rice synteny for chromosome 5H. Colored lines connect each barley locus to the position of the best BLAST hit on the rice genome. Table S5 (Additional File 15) lists the MAF values deter- mined during the design of BOPA1 and BOPA2 versus the observed MAF values in year 2006 and year 2007 Barley- CAP breeding germplasm. For example, 11 of 157 SNPs with a design MAF of 0.01 or lower had an observed MAF of at least 0.08 in year 2006 or 2007 breeding germplasm. Similarly, 25 of 283 SNPs with a design MAF of 0.024 or lower had an observed MAF of at least 0.10 in year 2006 or 2007 breeding germplasm. The differences between BOPA1 and BOPA2 should be carefully considered by potential users, and the characteristics of specific SNPs should be considered when selecting subsets of SNPs for other platforms. Other characteristics of the 2943 SNP map It is perhaps of relevance that there were significant differ- ences in the genetic length of some of the individual chro- mosomes in the different populations (Table 1). For example, the genetic length of chromosome 4H in the SxM population is expanded relative to the same chromo- some in any other population, and all of the other chro- mosomes have a longer genetic length in the OWB population than in the other populations. Also, the genetic map lengths are consistently higher than would be expected from cytogenetic counts of chiasmata per meio- sis for this species, as previously noted [19] despite the fact that methodological errors in genotyping can be ruled out in the present work because of the lack of any suspi- cious-looking singleton double recombinants. The nota- ble deviations from mean genetic distance values indicate that the genetic background as well as environmental fac- tors may have had a significant effect on recombination, and presumably also chiasmata counts, in this species. Also, although the broad patterns of synteny within grasses recognized previously by many investigators has been confirmed by this work, the hitherto unprecedented density of gene-derived markers enable further delinea- tion of several inversions and rearrangements of gene order at macro-, meso- and micro-synteny levels. Chro- mosome 5H (Figure 5) provides one example of such rear- rangements at the macrosynteny level. The HarvEST:Barley http://harvest.ucr.edu synteny viewer pro- vides zoom-in functionality to enable visualization at meso and micro-synteny levels as well. Access to the linkage map and SNP data The 2943 SNP linkage map can be accessed by several browsers including HarvEST:Barley [14] or [20], Grain- Genes [21], NCBI [22] and THT [23]. New versions of the map may become available as additional mapping popu- lations are applied to BOPA1 and BOPA2, linkage dise- quilibrium is used for mapping and the physical map and genome sequence are coupled to the genetic linkage map. Conclusion The unprecedented density of genic markers and marker bins enabled a high resolution comparison of the genomes of barley and rice. Low recombination in peri- centric regions is evident from bins containing many more than the average number of markers, meaning that a large number of genes are recombinationally locked into the genetic centromeric regions of several barley chromo- somes. Examination of US breeding germplasm illus- trated the usefulness of BOPA1 and BOPA2 in that they provide excellent marker density and sensitivity for detec- tion of minor alleles in this genetically narrow material. Methods Five 1536-SNP GoldenGate assays (Figure 1, Table 2) Three pilot-phase 1536-SNP GoldenGate assays were developed. These "pilot OPAs" are referred to as POPA1, POPA2 and POPA3. Two 1536-SNP production-scale OPAs, referred to as BOPA1 and BOPA2, were developed from SNPs tested on the pilot OPAs. All sequences used as SNP sources were generated using the Sanger dideoxy chain termination method. POPA1 and POPA2 The contents of POPA1 and POPA2 came from an initial list of SNPs comprised of the union of three intersecting lists from SCRI (1,658 SNPs), IPK (985 SNPs) and UCR (12,615 SNPs). SCRI and IPK SNPs were derived from PCR amplicon sequences, whereas UCR SNPs were derived nearly entirely from EST sequences. In the selec- tion of SNPs for the OPAs, preference was given to SNPs derived from amplicon sequences. Nearly all SNPs on POPA1 and about 60% of the SNPs on POPA2 targeted stress-regulated genes. The composition of POPA1 included 1524 barley SNPs, one per gene, of which 1033 Page 8 of 13 (page number not for citation purposes)