Time Course Analysis of Genome-Wide Identification of Mutations Induced by and Genes Expressed in Response to Carbon Ion Beam Irradiation in Rice (Oryza sativa L.)

Zhang, Jian; Peng, Ziai; Liu, Qiling; Yang, Gangyi; Zhou, Libin; Li, Wenjian; Wang, Hui; Chen, Zhiqiang; Guo, Tao

doi:10.3390/genes12091391

Cited by 7 publications

(5 citation statements)

References 38 publications

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“…The mutation rate increases with the increase in dose below 150 Gy, and the mutation effect decreases with the increase in dose above 150 Gy [16]. The mutation rate induced by 80 Gyd carbon ion beam is higher than that induced by 40 Gy carbon ion beam [26]. The relatively higher radiation dosage used in this study may lead to higher mutation frequency.…”

Section: The Mutation Rate Of Dehulled Rice Seeds Induced By Carbon I...mentioning

confidence: 58%

Genome-Wide Profile of Mutations Induced by Carbon Ion Beam Irradiation of Dehulled Rice Seeds

Ling,

Zhang,

Huang

et al. 2024

IJMS

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As a physical mutagen, carbon ion beam (CIB) irradiation can induce high-frequency mutation, which is user-friendly and environment-friendly in plant breeding. In this study, we resequenced eight mutant lines which were screened out from the progeny of the CIB-irradiated dehulled rice seeds. Among these mutants, CIB induced 135,535 variations, which include single base substitutions (SBSs), and small insertion and deletion (InDels). SBSs are the most abundant mutation, and account for 88% of all variations. Single base conversion is the main type of SBS, and the average ratio of transition and transversion is 1.29, and more than half of the InDels are short-segmented mutation (1–2 bp). A total of 69.2% of the SBSs and InDels induced by CIBs occurred in intergenic regions on the genome. Surprisingly, the average mutation frequency in our study is 9.8 × 10−5/bp and much higher than that of the previous studies, which may result from the relatively high irradiation dosage and the dehulling of seeds for irradiation. By analyzing the mutation of every 1 Mb in the genome of each mutant strain, we found some unusual high-frequency (HF) mutation regions, where SBSs and InDels colocalized. This study revealed the mutation mechanism of dehulled rice seeds by CIB irradiation on the genome level, which will enrich our understanding of the mutation mechanism of CIB radiation and improve mutagenesis efficiency.

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Section: The Mutation Rate Of Dehulled Rice Seeds Induced By Carbon I...mentioning

confidence: 58%

Genome-Wide Profile of Mutations Induced by Carbon Ion Beam Irradiation of Dehulled Rice Seeds

Ling,

Zhang,

Huang

et al. 2024

IJMS

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“…However, spontaneous mutation rates for higher plants are low, ranging from 10 –5 to 10 –8 , thus, mutagenesis is an important strategy to increase mutation frequencies 6 . The main mutagens are physical mutagens such as X-rays 7 – 9 , γ-irradiation 10 – 12 and ion beams 13 – 16 , chemical mutagens such as ethyl methane sulfonate 17 and sodium azide 18 , 19 . Scientists have developed rice varieties with various excellent traits, e.g.…”

Section: Introductionmentioning

confidence: 99%

A new method for mutation inducing in rice by using DC electrophoresis bath and its mutagenic effects

Zou

Sun

Zou

et al. 2023

Sci Rep

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Mutation breeding is a significant means of increasing breeding efficiency and accelerating breeding process. In present study, we explored a new method for mutations inducing in rice (Oryza sativa L.) by using direct current electrophoresis bath (DCEB). The results showed that 20 mM NaCl solution is the optimal buffer, and the mortality of rice seeds followed an upward trend with increasing voltage and processing time of DCEB. By exploring the mutagenic effects of γ-irradiation and DCEB on seed vigor and physiological damages, we found that the physiological damages induced by DCEB on seed vigor were significant compared with that by γ-irradiation. We screened two mutants with low filled grain percentage and one mutant with abnormal hull from the M2 generations. These three mutants were confirmed to be authentic mutants based on 48 SSR markers followed by the protocol NY/T 1433–2014. Whole-genome resequencing detected a total of 503 and 537 polymorphisms in the two mutants, respectively, and the DCEB mutagenesis induced mainly InDel variants, while the exon region of mutant genes occupied a large proportion, especially the SNP variants, which occupied about 20% of the mutation sites in the exon region.

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“…Heavy-ion beam irradiation can generate mutations in the form of substitutions, small insertion–deletion polymorphisms (InDels), and structure variants. Currently, it has been used for mutation breeding or genetic studies in many crops, such as wheat( Zhang et al., 2008 ; Fitzgerald et al., 2015 ; Li et al., 2022 ), rice( Belfield et al., 2012 ; Yang et al., 2019 ; Zhang et al., 2021 ), Arabidopsis thaliana ( Du et al., 2014 ; Du et al., 2017 ; Du et al., 2018 ), chrysanthemum ( Yamaguchi et al., 2010 ), and soybean ( Im et al., 2017 ; Kim et al., 2008 ). Many plant variations have been induced by CIB irradiation, and many novel experimental materials and practical cultivars have been generated.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide analysis of mutations induced by carbon ion beam irradiation in cotton

Liu

Zhao²,

Geng³

et al. 2023

Front. Plant Sci.

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Carbon ion beam (CIB) irradiation is a powerful way to create mutations in animals, plants, and microbes. Research on the mutagenic effects and molecular mechanisms of radiation is an important and multidisciplinary issue. However, the effect of carbon ion radiation on cotton is uncertain. In this study, five different upland cotton varieties and five CIB doses were used to identify the suitable irradiation dose for cotton. Three mutagenized progeny cotton lines from the wild-type Ji172 were re-sequenced. The effect of half-lethal dose on mutation induction indicated that 200 Gy with LETmax of 226.9 KeV/μm was the most effective heavy-ion dose for upland cotton and a total of 2,959-4,049 single-base substitutions (SBSs) and 610-947 insertion-deletion polymorphisms (InDels) were identified among the three mutants by resequencing. The ratio of transition to transversion in the three mutants ranged from 2.16 to 2.24. Among transversion events, G:C>C:G was significantly less common than three other types of mutations (A:T>C:G, A:T>T:A, and G:C>T:A). The proportions of six types of mutations were very similar in each mutant. The distributions of identified SBSs and InDels were similar with unevenly distributed across the genome and chromosomes. Some chromosomes had significantly more SBSs than others, and there were “hotspot” mutation regions at the ends of chromosomes. Overall, our study revealed a profile of cotton mutations caused by CIB irradiation, and these data could provide valuable information for cotton mutation breeding.

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Time Course Analysis of Genome-Wide Identification of Mutations Induced by and Genes Expressed in Response to Carbon Ion Beam Irradiation in Rice (Oryza sativa L.)

Cited by 7 publications

References 38 publications

Genome-Wide Profile of Mutations Induced by Carbon Ion Beam Irradiation of Dehulled Rice Seeds

Genome-Wide Profile of Mutations Induced by Carbon Ion Beam Irradiation of Dehulled Rice Seeds

A new method for mutation inducing in rice by using DC electrophoresis bath and its mutagenic effects

Genome-wide analysis of mutations induced by carbon ion beam irradiation in cotton

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