Fine Mapping and Genetic Effect Analysis of <i>Rf21(t)</i> for the Fertility Restoration of Chinsurah-Boro-II-Type Cytoplasmic Male Sterile <i>Oryza sativa</i> (ssp. <i>japonica</i>) Lines
The combination of Chinsurah Boro II (BT)-type cytoplasmic male sterility (CMS) and <i>Rf1</i>, the main fertility restorer gene (<i>Rf</i>) for CMS-BT, has been extensively utilized for the production of three-line commercial <i>japonica</i> hybrid seeds. The ide...
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2025-07-01
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| author | Yuanyue Du Liying Fan Yunhua Gu Chen Wang Kai Shi Yebin Qin Zhejun Li Qiaoquan Liu Shuzhu Tang Honggen Zhang Zuopeng Xu |
| author_facet | Yuanyue Du Liying Fan Yunhua Gu Chen Wang Kai Shi Yebin Qin Zhejun Li Qiaoquan Liu Shuzhu Tang Honggen Zhang Zuopeng Xu |
| author_sort | Yuanyue Du |
| collection | DOAJ |
| description | The combination of Chinsurah Boro II (BT)-type cytoplasmic male sterility (CMS) and <i>Rf1</i>, the main fertility restorer gene (<i>Rf</i>) for CMS-BT, has been extensively utilized for the production of three-line commercial <i>japonica</i> hybrid seeds. The identification of new <i>Rf</i> genes holds significance for the breeding of BT-type restorer lines, aiming to enhance the heterosis level of BT-type <i>japonica</i> hybrids. In the present study, ‘02428’, a wide-compatibility <i>japonica</i> variety, was observed to partially restore fertility to BT-type CMS lines. Genetic analysis revealed that ‘02428’ carries a dominant <i>Rf</i> gene, <i>Rf21(t)</i>, responsible for the fertility restoration of BT-type CMS lines. Leveraging bulked segregant analysis (BSA) resequencing technology and molecular markers, the <i>Rf21(t)</i> locus was identified, and mapped within a candidate interval of 6–12.5 Mb on chromosome 2. Using the iso-cytoplasmic restorer populations, <i>Rf21(t)</i> was ultimately mapped to an interval of approximately 77 kb, encompassing 12 predicted genes, including <i>LOC_Os02g17360</i>, encoding a PPR-domain-containing protein and <i>LOC_Os02g17380 (Rf2)</i>, a cloned <i>Rf</i> for Lead-rice-type CMS. A comparative sequence analysis, gene expression profiling and gene knockout experiments confirmed that <i>LOC_Os02g17360</i> and <i>LOC_Os02g17380</i> are the most likely candidates of <i>Rf21(t)</i>. Furthermore, <i>Rf21(t)</i> showed the dosage effect on the fertility restoration of BT-type CMS lines. This newly identified <i>Rf21(t)</i> represents a valuable genetic resource for the breeding of BT-type <i>japonica</i> restorer lines. Our findings offer practical insights for breeders interested in advancing BT-type <i>japonica</i> hybrid development. |
| format | Article |
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| institution | DOAJ |
| issn | 2073-4395 |
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| publishDate | 2025-07-01 |
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| spelling | doaj-art-00fc2113be8149b281e8695d103fef6f2025-08-20T02:45:42ZengMDPI AGAgronomy2073-43952025-07-01157169010.3390/agronomy15071690Fine Mapping and Genetic Effect Analysis of <i>Rf21(t)</i> for the Fertility Restoration of Chinsurah-Boro-II-Type Cytoplasmic Male Sterile <i>Oryza sativa</i> (ssp. <i>japonica</i>) LinesYuanyue Du0Liying Fan1Yunhua Gu2Chen Wang3Kai Shi4Yebin Qin5Zhejun Li6Qiaoquan Liu7Shuzhu Tang8Honggen Zhang9Zuopeng Xu10Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou 225009, ChinaJiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou 225009, ChinaJiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou 225009, ChinaJiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou 225009, ChinaJiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou 225009, ChinaJiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou 225009, ChinaJiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou 225009, ChinaJiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou 225009, ChinaJiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou 225009, ChinaJiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou 225009, ChinaJiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou 225009, ChinaThe combination of Chinsurah Boro II (BT)-type cytoplasmic male sterility (CMS) and <i>Rf1</i>, the main fertility restorer gene (<i>Rf</i>) for CMS-BT, has been extensively utilized for the production of three-line commercial <i>japonica</i> hybrid seeds. The identification of new <i>Rf</i> genes holds significance for the breeding of BT-type restorer lines, aiming to enhance the heterosis level of BT-type <i>japonica</i> hybrids. In the present study, ‘02428’, a wide-compatibility <i>japonica</i> variety, was observed to partially restore fertility to BT-type CMS lines. Genetic analysis revealed that ‘02428’ carries a dominant <i>Rf</i> gene, <i>Rf21(t)</i>, responsible for the fertility restoration of BT-type CMS lines. Leveraging bulked segregant analysis (BSA) resequencing technology and molecular markers, the <i>Rf21(t)</i> locus was identified, and mapped within a candidate interval of 6–12.5 Mb on chromosome 2. Using the iso-cytoplasmic restorer populations, <i>Rf21(t)</i> was ultimately mapped to an interval of approximately 77 kb, encompassing 12 predicted genes, including <i>LOC_Os02g17360</i>, encoding a PPR-domain-containing protein and <i>LOC_Os02g17380 (Rf2)</i>, a cloned <i>Rf</i> for Lead-rice-type CMS. A comparative sequence analysis, gene expression profiling and gene knockout experiments confirmed that <i>LOC_Os02g17360</i> and <i>LOC_Os02g17380</i> are the most likely candidates of <i>Rf21(t)</i>. Furthermore, <i>Rf21(t)</i> showed the dosage effect on the fertility restoration of BT-type CMS lines. This newly identified <i>Rf21(t)</i> represents a valuable genetic resource for the breeding of BT-type <i>japonica</i> restorer lines. Our findings offer practical insights for breeders interested in advancing BT-type <i>japonica</i> hybrid development.https://www.mdpi.com/2073-4395/15/7/1690<i>japonica</i>BT-type CMSfertility restorer gene (<i>Rf</i>)gene mapping |
| spellingShingle | Yuanyue Du Liying Fan Yunhua Gu Chen Wang Kai Shi Yebin Qin Zhejun Li Qiaoquan Liu Shuzhu Tang Honggen Zhang Zuopeng Xu Fine Mapping and Genetic Effect Analysis of <i>Rf21(t)</i> for the Fertility Restoration of Chinsurah-Boro-II-Type Cytoplasmic Male Sterile <i>Oryza sativa</i> (ssp. <i>japonica</i>) Lines Agronomy <i>japonica</i> BT-type CMS fertility restorer gene (<i>Rf</i>) gene mapping |
| title | Fine Mapping and Genetic Effect Analysis of <i>Rf21(t)</i> for the Fertility Restoration of Chinsurah-Boro-II-Type Cytoplasmic Male Sterile <i>Oryza sativa</i> (ssp. <i>japonica</i>) Lines |
| title_full | Fine Mapping and Genetic Effect Analysis of <i>Rf21(t)</i> for the Fertility Restoration of Chinsurah-Boro-II-Type Cytoplasmic Male Sterile <i>Oryza sativa</i> (ssp. <i>japonica</i>) Lines |
| title_fullStr | Fine Mapping and Genetic Effect Analysis of <i>Rf21(t)</i> for the Fertility Restoration of Chinsurah-Boro-II-Type Cytoplasmic Male Sterile <i>Oryza sativa</i> (ssp. <i>japonica</i>) Lines |
| title_full_unstemmed | Fine Mapping and Genetic Effect Analysis of <i>Rf21(t)</i> for the Fertility Restoration of Chinsurah-Boro-II-Type Cytoplasmic Male Sterile <i>Oryza sativa</i> (ssp. <i>japonica</i>) Lines |
| title_short | Fine Mapping and Genetic Effect Analysis of <i>Rf21(t)</i> for the Fertility Restoration of Chinsurah-Boro-II-Type Cytoplasmic Male Sterile <i>Oryza sativa</i> (ssp. <i>japonica</i>) Lines |
| title_sort | fine mapping and genetic effect analysis of i rf21 t i for the fertility restoration of chinsurah boro ii type cytoplasmic male sterile i oryza sativa i ssp i japonica i lines |
| topic | <i>japonica</i> BT-type CMS fertility restorer gene (<i>Rf</i>) gene mapping |
| url | https://www.mdpi.com/2073-4395/15/7/1690 |
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