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Title: The Sequences of 1,504 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];  [2];  [3];  [1];  [3];  [3];  [4];  [2];  [5];  [1];  [3];  [3];  [3];  [6];  [1]
  1. Univ. of California, Davis, CA (United States). Dept. of Plant Pathology and the Genome Center; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Grass Genetics/Joint BioEnergy Inst. and Environmental Genomics and Systems Biology
  2. Univ. of California, Davis, CA (United States). Dept. of Plant Pathology and the Genome Center; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Grass Genetics/Joint BioEnergy Inst.
  3. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  4. Univ. of California, Davis, CA (United States). Dept. of Plant Pathology and the Genome Center
  5. Univ. of California, Davis, CA (United States). Dept. of Plant Pathology and the Genome Center; Xiamen Univ., Xiamen (China). School of Life Sciences
  6. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); HudsonAlpha Inst. for Biotechnology, Huntsville, AL (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23); 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 Volume: 29; Journal Issue: 6; Journal ID: ISSN 1040-4651
Publisher:
American Society of Plant Biologists
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 1,504 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 1,504 Mutants in the Model Rice Variety Kitaake Facilitate Rapid Functional Genomic Studies. United States. 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, and Ronald, Pamela C. Fri . "The Sequences of 1,504 Mutants in the Model Rice Variety Kitaake Facilitate Rapid Functional Genomic Studies". United States. doi:10.1105/tpc.17.00154.
@article{osti_1573127,
title = {The Sequences of 1,504 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 = {2017},
month = {6}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1105/tpc.17.00154

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Cited by: 16 works
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Works referencing / citing this record:

CRISPR/Cas9-targeted mutagenesis of Os8N3 in rice to confer resistance to Xanthomonas oryzae pv. oryzae
journal, August 2019