BMC Genomics 2009, 10:582 http://www.biomedcentral.com/1471-2164/10/582 SFeigmureent4of a consensus directed acyclic graph Segment of a consensus directed acyclic graph. A typ- ical segment of a directed acyclic graph representing the con- sensus map of one barley linkage group is shown. Each oval represents one bin of SNP markers, using POPA names for SNPs. Where an oval contains more than one SNP, it means that there was no evidence of recombination in any mapping population between those markers. The observed recombi- nation frequencies between marker bins are shown. The exact order of marker bins cannot be solved with certainty unless markers are shared between maps. Recombination frequencies are often not proportional to physical distance, nor consistent, when comparing two or more maps from dif- ferent mapping populations. Therefore directed acyclic graphs provide a more exact description of the limit of knowledge of the marker order than does a linear map derived using approximations based on recombination val- ues. See the text for further discussion. sion 5 to version 6. It is interesting that 14 of the 36 (39%) changes in the rice genome annotations brought rice-bar- ley synteny into line with the barley genetic map, 9 of the 36 (25%) changes degraded rice-barley synteny and 12 (33%) had a neutral effect because neither the version 5 nor 6 rice annotations were syntenic with barley. One had a neutral effect because both BLAST hits were consistent with syntenic duplications in the barley and rice genomes. It is not unusual to find imperfect synteny such as the 12 of 36 (33%) revised but non-syntenic positions; in fact 745 of the 2703 mapped barley SNP source sequences (27.6%) do not point to a best rice BLASTX within the major synteny block. However, from this comparison of the edited positions in rice versions 5 versus 6 to the 2943 SNP barley genetic linkage map, it appears that the barley SNP map is the more stable point of reference. Conse- quently, it may be of some benefit to use the barley genetic map for further revisions of the rice genome sequence. BOPA1 and BOPA2 elements and performance As discussed above, the two production OPAs, BOPA1 and BOPA2, had somewhat different design elements. These differences have been reflected in the performance of BOPA1 and BOPA2 for the genotyping of breeding germplasm within the BarleyCAP project [17]. Table 2 provides a comparison of BOPA1 and BOPA2 in relation to both SNP representation and the performance on 960 year 2006 US breeder DNA samples in the BarleyCAP project. Table 2 also summarizes information provided in greater detail in Table S4 (Additional File 14) on the rela- tionship of BOPA SNPs to probe sets on the Affymetrix Barley1 GeneChip [18] and the 2943 mapped SNPs in the present work. Extensive analyses of the diversity of breed- ing germplasm will be the subject of other papers; here we emphasize only the elements and fundamental perform- ance characteristics of BOPA1 and BOPA2. One can see that BOPA1, which was designed using only SNPs with a minor allele frequency (MAF) of at least 0.08 in the design germplasm, yielded MAF values less than 0.05 for only 164 SNPs (10.7%) in the US breeding materials. In con- trast BOPA2, which targeted 615 SNPs with MAF less than 0.08 in the design germplasm, yielded MAF values less than 0.05 for 585 SNPs (38.1%) in the breeding germ- plasm. This included about three times as many SNPs with MAF = 0 (301 versus 99) and 4.4 times as many SNPs (284/65) with MAF between 0 and 0.05. Thus, BOPA2 has greater sensitivity to detect rare alleles than does BOPA1, some of which may be important for the development of new varieties containing uncommon alleles of certain genes. But, this increased sensitivity is counterbalanced by a compromise in the reduced frequency of informative SNPs in general. Page 7 of 13 (page number not for citation purposes)