The Sequences of 1504 Mutants in the Model Rice Variety Kitaake Facilitate Rapid Functional Genomic Studies
Abstract
The availability of a whole-genome sequenced mutant population and the cataloging of mutations of each line at a single-nucleotide resolution facilitate functional genomic analysis. To this end, we generated and sequenced a fast-neutron-induced mutant population in the model rice cultivar Kitaake (Oryza sativa ssp japonica), which completes its life cycle in 9 weeks. We sequenced 1504 mutant lines at 45-fold coverage and identified 91,513 mutations affecting 32,307 genes, i.e., 58% of all rice genes. We detected an average of 61 mutations per line. Mutation types include single-base substitutions, deletions, insertions, inversions, translocations, and tandem duplications. We observed a high proportion of loss-of-function mutations. We identified an inversion affecting a single gene as the causative mutation for the short-grain phenotype in one mutant line. This result reveals the usefulness of the resource for efficient, cost-effective identification of genes conferring specific phenotypes. To facilitate public access to this genetic resource, we established an open access database called KitBase that provides access to sequence data and seed stocks. This population complements other available mutant collections and gene-editing technologies. In conclusion, this work demonstrates how inexpensive next-generation sequencing can be applied to generate a high-density catalog of mutations.
- Authors:
-
[1];
[1];
[1];
[3];
[5];
[3];
[1]
- Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616, Grass Genetics, Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616, Grass Genetics, Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California 94598
- Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616
- Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616, School of Life Sciences, Xiamen University, Xiamen 361102, China
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California 94598, HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER); National Institutes of Health (NIH); National Science Foundation (NSF)
- OSTI Identifier:
- 1573127
- Alternate Identifier(s):
- OSTI ID: 1425420
- Grant/Contract Number:
- AC02-05CH11231; GM59962; IOS-1237975
- Resource Type:
- Published Article
- Journal Name:
- Plant Cell
- Additional Journal Information:
- Journal Name: Plant Cell Journal Volume: 29 Journal Issue: 6; Journal ID: ISSN 1040-4651
- Publisher:
- Oxford University Press
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 54 ENVIRONMENTAL SCIENCES
Citation Formats
Li, Guotian, Jain, Rashmi, Chern, Mawsheng, Pham, Nikki T., Martin, Joel A., Wei, Tong, Schackwitz, Wendy S., Lipzen, Anna M., Duong, Phat Q., Jones, Kyle C., Jiang, Liangrong, Ruan, Deling, Bauer, Diane, Peng, Yi, Barry, Kerrie W., Schmutz, Jeremy, and Ronald, Pamela C. The Sequences of 1504 Mutants in the Model Rice Variety Kitaake Facilitate Rapid Functional Genomic Studies. United States: N. p., 2017.
Web. doi:10.1105/tpc.17.00154.
Li, Guotian, Jain, Rashmi, Chern, Mawsheng, Pham, Nikki T., Martin, Joel A., Wei, Tong, Schackwitz, Wendy S., Lipzen, Anna M., Duong, Phat Q., Jones, Kyle C., Jiang, Liangrong, Ruan, Deling, Bauer, Diane, Peng, Yi, Barry, Kerrie W., Schmutz, Jeremy, & Ronald, Pamela C. The Sequences of 1504 Mutants in the Model Rice Variety Kitaake Facilitate Rapid Functional Genomic Studies. United States. https://doi.org/10.1105/tpc.17.00154
Li, Guotian, Jain, Rashmi, Chern, Mawsheng, Pham, Nikki T., Martin, Joel A., Wei, Tong, Schackwitz, Wendy S., Lipzen, Anna M., Duong, Phat Q., Jones, Kyle C., Jiang, Liangrong, Ruan, Deling, Bauer, Diane, Peng, Yi, Barry, Kerrie W., Schmutz, Jeremy, and Ronald, Pamela C. Fri .
"The Sequences of 1504 Mutants in the Model Rice Variety Kitaake Facilitate Rapid Functional Genomic Studies". United States. https://doi.org/10.1105/tpc.17.00154.
@article{osti_1573127,
title = {The Sequences of 1504 Mutants in the Model Rice Variety Kitaake Facilitate Rapid Functional Genomic Studies},
author = {Li, Guotian and Jain, Rashmi and Chern, Mawsheng and Pham, Nikki T. and Martin, Joel A. and Wei, Tong and Schackwitz, Wendy S. and Lipzen, Anna M. and Duong, Phat Q. and Jones, Kyle C. and Jiang, Liangrong and Ruan, Deling and Bauer, Diane and Peng, Yi and Barry, Kerrie W. and Schmutz, Jeremy and Ronald, Pamela C.},
abstractNote = {The availability of a whole-genome sequenced mutant population and the cataloging of mutations of each line at a single-nucleotide resolution facilitate functional genomic analysis. To this end, we generated and sequenced a fast-neutron-induced mutant population in the model rice cultivar Kitaake (Oryza sativa ssp japonica), which completes its life cycle in 9 weeks. We sequenced 1504 mutant lines at 45-fold coverage and identified 91,513 mutations affecting 32,307 genes, i.e., 58% of all rice genes. We detected an average of 61 mutations per line. Mutation types include single-base substitutions, deletions, insertions, inversions, translocations, and tandem duplications. We observed a high proportion of loss-of-function mutations. We identified an inversion affecting a single gene as the causative mutation for the short-grain phenotype in one mutant line. This result reveals the usefulness of the resource for efficient, cost-effective identification of genes conferring specific phenotypes. To facilitate public access to this genetic resource, we established an open access database called KitBase that provides access to sequence data and seed stocks. This population complements other available mutant collections and gene-editing technologies. In conclusion, this work demonstrates how inexpensive next-generation sequencing can be applied to generate a high-density catalog of mutations.},
doi = {10.1105/tpc.17.00154},
journal = {Plant Cell},
number = 6,
volume = 29,
place = {United States},
year = {Fri Jun 02 00:00:00 EDT 2017},
month = {Fri Jun 02 00:00:00 EDT 2017}
}
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https://doi.org/10.1105/tpc.17.00154
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