start-ver=1.4 cd-journal=joma no-vol=10 cd-vols= no-issue= article-no= start-page= end-page= dt-received= dt-revised= dt-accepted= dt-pub-year=2009 dt-pub=20091204 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Development and implementation of high-throughput SNP genotyping in barley en-subtitle= kn-subtitle= en-abstract= kn-abstract=Background: High density genetic maps of plants have, nearly without exception, made use of marker datasets containing missing or questionable genotype calls derived from a variety of genic and non-genic or anonymous markers, and been presented as a single linear order of genetic loci for each linkage group. The consequences of missing or erroneous data include falsely separated markers, expansion of cM distances and incorrect marker order. These imperfections are amplified in consensus maps and problematic when fine resolution is critical including comparative genome analyses and map-based cloning. Here we provide a new paradigm, a high-density consensus genetic map of barley based only on complete and error-free datasets and genic markers, represented accurately by graphs and approximately by a best-fit linear order, and supported by a readily available SNP genotyping resource. Results: Approximately 22,000 SNPs were identified from barley ESTs and sequenced amplicons; 4,596 of them were tested for performance in three pilot phase Illumina GoldenGate assays. Data from three barley doubled haploid mapping populations supported the production of an initial consensus map. Over 200 germplasm selections, principally European and US breeding material, were used to estimate minor allele frequency (MAF) for each SNP. We selected 3,072 of these tested SNPs based on technical performance, map location, MAF and biological interest to fill two 1536-SNP "production" assays (BOPA1 and BOPA2), which were made available to the barley genetics community. Data were added using BOPA1 from a fourth mapping population to yield a consensus map containing 2,943 SNP loci in 975 marker bins covering a genetic distance of 1099 cM. 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 pericentric 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 chromosomes. Examination of US breeding germplasm illustrated the usefulness of BOPA1 and BOPA2 in that they provide excellent marker density and sensitivity for detection of minor alleles in this genetically narrow material. en-copyright= kn-copyright= en-aut-name=CloseTimothy J. en-aut-sei=Close en-aut-mei=Timothy J. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=BhatPrasanna R. en-aut-sei=Bhat en-aut-mei=Prasanna R. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=LonardiStefano en-aut-sei=Lonardi en-aut-mei=Stefano kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=WuYonghui en-aut-sei=Wu en-aut-mei=Yonghui kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=RostoksNils en-aut-sei=Rostoks en-aut-mei=Nils kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=RamsayLuke en-aut-sei=Ramsay en-aut-mei=Luke kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= en-aut-name=DrukaArnis en-aut-sei=Druka en-aut-mei=Arnis kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= en-aut-name=SteinNils en-aut-sei=Stein en-aut-mei=Nils kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=8 ORCID= en-aut-name=SvenssonJan T. en-aut-sei=Svensson en-aut-mei=Jan T. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=9 ORCID= en-aut-name=WanamakerSteve en-aut-sei=Wanamaker en-aut-mei=Steve kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=10 ORCID= en-aut-name=BozdagSerdar en-aut-sei=Bozdag en-aut-mei=Serdar kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=11 ORCID= en-aut-name=RooseMikeal L. en-aut-sei=Roose en-aut-mei=Mikeal L. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=12 ORCID= en-aut-name=MoscouMatthew J. en-aut-sei=Moscou en-aut-mei=Matthew J. