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https://hdl.handle.net/20.500.14094/90004528
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2024-03-29
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90004528 (fulltext)
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メタデータID
90004528
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open access
出版タイプ
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タイトル
IntroMap: a signal analysis based method for the detection of genomic introgressions
著者
Shea, Daniel J. ; Shimizu, Motoki ; Nishida, Namiko ; Fukai, Eigo ; Abe, Takashi ; Fujimoto, Ryo ; Okazaki, Keiichi
著者名
Shea, Daniel J.
著者名
Shimizu, Motoki
著者名
Nishida, Namiko
著者名
Fukai, Eigo
著者名
Abe, Takashi
著者ID
A0337
研究者ID
1000060620375
KUID
https://kuid-rm-web.ofc.kobe-u.ac.jp/profile/ja.2d794652078d165f520e17560c007669.html
著者名
Fujimoto, Ryo
藤本, 龍
フジモト, リョウ
所属機関名
農学研究科
著者名
Okazaki, Keiichi
収録物名
BMC Genetics
巻(号)
18
ページ
101-101
出版者
BioMed Central
刊行日
2017-12-04
公開日
2018-01-23
抄録
Background: Breeding programs often rely on marker-assisted tests or variant calling of next generation sequence (NGS) data to identify regions of genomic introgression arising from the hybridization of two plant species. In this paper we present IntroMap, a bioinformatics pipeline for the screening of candidate plants through the application of signal processing techniques to NGS data, using alignment to a reference genome sequence (annotation is not required) that shares homology with the recurrent parental cultivar, and without the need for de novo assembly of the read data or variant calling. Results: We show the accurate identification of introgressed genomic regions using both in silico simulated genomes, and a hybridized cultivar data set using our pipeline. Additionally we show, through targeted marker-based assays, validation of the IntroMap predicted regions for the hybrid cultivar. Conclusions: This approach can be used to automate the screening of large populations, reducing the time and labor required, and can improve the accuracy of the detection of introgressed regions in comparison to a marker-based approach. In contrast to other approaches that generally rely upon a variant calling step, our method achieves accurate identification of introgressed regions without variant calling, relying solely upon alignment.
キーワード
Plant breeding
Interspecific hybridization
Introgression
Signal analysis
カテゴリ
農学研究科
学術雑誌論文
権利
© The Author(s). 2017
This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
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journal article
言語
English (英語)
eISSN
1471-2156
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関連情報
DOI
https://doi.org/10.1186/s12863-017-0568-5
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