ID | 57453 |
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著者 |
Tanaka, Tsuyoshi
Breeding Informatics Research Unit, Division of Basic Research, Institute of Crop Science, National Agriculture and Food Research Organization (NARO),
Ishikawa, Goro
Breeding Strategies Research Unit, Division of Basic Research, Institute of Crop Science, National Agriculture and Food Research Organization (NARO)
Ogiso-Tanaka, Eri
Soybean and Field Crop Applied Genomics Research Unit, Division of Field Crop Research, Institute of Crop Science, National Agriculture and Food Research Organization (NARO)
Yanagisawa, Takashi
Wheat and Barley Breeding Unit, Division of Wheat and Barley Research, Institute of Crop Science, National Agriculture and Food Research Organization (NARO)
Sato, Kazuhiro
Group of Genome Diversity, Institute of Plant Science and Resources, Okayama University
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抄録 | Marker-assisted selection of crop plants requires DNA markers that can distinguish between the closely related strains often used in breeding. The availability of reference genome sequence facilitates the generation of markers, by elucidating the genomic positions of new markers as well as of their neighboring sequences. In 2017, a high quality genome sequence was released for the six-row barley (Hordeum vulgare) cultivar Morex. Here, we developed a de novo RNA-Seq-based genotyping procedure for barley strains used in Japanese breeding programs. Using RNA samples from the seedling shoot, seedling root, and immature flower spike, we mapped next-generation sequencing reads onto the transcribed regions, which correspond to ∼590 Mb of the whole ∼4.8-Gbp reference genome sequence. Using 150 samples from 108 strains, we detected 181,567 SNPs and 45,135 indels located in the 28,939 transcribed regions distributed throughout the Morex genome. We evaluated the quality of this polymorphism detection approach by analyzing 387 RNA-Seq-derived SNPs using amplicon sequencing. More than 85% of the RNA-Seq SNPs were validated using the highly redundant reads from the amplicon sequencing, although half of the indels and multiple-allele loci showed different polymorphisms between the platforms. These results demonstrated that our RNA-Seq-based de novo polymorphism detection system generates genome-wide markers, even in the closely related barley genotypes used in breeding programs.
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キーワード | Japanese barley breeding
RNA-Seq
amplicon sequencing
barley; genotyping
barley
genotyping
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発行日 | 2019-05-10
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出版物タイトル |
Frontiers in plant science.
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巻 | 577巻
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出版者 | Frontiers Research Foundation
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開始ページ | 577
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ISSN | 1664-462X
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資料タイプ |
学術雑誌論文
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言語 |
英語
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OAI-PMH Set |
岡山大学
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著作権者 | Copyright © 2019 Tanaka, Ishikawa, Ogiso-Tanaka, Yanagisawa and Sato.
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論文のバージョン | publisher
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関連URL | isVersionOf https://doi.org/10.3389/fpls.2019.00577
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ライセンス | http://creativecommons.org/licenses/by/4.0/
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Citation | Tanaka T, Ishikawa G, Ogiso-Tanaka E, Yanagisawa T and Sato K (2019) Development of Genome-Wide SNP Markers for Barley via Reference- Based RNA-Seq Analysis. Front. Plant Sci. 10:577. doi: 10.3389/fpls.2019.00577
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