Whole-Genome Sequencing of Rice Mutant Library Members Induced by N-Methyl-N-Nitrosourea Mutagenesis of Fertilized Egg Cells
Abstract Although targeted genome editing technology has become a powerful reverse genetic approach for accelerating functional genomics, conventional mutant libraries induced by chemical mutagens remain valuable for plant studies. Plants containing chemically induced mutations are simple yet effect...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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SpringerOpen
2022-07-01
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| Series: | Rice |
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| Online Access: | https://doi.org/10.1186/s12284-022-00585-1 |
| _version_ | 1811293819212136448 |
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| author | Takahiko Kubo Yoshiyuki Yamagata Hiroaki Matsusaka Atsushi Toyoda Yutaka Sato Toshihiro Kumamaru |
| author_facet | Takahiko Kubo Yoshiyuki Yamagata Hiroaki Matsusaka Atsushi Toyoda Yutaka Sato Toshihiro Kumamaru |
| author_sort | Takahiko Kubo |
| collection | DOAJ |
| description | Abstract Although targeted genome editing technology has become a powerful reverse genetic approach for accelerating functional genomics, conventional mutant libraries induced by chemical mutagens remain valuable for plant studies. Plants containing chemically induced mutations are simple yet effective genetic tools that can be grown without regard for biosafety issues. Whole-genome sequencing of mutant individuals reduces the effort required for mutant screening, thereby increasing their utility. In this study, we sequenced members of a mutant library of Oryza sativa cv. Nipponbare derived from treating single fertilized egg cells with N-methyl-N-nitrosourea (MNU). By whole-genome sequencing 266 M1 plants in this mutant library, we identified a total of 0.66 million induced point mutations. This result represented one mutation in every 146-kb of genome sequence in the 373 Mb assembled rice genome. These point mutations were uniformly distributed throughout the rice genome, and over 70,000 point mutations were located within coding sequences. Although this mutant library was a small population, nonsynonymous mutations were found in nearly 61% of all annotated rice genes, and 8.6% (3248 genes) had point mutations with large effects on gene function, such as gaining a stop codon or losing a start codon. WGS showed MNU-mutagenesis using rice fertilized egg cells induces mutations efficiently and is suitable for constructing mutant libraries for an in silico mutant screening system. Expanding this mutant library and its database will provide a useful in silico screening tool that facilitates functional genomics studies with a special emphasis on rice. |
| first_indexed | 2024-04-13T05:07:27Z |
| format | Article |
| id | doaj.art-5c3ed375e47f412eb48748f6f56ac1cd |
| institution | Directory Open Access Journal |
| issn | 1939-8425 1939-8433 |
| language | English |
| last_indexed | 2024-04-13T05:07:27Z |
| publishDate | 2022-07-01 |
| publisher | SpringerOpen |
| record_format | Article |
| series | Rice |
| spelling | doaj.art-5c3ed375e47f412eb48748f6f56ac1cd2022-12-22T03:01:08ZengSpringerOpenRice1939-84251939-84332022-07-011511810.1186/s12284-022-00585-1Whole-Genome Sequencing of Rice Mutant Library Members Induced by N-Methyl-N-Nitrosourea Mutagenesis of Fertilized Egg CellsTakahiko Kubo0Yoshiyuki Yamagata1Hiroaki Matsusaka2Atsushi Toyoda3Yutaka Sato4Toshihiro Kumamaru5Faculty of Agriculture, Kyushu UniversityFaculty of Agriculture, Kyushu UniversityFaculty of Agriculture, Kyushu UniversityNational Institute of GeneticsNational Institute of GeneticsFaculty of Agriculture, Kyushu UniversityAbstract Although targeted genome editing technology has become a powerful reverse genetic approach for accelerating functional genomics, conventional mutant libraries induced by chemical mutagens remain valuable for plant studies. Plants containing chemically induced mutations are simple yet effective genetic tools that can be grown without regard for biosafety issues. Whole-genome sequencing of mutant individuals reduces the effort required for mutant screening, thereby increasing their utility. In this study, we sequenced members of a mutant library of Oryza sativa cv. Nipponbare derived from treating single fertilized egg cells with N-methyl-N-nitrosourea (MNU). By whole-genome sequencing 266 M1 plants in this mutant library, we identified a total of 0.66 million induced point mutations. This result represented one mutation in every 146-kb of genome sequence in the 373 Mb assembled rice genome. These point mutations were uniformly distributed throughout the rice genome, and over 70,000 point mutations were located within coding sequences. Although this mutant library was a small population, nonsynonymous mutations were found in nearly 61% of all annotated rice genes, and 8.6% (3248 genes) had point mutations with large effects on gene function, such as gaining a stop codon or losing a start codon. WGS showed MNU-mutagenesis using rice fertilized egg cells induces mutations efficiently and is suitable for constructing mutant libraries for an in silico mutant screening system. Expanding this mutant library and its database will provide a useful in silico screening tool that facilitates functional genomics studies with a special emphasis on rice.https://doi.org/10.1186/s12284-022-00585-1Rice mutant libraryN-methyl-N-nitrosourea (MNU)Single nucletide variant (SNV)NGSIn silico TILLINGOryza sativa |
| spellingShingle | Takahiko Kubo Yoshiyuki Yamagata Hiroaki Matsusaka Atsushi Toyoda Yutaka Sato Toshihiro Kumamaru Whole-Genome Sequencing of Rice Mutant Library Members Induced by N-Methyl-N-Nitrosourea Mutagenesis of Fertilized Egg Cells Rice Rice mutant library N-methyl-N-nitrosourea (MNU) Single nucletide variant (SNV) NGS In silico TILLING Oryza sativa |
| title | Whole-Genome Sequencing of Rice Mutant Library Members Induced by N-Methyl-N-Nitrosourea Mutagenesis of Fertilized Egg Cells |
| title_full | Whole-Genome Sequencing of Rice Mutant Library Members Induced by N-Methyl-N-Nitrosourea Mutagenesis of Fertilized Egg Cells |
| title_fullStr | Whole-Genome Sequencing of Rice Mutant Library Members Induced by N-Methyl-N-Nitrosourea Mutagenesis of Fertilized Egg Cells |
| title_full_unstemmed | Whole-Genome Sequencing of Rice Mutant Library Members Induced by N-Methyl-N-Nitrosourea Mutagenesis of Fertilized Egg Cells |
| title_short | Whole-Genome Sequencing of Rice Mutant Library Members Induced by N-Methyl-N-Nitrosourea Mutagenesis of Fertilized Egg Cells |
| title_sort | whole genome sequencing of rice mutant library members induced by n methyl n nitrosourea mutagenesis of fertilized egg cells |
| topic | Rice mutant library N-methyl-N-nitrosourea (MNU) Single nucletide variant (SNV) NGS In silico TILLING Oryza sativa |
| url | https://doi.org/10.1186/s12284-022-00585-1 |
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