Genome-Wide Profile of Mutations Induced by Carbon Ion Beam Irradiation of Dehulled Rice Seeds
Abstract
:1. Introduction
2. Results
2.1. Summarized Information of CIB-Induced Mutations
2.2. Frequency and Distribution of Mutations for CIB Irradiation
2.2.1. Distribution of Mutations on Chromosomes
2.2.2. Theoretical Mutation Frequency of the M1 Generation
2.3. Characteristics of Mutations Induced by CIB Irradiation
2.4. Effect of CIB-Induced Mutation on Gene Function
2.5. Verification of the Identified Mutation Sites
3. Discussion
3.1. The Mutation Rate of Dehulled Rice Seeds Induced by Carbon Ion Beam
3.2. SBSs and InDels Are the Two Main Mutation Types Occurring under CIB Irradiation
3.3. Gene Function-Affecting Mutations Provide Some Clues to Gene Identification
4. Materials and Methods
4.1. Plant Material, Mutagenesis, and Mutant Screening
4.2. Whole-Genome Sequencing and Clean Read Filtering
4.3. SNP and InDel Identification
Variant Annotation and Gene Function Prediction
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Type | Line | Sequenced Generation | HQ_Clean_ Data(bp) | Theoretical Genome Coverage | Genome Coverage of 10× Sequencing Depth (%) | Genome Coverage of 20× Sequencing Depth (%) | Genome Coverage of 30× Sequencing Depth (%) |
---|---|---|---|---|---|---|---|
WT | H492 | M6 | 16.0 | 42.9 | 93.79 | 90.22 | 80.01 |
Mutant | H494 | M6 | 16.2 | 43.5 | 88.05 | 77.08 | 62.57 |
Mutant | H495 | M6 | 16.2 | 43.3 | 88.72 | 77.47 | 62.03 |
Mutant | H496 | M6 | 16.4 | 44.1 | 89.67 | 79.73 | 65.36 |
WT | H499 | M6 | 13.6 | 36.5 | 79.55 | 64.22 | 45.77 |
Mutant | H512 | M6 | 14.2 | 38.0 | 80.63 | 66.28 | 48.47 |
WT | H574 | M6 | 15.6 | 41.9 | 85.99 | 79.55 | 64.71 |
Mutant | H579 | M6 | 15.9 | 42.7 | 86.62 | 79.67 | 64.11 |
Mutant | H580 | M6 | 16.9 | 45.3 | 86.95 | 80.7 | 67.93 |
Mutant | H592 | M6 | 16.2 | 43.4 | 86.38 | 79.72 | 65.78 |
Mutant | H593 | M6 | 16.2 | 43.4 | 86.51 | 80.5 | 66.75 |
Average | 15.8 | 42.3 | 86.6 | 77.7 | 63.0 |
WT | Mutant | Total | SBSs | InDels | The Estimated Mutations in M1 | Mutation Rate in M1 |
---|---|---|---|---|---|---|
H492 | H494 | 2455 | 2101 | 354 | 4910 | 12.3 × 10−5 |
H495 | 145 | 110 | 35 | 290 | ||
H496 | 66,813 | 59,315 | 7498 | 133,626 | ||
H499 | H512 | 21,101 | 18,860 | 2241 | 42,202 | 11.3 × 10−5 |
H574 | H579 | 8503 | 7257 | 1246 | 17,006 | 6.0 × 10−5 |
H580 | 6196 | 5528 | 668 | 12,392 | ||
H592 | 23,689 | 20,548 | 3141 | 47,378 | ||
H593 | 6633 | 5860 | 773 | 13,266 | ||
Average | 16,942 | 14,947 | 1995 | 33,884 | 9.8 × 10−5 |
Category | Mutant | Synonymous Mutation | Non-Synonymous Mutation | Nonsense Mutation | Frameshift Mutation |
---|---|---|---|---|---|
MP1 | H494 | 63 | 62 | 1 | 3 |
H495 | 0 | 2 | 1 | 0 | |
H496 | 1411 | 1728 | 39 | 75 | |
MP2 | H512 | 328 | 465 | 10 | 22 |
MP3 | H579 | 327 | 302 | 11 | 15 |
H580 | 105 | 130 | 3 | 7 | |
H592 | 593 | 496 | 7 | 20 | |