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=13 ORCID= en-aut-name=ChaoShiaoman en-aut-sei=Chao en-aut-mei=Shiaoman kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=14 ORCID= en-aut-name=VarshneyRajeev K. en-aut-sei=Varshney en-aut-mei=Rajeev K. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=15 ORCID= en-aut-name=SzuecsPeter en-aut-sei=Szuecs en-aut-mei=Peter kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=16 ORCID= en-aut-name=SatoKazuhiro en-aut-sei=Sato en-aut-mei=Kazuhiro kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=17 ORCID= en-aut-name=HayesPatrick M. en-aut-sei=Hayes en-aut-mei=Patrick M. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=18 ORCID= en-aut-name=MatthewsDavid E. en-aut-sei=Matthews en-aut-mei=David E. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=19 ORCID= en-aut-name=KleinhofsAndris en-aut-sei=Kleinhofs en-aut-mei=Andris kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=20 ORCID= en-aut-name=MuehlbauerGary J. en-aut-sei=Muehlbauer en-aut-mei=Gary J. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=21 ORCID= en-aut-name=DeYoungJoseph en-aut-sei=DeYoung en-aut-mei=Joseph kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=22 ORCID= en-aut-name=MarshallDavid F. en-aut-sei=Marshall en-aut-mei=David F. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=23 ORCID= en-aut-name=MadishettyKavitha en-aut-sei=Madishetty en-aut-mei=Kavitha kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=24 ORCID= en-aut-name=FentonRaymond D. en-aut-sei=Fenton en-aut-mei=Raymond D. kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=25 ORCID= en-aut-name=CondaminePascal en-aut-sei=Condamine en-aut-mei=Pascal kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=26 ORCID= en-aut-name=GranerAndreas en-aut-sei=Graner en-aut-mei=Andreas kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=27 ORCID= en-aut-name=WaughRobbie en-aut-sei=Waugh en-aut-mei=Robbie kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=28 ORCID= affil-num=1 en-affil= kn-affil=Univ Calif Riverside, Dept Bot & Plant Sci affil-num=2 en-affil= kn-affil=Univ Calif Riverside, Dept Bot & Plant Sci affil-num=3 en-affil= kn-affil=Univ Calif Riverside, Dept Comp Sci affil-num=4 en-affil= kn-affil=Univ Calif Riverside, Dept Comp Sci affil-num=5 en-affil= kn-affil=Scottish Crop Res Inst affil-num=6 en-affil= kn-affil=Scottish Crop Res Inst affil-num=7 en-affil= kn-affil=Scottish Crop Res Inst affil-num=8 en-affil= kn-affil=Leibniz Inst Plant Genet & Crop Plant Res IPK affil-num=9 en-affil= kn-affil=Univ Calif Riverside, Dept Bot & Plant Sci affil-num=10 en-affil= kn-affil=Univ Calif Riverside, Dept Bot & Plant Sci affil-num=11 en-affil= kn-affil=Univ Calif Riverside, Dept Comp Sci affil-num=12 en-affil= kn-affil=Univ Calif Riverside, Dept Bot & Plant Sci affil-num=13 en-affil= kn-affil=Univ Calif Riverside, Dept Bot & Plant Sci affil-num=14 en-affil= kn-affil=USDA ARS, Biosci Res Lab affil-num=15 en-affil= kn-affil=Leibniz Inst Plant Genet & Crop Plant Res IPK affil-num=16 en-affil= kn-affil=Oregon State Univ, Dept Crop & Soil Sci affil-num=17 en-affil= kn-affil=Okayama Univ, Bioresources Res Inst affil-num=18 en-affil= kn-affil=Oregon State Univ, Dept Crop & Soil Sci affil-num=19 en-affil= kn-affil=Cornell Univ, USDA ARS affil-num=20 en-affil= kn-affil=Washington State Univ, Dept Crop & Soil Sci affil-num=21 en-affil= kn-affil=Univ Minnesota, Dept Agron & Plant Genet affil-num=22 en-affil= kn-affil=Univ Calif Los Angeles, So Calif Genotyping Consortium affil-num=23 en-affil= kn-affil=Scottish Crop Res Inst affil-num=24 en-affil= kn-affil=Univ Calif Riverside, Dept Bot & Plant Sci affil-num=25 en-affil= kn-affil=Univ Calif Riverside, Dept Bot & Plant Sci affil-num=26 en-affil= kn-affil=Univ Calif Riverside, Dept Bot & Plant Sci affil-num=27 en-affil= kn-affil=Leibniz Inst Plant Genet & Crop Plant Res IPK affil-num=28 en-affil= kn-affil=Scottish Crop Res Inst END