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MiRiQ Database: A Platform for In Silico Rice Mutant Screening
Takahiko Kubo1, Yoshiyuki Yamagata1, Hiroaki Matsusaka1
1Faculty of Agriculture, Kyushu University, 744 Motooka Nishi-ku, Fukuoka, 819-0395 Japan.
Plant & Cell Physiology
|November 6, 2023
Summary
Researchers developed the Mutation-induced Rice in Kyushu University (MiRiQ) database, offering a powerful tool for in silico screening of rice mutants. This resource accelerates plant gene function discovery and crop improvement by providing access to millions of genetic variations.
Area of Science:
- Plant Genomics
- Functional Genomics
- Crop Science
Background:
- Genetic studies are crucial for understanding plant gene function.
- Next-generation sequencing enables large-scale mutant library analysis.
- Efficient tools are needed for in silico mutant screening.
Purpose of the Study:
- To create and release an open-access database for in silico mutant screening.
- To provide easy access to a whole-genome-sequenced rice mutant library.
- To facilitate functional genomic research and crop improvement.
Main Methods:
- Development of the Mutation-induced Rice in Kyushu University (MiRiQ) database.
- Whole-genome sequencing of 721 M1 mutant rice plants (Nipponbare).
- Incorporation of 1.6 million single-nucleotide variants (SNVs) and InDels.
Main Results:
- The MiRiQ database (version 1.0) is now publicly accessible.
- Mutations identified in 87% of annotated protein-coding genes.
- Database includes search tools and JBrowse for mutation analysis.
Conclusions:
- The MiRiQ database accelerates mutant identification and functional analysis.
- It provides a valuable resource for the plant science community and breeders.
- Facilitates efficient crop improvement through genetic variation data.
Related Concept Videos
01:16In-vitro Mutagenesis
To learn more about the function of a gene, researchers can observe what happens when the gene is inactivated or “knocked out,” by creating genetically engineered knockout animals. Knockout mice have been particularly useful as models for human diseases such as cancer, Parkinson’s disease, and diabetes.
01:16In vitro Mutagenesis
To learn more about the function of a gene, researchers can observe what happens when the gene is inactivated or “knocked out,” by creating genetically engineered knockout animals. Knockout mice have been particularly useful as models for human diseases such as cancer, Parkinson’s disease, and diabetes.
02:46Genetic Screens
Genetic screens are tools used to identify genes and mutations responsible for phenotypes of interest. Genetic screens help identify individuals or a group of people at risk of developing genetic diseases and help them with early intervention, targeted therapy, and reproductive options.
Forward genetic screens
Forward or “classical” genetic screens involve creating random mutations in an organism’s DNA using radiation, mutagens, or insertion of additional bases, which result in visible changes...
Forward genetic screens
Forward or “classical” genetic screens involve creating random mutations in an organism’s DNA using radiation, mutagens, or insertion of additional bases, which result in visible changes...