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Detection and characterization of genome-wide mutations in M1 vegetative cells of gamma-irradiated Arabidopsis

Radiation-induced mutations have been detected by whole-genome sequencing analyses of self-pollinated generations of mutagenized plants. However, large DNA alterations and mutations in non-germline cells were likely missed. In this study, in order to detect various types of mutations in mutagenized...

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Autores principales: Kitamura, Satoshi, Satoh, Katsuya, Oono, Yutaka
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8775353/
https://www.ncbi.nlm.nih.gov/pubmed/35051177
http://dx.doi.org/10.1371/journal.pgen.1009979
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author Kitamura, Satoshi
Satoh, Katsuya
Oono, Yutaka
author_facet Kitamura, Satoshi
Satoh, Katsuya
Oono, Yutaka
author_sort Kitamura, Satoshi
collection PubMed
description Radiation-induced mutations have been detected by whole-genome sequencing analyses of self-pollinated generations of mutagenized plants. However, large DNA alterations and mutations in non-germline cells were likely missed. In this study, in order to detect various types of mutations in mutagenized M1 plants, anthocyanin pigmentation was used as a visible marker of mutations. Arabidopsis seeds heterozygous for the anthocyanin biosynthetic genes were irradiated with gamma-rays. Anthocyanin-less vegetative sectors resulting from a loss of heterozygosity were isolated from the gamma-irradiated M1 plants. The whole-genome sequencing analysis of the sectors detected various mutations, including structural variations (SVs) and large deletions (≥100 bp), both of which have been less characterized in the previous researches using gamma-irradiated plant genomes of M2 or later generations. Various types of rejoined sites were found in SVs, including no-insertion/deletion (indel) sites, only-deletion sites, only-insertion sites, and indel sites, but the rejoined sites with 0–5 bp indels represented most of the SVs. Examinations of the junctions of rearrangements (SVs and large deletions), medium deletions (10–99 bp), and small deletions (2–9 bp) revealed unique features (i.e., frequency of insertions and microhomology) at the rejoined sites. These results suggest that they were formed preferentially via different processes. Additionally, mutations that occurred in putative single M1 cells were identified according to the distribution of their allele frequency. The estimated mutation frequencies and spectra of the M1 cells were similar to those of previously analyzed M2 cells, with the exception of the greater proportion of rearrangements in the M1 cells. These findings suggest there are no major differences in the small mutations (<100 bp) between vegetative and germline cells. Thus, this study generated valuable information that may help clarify the nature of gamma-irradiation-induced mutations and their occurrence in cells that develop into vegetative or reproductive tissues.
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spelling pubmed-87753532022-01-21 Detection and characterization of genome-wide mutations in M1 vegetative cells of gamma-irradiated Arabidopsis Kitamura, Satoshi Satoh, Katsuya Oono, Yutaka PLoS Genet Research Article Radiation-induced mutations have been detected by whole-genome sequencing analyses of self-pollinated generations of mutagenized plants. However, large DNA alterations and mutations in non-germline cells were likely missed. In this study, in order to detect various types of mutations in mutagenized M1 plants, anthocyanin pigmentation was used as a visible marker of mutations. Arabidopsis seeds heterozygous for the anthocyanin biosynthetic genes were irradiated with gamma-rays. Anthocyanin-less vegetative sectors resulting from a loss of heterozygosity were isolated from the gamma-irradiated M1 plants. The whole-genome sequencing analysis of the sectors detected various mutations, including structural variations (SVs) and large deletions (≥100 bp), both of which have been less characterized in the previous researches using gamma-irradiated plant genomes of M2 or later generations. Various types of rejoined sites were found in SVs, including no-insertion/deletion (indel) sites, only-deletion sites, only-insertion sites, and indel sites, but the rejoined sites with 0–5 bp indels represented most of the SVs. Examinations of the junctions of rearrangements (SVs and large deletions), medium deletions (10–99 bp), and small deletions (2–9 bp) revealed unique features (i.e., frequency of insertions and microhomology) at the rejoined sites. These results suggest that they were formed preferentially via different processes. Additionally, mutations that occurred in putative single M1 cells were identified according to the distribution of their allele frequency. The estimated mutation frequencies and spectra of the M1 cells were similar to those of previously analyzed M2 cells, with the exception of the greater proportion of rearrangements in the M1 cells. These findings suggest there are no major differences in the small mutations (<100 bp) between vegetative and germline cells. Thus, this study generated valuable information that may help clarify the nature of gamma-irradiation-induced mutations and their occurrence in cells that develop into vegetative or reproductive tissues. Public Library of Science 2022-01-20 /pmc/articles/PMC8775353/ /pubmed/35051177 http://dx.doi.org/10.1371/journal.pgen.1009979 Text en © 2022 Kitamura et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Kitamura, Satoshi
Satoh, Katsuya
Oono, Yutaka
Detection and characterization of genome-wide mutations in M1 vegetative cells of gamma-irradiated Arabidopsis
title Detection and characterization of genome-wide mutations in M1 vegetative cells of gamma-irradiated Arabidopsis
title_full Detection and characterization of genome-wide mutations in M1 vegetative cells of gamma-irradiated Arabidopsis
title_fullStr Detection and characterization of genome-wide mutations in M1 vegetative cells of gamma-irradiated Arabidopsis
title_full_unstemmed Detection and characterization of genome-wide mutations in M1 vegetative cells of gamma-irradiated Arabidopsis
title_short Detection and characterization of genome-wide mutations in M1 vegetative cells of gamma-irradiated Arabidopsis
title_sort detection and characterization of genome-wide mutations in m1 vegetative cells of gamma-irradiated arabidopsis
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8775353/
https://www.ncbi.nlm.nih.gov/pubmed/35051177
http://dx.doi.org/10.1371/journal.pgen.1009979
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