2013 Fiscal Year Final Research Report
Pilot studies for high throughput analysis of Arabidopsis GWAS
| Project/Area Number |
24657029
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| Research Category |
Grant-in-Aid for Challenging Exploratory Research
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| Allocation Type | Single-year Grants |
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| Research Field |
Plant molecular biology/Plant physiology
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| Research Institution | Gifu University |
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Principal Investigator |
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| Co-Investigator(Renkei-kenkyūsha) |
KOBAYASHI Yuriko 岐阜大学, 応用生物科学部, 助教 (40610952)
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| Project Period (FY) |
2012-04-01 – 2014-03-31
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| Keywords | GWAS / 環境ストレス / 光合成 |
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| Research Abstract |
In this study, we tried GWAS mapping using Arabidopsis 80 accessions whose genome sequences have been published (Cao et al, 2011). DNA polymorphism data has been prepared from the genome sequences, and 1.5 M SNPs have been extracted. As for the phenotyping, environmental stress resistance has been measured using photoinhibition as a parameter of resistance. Association mapping was done using TASSEL (Bradbury et al, 2007) and STRUCTURE (Pritchard et al, 2000). Survey of the obtained GWAS signals revealed some differences from human GWAS signals in the peak height and distribution, and the differences are suggested to be due to different population structures between human and Arabidopsis. These differences are to be considered for modification of the human GWAS calculation methods to fit with Arabidopsis studies. As expected, false-positive GWAS signals were observed in our GWAS calculations, and they could be removed by deletion of minority SNP loci from the calculation.
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[Journal Article] ppdb: plant promoter database version 3.02014
Author(s)
Hieno A, Naznin HA, Hyakumachi M, Sakurai T, Tokizawa M, Koyama H, Sato N, Nishiyama T, Hasebe M, Zimmer AD, Lang D, Reski R, Rensing SA, Obokata J, and Yamamoto YY
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Journal Title
Nucleic Acids Res
Volume: 41
Pages: D1188-1192
DOI
Peer Reviewed
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[Presentation] Plant promoter analysis in the genomic age2012
Author(s)
Yohei Yoshioka, Mitsuro Hyakucachi, Yuriko Kobayashi, Hiroyuki Koyama, Satoshi Iuchi, Masatomo Kobayashi, Yutaka Suzuki, Sumio Sugano, Tetsuya Sakurai, Kazuo Shinozaki, Nobutaka Mitsuda, Masaru Ohme-Takagi, Yasuomi Tada, Yoshiharu Y. Yamamoto
Organizer
77th CSHL Symposium : The Biology of Plants 2012
Place of Presentation
Cold Spring Harbor Laboratory, USA
Year and Date
20120600
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