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Plant Reprod. 2018 Mar;31(1):117-128. doi: 10.1007/s00497-018-0331-8. Epub 2018 Mar 1.

Development of the Mitsucal computer system to identify causal mutation with a high-throughput sequencer.

Author information

1
Division of Biological Sciences, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan. takamasa@thaliana.myhome.cx.
2
Exploratory Research for Advanced Technology (ERATO), Higashiyama Live-Holonics Project, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan. takamasa@thaliana.myhome.cx.
3
Department of Biological Chemistry, College of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501, Japan. takamasa@thaliana.myhome.cx.
4
Department of Biological Chemistry, College of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501, Japan.
5
Laboratory of Biochemistry, Graduate School of Bio-agricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan.
6
Division of Biological Sciences, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan.
7
Exploratory Research for Advanced Technology (ERATO), Higashiyama Live-Holonics Project, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan.
8
Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan.

Abstract

Development of Mitsucal. Recent advances in DNA sequencing technology have facilitated whole-genome sequencing of mutants and variants. However, the analyses of large sequence datasets using a computer remain more difficult than operating a sequencer. Forward genetic approach is powerful even in sexual reproduction to identify key genes. Therefore, we developed the Mitsucal computer system for identifying causal genes of mutants, using whole-genome sequence data. Mitsucal includes a user-friendly web interface to configure analysis variables, such as background and crossed strains. Other than configuration, users are only required to upload short reads. All results are presented through a web interface where users can easily obtain a short list of candidate mutations. In the present study, we present three examples of Arabidopsis mutants defective in sexual reproduction in which Mitsucal is used to identify causal mutation. One mutant was screened from seeds of a transgenic line with a reporter gene to elucidate the mechanisms involved in the regulation of seed oil storage. The identified gene codes for a protein may be involved in mRNA splicing. Other two mutants had defects in the surface walls on pollen termed exine. Both causal genes were identified, and mutants were found to be allele of known mutants. These results show that Mitsucal could facilitate identification of causal genes.

KEYWORDS:

Arabidopsis mutant; Bioinformatics; Bulk segregant analysis; Whole-genome sequence

PMID:
29497825
DOI:
10.1007/s00497-018-0331-8
[Indexed for MEDLINE]

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