H593 | 123 | 116 | 3 | 7 | |
Total | 2950 | 3301 | 75 | 149 | |
Average | 368.8 | 412.6 | 9.4 | 18.6 |
Mutant | Gene ID | Whether in HF Mutation Region | Gene Description | Possibly Affected Phenotype | Cloned or Not |
---|---|---|---|---|---|
H494 | Os06g0247500 | No | Pyrophosphate-fructose 6-phosphate 1-phosphotransferase | Plant height, grain shape | Yes |
H495 | Os02g0278400 | No | Cytochrome P450 | Plant height, grain shape | No |
H496 | Os05g0374200 | No | Cytokinin oxidase/dehydrogenase 9 | Plant height, grain shape, setting percentage | Yes |
H496 | Os01g0826400 | No | WRKY transcription factor | Plant height, grain shape | Yes |
H496 | Os07g0214300 | No | α-amylase/trypsin inhibitor | Grain shape | Yes |
H496 | Os07g0235800 | No | APETALA2-like transcription factor | Grain shape | Yes |
H496 | Os07g0583700 | No | WRKY transcription factor 78 | Plant height, grain shape | Yes |
H496 | Os12g0428600 | Yes | HECT-domain E3 ubiquitin ligase | Plant height, grain shape | Yes |
H496 | Os12g0496900 | No | GRF-INTERACTING FACTOR 2 | Plant height, grain shape | No |
H496 | Os12g0552600 | No | Grain Weight (qTGW12a) | Grain shape | Yes |
H512 | Os01g0972800 | No | WRKY transcription factor | Plant height, grain length | No |
H512 | Os03g0430000 | Yes | defective embryo sac1 | Setting percentage | Yes |
H512 | Os05g0547850 | No | Programmed cell death 5 | Plant height, grain shape | Yes |
H580 | Os04g0396500 | No | lax panicle2 | Panicle type | Yes |
H592 | Os03g0267800 | No | Ubiquitin-interacting motif-containing ubiquitin receptor | Grain shape | Yes |
H592 | Os03g0274800 | Yes | Receptor-like cytoplasmic kinase | Plant archetechture, setting percentage | Yes |
H592 | Os07g0192300 | Yes | NARROW LEAF 11 | Plant archetechture, panicle type | Yes |
H592 | Os07g0232100 | Yes | B3 domain transcription factor | Panicle type | Yes |
H592 | Os07g0233300 | Yes | Alfin-like gene | Grain length | Yes |
H592 | Os07g0235800 | Yes | APETALA2-like transcription factor | Grain shape | Yes |
H592 | Os09g0281900 | No | Mediator subunit gene | Plant height, grain shape, setting percentage | No |
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Ling, Y.; Zhang, Y.; Huang, M.; Guo, T.; Yang, G. Genome-Wide Profile of Mutations Induced by Carbon Ion Beam Irradiation of Dehulled Rice Seeds. Int. J. Mol. Sci. 2024, 25, 5195. https://doi.org/10.3390/ijms25105195
Ling Y, Zhang Y, Huang M, Guo T, Yang G. Genome-Wide Profile of Mutations Induced by Carbon Ion Beam Irradiation of Dehulled Rice Seeds. International Journal of Molecular Sciences. 2024; 25(10):5195. https://doi.org/10.3390/ijms25105195
Chicago/Turabian StyleLing, Ying, Yuming Zhang, Ming Huang, Tao Guo, and Guili Yang. 2024. "Genome-Wide Profile of Mutations Induced by Carbon Ion Beam Irradiation of Dehulled Rice Seeds" International Journal of Molecular Sciences 25, no. 10: 5195. https://doi.org/10.3390/ijms25105195