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ID 52278
フルテキストURL
著者
Close, Timothy J. Univ Calif Riverside, Dept Bot & Plant Sci
Bhat, Prasanna R. Univ Calif Riverside, Dept Bot & Plant Sci
Lonardi, Stefano Univ Calif Riverside, Dept Comp Sci
Wu, Yonghui Univ Calif Riverside, Dept Comp Sci
Rostoks, Nils Scottish Crop Res Inst
Ramsay, Luke Scottish Crop Res Inst
Druka, Arnis Scottish Crop Res Inst
Stein, Nils Leibniz Inst Plant Genet & Crop Plant Res IPK
Svensson, Jan T. Univ Calif Riverside, Dept Bot & Plant Sci
Wanamaker, Steve Univ Calif Riverside, Dept Bot & Plant Sci
Bozdag, Serdar Univ Calif Riverside, Dept Comp Sci
Roose, Mikeal L. Univ Calif Riverside, Dept Bot & Plant Sci
Moscou, Matthew J. Univ Calif Riverside, Dept Bot & Plant Sci
Chao, Shiaoman USDA ARS, Biosci Res Lab
Varshney, Rajeev K. Leibniz Inst Plant Genet & Crop Plant Res IPK
Szuecs, Peter Oregon State Univ, Dept Crop & Soil Sci
Sato, Kazuhiro Okayama Univ, Bioresources Res Inst
Hayes, Patrick M. Oregon State Univ, Dept Crop & Soil Sci
Matthews, David E. Cornell Univ, USDA ARS
Kleinhofs, Andris Washington State Univ, Dept Crop & Soil Sci
Muehlbauer, Gary J. Univ Minnesota, Dept Agron & Plant Genet
DeYoung, Joseph Univ Calif Los Angeles, So Calif Genotyping Consortium
Marshall, David F. Scottish Crop Res Inst
Madishetty, Kavitha Univ Calif Riverside, Dept Bot & Plant Sci
Fenton, Raymond D. Univ Calif Riverside, Dept Bot & Plant Sci
Condamine, Pascal Univ Calif Riverside, Dept Bot & Plant Sci
Graner, Andreas Leibniz Inst Plant Genet & Crop Plant Res IPK
Waugh, Robbie Scottish Crop Res Inst
抄録
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.
発行日
2009-12-04
出版物タイトル
BMC Genomics
10巻
出版者
Biomed Central Ltd
ISSN
1471-2164
資料タイプ
学術雑誌論文
言語
English
OAI-PMH Set
岡山大学
著作権者
© 2009 Close et al; licensee BioMed Central Ltd.
論文のバージョン
publisher
査読
有り
DOI
Web of Sience KeyUT