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Title: Genome-Wide Sequencing of 41 Rice (Oryza sativa L.) Mutated Lines Reveals Diverse Mutations Induced by Fast-Neutron Irradiation

Abstract

Fast-neutron (FN) irradiation has been used to create mutagen-ized collections of many plant species (Bolon et al., 2014). FN-induced mutagenesis has clear advantages: it is an efficientmeans of saturating the genome, and it does not involve time-consuming plant transformation or tissue culture. In rice, mostmutant collections, although highly valuable, were generated us-ing either T-DNA insertion or transposon tagging approaches thatoften induce mutations unlinked to the insertion and complicatinganalysis (Wang et al., 2013). Another disadvantage of some ofthese collections is that they were created in rice varieties thatare photoperiod-sensitive and often have long generation times.

Authors:
; ; ; ; ; ; ; ; ; ;
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)
OSTI Identifier:
1460494
Alternate Identifier(s):
OSTI ID: 1616049
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Published Article
Journal Name:
Molecular Plant
Additional Journal Information:
Journal Name: Molecular Plant Journal Volume: 9 Journal Issue: 7; Journal ID: ISSN 1674-2052
Publisher:
Elsevier
Country of Publication:
United Kingdom
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Li, Guotian, Chern, Mawsheng, Jain, Rashmi, Martin, Joel A., Schackwitz, Wendy S., Jiang, Liangrong, Vega-Sánchez, Miguel E., Lipzen, Anna M., Barry, Kerrie W., Schmutz, Jeremy, and Ronald, Pamela C. Genome-Wide Sequencing of 41 Rice (Oryza sativa L.) Mutated Lines Reveals Diverse Mutations Induced by Fast-Neutron Irradiation. United Kingdom: N. p., 2016. Web. doi:10.1016/j.molp.2016.03.009.
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Li, Guotian, Chern, Mawsheng, Jain, Rashmi, Martin, Joel A., Schackwitz, Wendy S., Jiang, Liangrong, Vega-Sánchez, Miguel E., Lipzen, Anna M., Barry, Kerrie W., Schmutz, Jeremy, & Ronald, Pamela C. Genome-Wide Sequencing of 41 Rice (Oryza sativa L.) Mutated Lines Reveals Diverse Mutations Induced by Fast-Neutron Irradiation. United Kingdom. https://doi.org/10.1016/j.molp.2016.03.009
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Li, Guotian, Chern, Mawsheng, Jain, Rashmi, Martin, Joel A., Schackwitz, Wendy S., Jiang, Liangrong, Vega-Sánchez, Miguel E., Lipzen, Anna M., Barry, Kerrie W., Schmutz, Jeremy, and Ronald, Pamela C. Fri . "Genome-Wide Sequencing of 41 Rice (Oryza sativa L.) Mutated Lines Reveals Diverse Mutations Induced by Fast-Neutron Irradiation". United Kingdom. https://doi.org/10.1016/j.molp.2016.03.009.
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@article{osti_1460494,
title = {Genome-Wide Sequencing of 41 Rice (Oryza sativa L.) Mutated Lines Reveals Diverse Mutations Induced by Fast-Neutron Irradiation},
author = {Li, Guotian and Chern, Mawsheng and Jain, Rashmi and Martin, Joel A. and Schackwitz, Wendy S. and Jiang, Liangrong and Vega-Sánchez, Miguel E. and Lipzen, Anna M. and Barry, Kerrie W. and Schmutz, Jeremy and Ronald, Pamela C.},
abstractNote = {Fast-neutron (FN) irradiation has been used to create mutagen-ized collections of many plant species (Bolon et al., 2014). FN-induced mutagenesis has clear advantages: it is an efficientmeans of saturating the genome, and it does not involve time-consuming plant transformation or tissue culture. In rice, mostmutant collections, although highly valuable, were generated us-ing either T-DNA insertion or transposon tagging approaches thatoften induce mutations unlinked to the insertion and complicatinganalysis (Wang et al., 2013). Another disadvantage of some ofthese collections is that they were created in rice varieties thatare photoperiod-sensitive and often have long generation times.},
doi = {10.1016/j.molp.2016.03.009},
journal = {Molecular Plant},
number = 7,
volume = 9,
place = {United Kingdom},
year = {Fri Jul 01 00:00:00 EDT 2016},
month = {Fri Jul 01 00:00:00 EDT 2016}
}
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Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1016/j.molp.2016.03.009
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Cited by: 58 works
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Figures / Tables:

Figure 1 Figure 1: (A) Strategy for generating and sequencing the rice FN-mutagenized population. Seeds from individual M1 plants were collected separately and stored. Genomic DNA isolated from a single M3 plant was used in sequencing. (B) Representation of the diversity of mutations induced by FN irradiation. The inner pie chart indicatesmore » the number of each type of mutation in the 41 sequenced M3 lines. The outer circle shows the number of genes affected by each type of mutation. SBS, single base substitutions; DEL, deletions; INS, insertions; INV, inversions; TRA, translocations; and DUP, tandem duplications. (C) Comparisons between FN-induced SBSs and the SNPs present between X.Kitaake and the Nipponbare reference genome. Ti, transitions; Tv, transversions. (D) Size distribution of FN-induced deletions the 41 rice mutant lines. The x axis shows deletion size in the log10 scale, and the y axis depicts the number of deletion events in the log2 scale. (E) Representation of the 12 rice chromosomes on an Mb scale. The centromere is indicated by a black line. (F) Representation of repetitive sequences in the reference genome in non-overlapping windows (window size = 500 kb). The darker the color, the higher content of repetitive sequence. Repeat data were derived from RGAP version 7. (G) The sequencing depth of the 42 rice lines, including the 41 M3 lines and the nonirradiated parental line X.Kitaake. (H) Genome-wide distribution of FN-induced mutations in non-overlapping 500-kb windows. The highest bar shown in chromosome 1 equates to 17 mutations/500 kb. (I) Translocations. Each line is colored according to the smaller number chromosome that the translocation involves. (J) The frequency of the number of FN-induced mutations per mutant line in the 41 M3 lines. (K) The frequency of the number of genes affected per mutant line in the 41 M3 lines.« less
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