BMC Genomics 2009, 10:582 http://www.biomedcentral.com/1471-2164/10/582 BFaigrluerye-ri6ce synteny summary Barley-rice synteny summary. Seven barley linkage groups represented as rice synteny blocks. Numbers inside each barley chromosome indicate syntenic rice chromosome arm. were derived from ESTs and 491 from amplicon sequences. The composition of POPA2 included 1536 barley SNPs, one per gene including 258 genes repre- sented on POPA1, of which 1456 were from ESTs and 80 from amplicon sequences. BOPA1 BOPA1 represented 705 SNPs from POPA1 and 832 from POPA2, including one SNP in common. All BOPA1 SNPs had a satisfactory technical performance on POPA1 or POPA2 and a minor allele frequency of at least 0.08. To the extent of results presented in this manuscript, BOPA1 included 1414 mapped and 122 unmapped SNPs. POPA3 Residual SNPs from the sources of POPA1 and POPA2 were insufficient to complete the design of POPA3 with- out compromising on the SNP selection criteria. Addi- tional SNPs for POPA3 came from three sources: 1) an extended list of 5,732 SNPs identified in SCRI amplicon sequences, 2) colleagues who contributed SNPs from amplicon sequences of specific genes of biological interest and 3) an expanded barley EST resource. The first two of these additional sources were exhausted for POPA3 design. In the selection of EST-derived SNPs, priority was given to genes previously classified as having interesting expression patterns during malting or upon exposure to pathogens, or relevant to malting, brewing quality, abiotic stress or phenology. The composition of POPA3 included 1536 barley SNPs, in many cases more than one per gene and in some cases including genes represented on POPA1 or POPA2. In total, 967 POPA3 SNPs were derived from ESTs and 569 from amplicon sequences. BOPA2 BOPA2 represented 406 SNPs from POPA1, 178 from POPA2 and 952 from POPA3. The primary emphases of BOPA2 were representation of mapped SNPs that were not included on BOPA1 and inclusion of multiple SNPs for certain genes to reveal haplotypes at these loci, with some weight given to MAF. BOPA2 contained 921 SNPs with MAF at least 0.08, 256 SNPs with MAF at least 0.04 but less than 0.08, 345 SNPs with MAF least 0.005 but less than 0.04, and 14 SNPs with only one allele (MAF = 0) in the germplasm examined using POPA3. To the extent of results presented in this manuscript, BOPA2 included 1263 mapped and 273 unmapped SNPs. A total of 967 SNPs were from ESTs and 569 from amplicon sequences. SNP annotations Table S4 (Additional File 14) provides alternative SNP names arising from this work, and several annotation fields for all SNPs represented on POPA1, POPA2, POPA3, BOPA1 and BOPA2. The annotations include BLAST hits to the rice and Arabidopsis genomes and Uni- Prot, the relationship of SNP source sequences to Har- vEST:Barley unigenes and probe sets on the Affymetrix Barley1 GeneChip and source consensus sequences. To assign SNP loci on the genetic map to chromosome arms, centromere positions were identified using flow-sorted chromosome arms following the method described in Simkova et al. [24]; results of this work will be described elsewhere (Bhat et al., in preparation). The annotation information in Table S4 (Additional File 14) is also avail- able from HarvEST:Barley [14] and [20]. The HarvEST BLAST server [25] provides the 2943 mapped SNP uni- gene sequences as a searchable database. DNA sources Genomic DNAs of 93 doubled haploid maplines and the parents (Dom, Rec) of the Oregon Wolfe Barley (OWB) population [26,27] 148 doubled haploids and the parents of the Steptoe × Morex (SxM) population [7,28], 95 dou- bled haploid maplines and the parents of the Haruna Nijo × OHU602 (HxO) population and 213 additional germ- plasm samples were purified using Plant DNeasy (Qiagen, Valencia, CA, USA) starting with 100-300 mg of young seedling leaves. Genomic DNAs of 93 doubled haploid maplines and the Barke parent from the Morex × Barke population (Stein et al. unpublished) were produced using a CTAB method. All DNA samples were checked for concentration using UV spectroscopy and Quant-iT PicoGreen (Invitrogen, Carlsbad, CA, USA) and adjusted to approximately 120 ng/μl in TE buffer. Page 9 of 13 (page number not for citation purposes)