Transcriptome Analysis Between Parents and Offspring Revealed the Early Salt Tolerance Mechanism of Rice NGY1
Abstract Salt stress poses a severe threat to global rice productivity, and developing salt-tolerant cultivars represents a critical strategy to address this challenge. However, the molecular mechanisms underlying salt tolerance in rice remain elusive. This study focuses on NGY1, a crossbred offspri...
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| Format: | Article |
| Language: | English |
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SpringerOpen
2025-06-01
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| Series: | Rice |
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| Online Access: | https://doi.org/10.1186/s12284-025-00802-7 |
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| author | Cheng Li Kai Lu Wen-Hua Liang Tao Chen Shu Yao Lei He Xiao-Dong Wei Ling Zhao Li-Hui Zhou Chun-Fang Zhao Qing-Yong Zhao Zhen Zhu Cai-Lin Wang Ya-Dong Zhang |
| author_facet | Cheng Li Kai Lu Wen-Hua Liang Tao Chen Shu Yao Lei He Xiao-Dong Wei Ling Zhao Li-Hui Zhou Chun-Fang Zhao Qing-Yong Zhao Zhen Zhu Cai-Lin Wang Ya-Dong Zhang |
| author_sort | Cheng Li |
| collection | DOAJ |
| description | Abstract Salt stress poses a severe threat to global rice productivity, and developing salt-tolerant cultivars represents a critical strategy to address this challenge. However, the molecular mechanisms underlying salt tolerance in rice remain elusive. This study focuses on NGY1, a crossbred offspring between YF47 and SN9903, which showed superior salt tolerance compared to its parent lines during the seedling stage. RNA sequencing (RNA-seq) of seedlings harvested at distinct temporal stages of salt stress identified over 10,000 differentially expressed genes (DEGs). Functional enrichment analyses (GO and KEGG) revealed that NGY1 uniquely mobilized a broader repertoire of stress-responsive genes within shorter timeframes than its parents lines, particularly those associated with redox homeostasis, phytohormone signaling, and MAPK cascades. Meanwhile, NGY1 can rapidly upregulate genes related to salt tolerance compared to its parent during the initial stress phase. Additionally, differences in salt tolerance between NGY1 and its parents were linked to variations in alternative splicing and the high expression of certain NBS-LRR protein genes early in salt stress exposure. These findings not only provide new insights into the molecular mechanisms of salt tolerance, but also provide a theoretical basis for genetic improvement of salt tolerance in rice. |
| format | Article |
| id | doaj-art-13092f9a23f848d2ba62ad9d0f20c8a5 |
| institution | OA Journals |
| issn | 1939-8425 1939-8433 |
| language | English |
| publishDate | 2025-06-01 |
| publisher | SpringerOpen |
| record_format | Article |
| series | Rice |
| spelling | doaj-art-13092f9a23f848d2ba62ad9d0f20c8a52025-08-20T02:31:09ZengSpringerOpenRice1939-84251939-84332025-06-0118111310.1186/s12284-025-00802-7Transcriptome Analysis Between Parents and Offspring Revealed the Early Salt Tolerance Mechanism of Rice NGY1Cheng Li0Kai Lu1Wen-Hua Liang2Tao Chen3Shu Yao4Lei He5Xiao-Dong Wei6Ling Zhao7Li-Hui Zhou8Chun-Fang Zhao9Qing-Yong Zhao10Zhen Zhu11Cai-Lin Wang12Ya-Dong Zhang13Institute of Food Crops/Nanjing Branch of China National Center for Rice Improvement/National Center of Technology Innovation for Saline-Alkali Tolerant Rice/Zhongshan Biological Breeding Laboratory/Jiangsu Academy of Agricultural ScienceInstitute of Food Crops/Nanjing Branch of China National Center for Rice Improvement/National Center of Technology Innovation for Saline-Alkali Tolerant Rice/Zhongshan Biological Breeding Laboratory/Jiangsu Academy of Agricultural ScienceInstitute of Food Crops/Nanjing Branch of China National Center for Rice Improvement/National Center of Technology Innovation for Saline-Alkali Tolerant Rice/Zhongshan Biological Breeding Laboratory/Jiangsu Academy of Agricultural ScienceInstitute of Food Crops/Nanjing Branch of China National Center for Rice Improvement/National Center of Technology Innovation for Saline-Alkali Tolerant Rice/Zhongshan Biological Breeding Laboratory/Jiangsu Academy of Agricultural ScienceInstitute of Food Crops/Nanjing Branch of China National Center for Rice Improvement/National Center of Technology Innovation for Saline-Alkali Tolerant Rice/Zhongshan Biological Breeding Laboratory/Jiangsu Academy of Agricultural ScienceInstitute of Food Crops/Nanjing Branch of China National Center for Rice Improvement/National Center of Technology Innovation for Saline-Alkali Tolerant Rice/Zhongshan Biological Breeding Laboratory/Jiangsu Academy of Agricultural ScienceInstitute of Food Crops/Nanjing Branch of China National Center for Rice Improvement/National Center of Technology Innovation for Saline-Alkali Tolerant Rice/Zhongshan Biological Breeding Laboratory/Jiangsu Academy of Agricultural ScienceInstitute of Food Crops/Nanjing Branch of China National Center for Rice Improvement/National Center of Technology Innovation for Saline-Alkali Tolerant Rice/Zhongshan Biological Breeding Laboratory/Jiangsu Academy of Agricultural ScienceInstitute of Food Crops/Nanjing Branch of China National Center for Rice Improvement/National Center of Technology Innovation for Saline-Alkali Tolerant Rice/Zhongshan Biological Breeding Laboratory/Jiangsu Academy of Agricultural ScienceInstitute of Food Crops/Nanjing Branch of China National Center for Rice Improvement/National Center of Technology Innovation for Saline-Alkali Tolerant Rice/Zhongshan Biological Breeding Laboratory/Jiangsu Academy of Agricultural ScienceInstitute of Food Crops/Nanjing Branch of China National Center for Rice Improvement/National Center of Technology Innovation for Saline-Alkali Tolerant Rice/Zhongshan Biological Breeding Laboratory/Jiangsu Academy of Agricultural ScienceInstitute of Food Crops/Nanjing Branch of China National Center for Rice Improvement/National Center of Technology Innovation for Saline-Alkali Tolerant Rice/Zhongshan Biological Breeding Laboratory/Jiangsu Academy of Agricultural ScienceInstitute of Food Crops/Nanjing Branch of China National Center for Rice Improvement/National Center of Technology Innovation for Saline-Alkali Tolerant Rice/Zhongshan Biological Breeding Laboratory/Jiangsu Academy of Agricultural ScienceInstitute of Food Crops/Nanjing Branch of China National Center for Rice Improvement/National Center of Technology Innovation for Saline-Alkali Tolerant Rice/Zhongshan Biological Breeding Laboratory/Jiangsu Academy of Agricultural ScienceAbstract Salt stress poses a severe threat to global rice productivity, and developing salt-tolerant cultivars represents a critical strategy to address this challenge. However, the molecular mechanisms underlying salt tolerance in rice remain elusive. This study focuses on NGY1, a crossbred offspring between YF47 and SN9903, which showed superior salt tolerance compared to its parent lines during the seedling stage. RNA sequencing (RNA-seq) of seedlings harvested at distinct temporal stages of salt stress identified over 10,000 differentially expressed genes (DEGs). Functional enrichment analyses (GO and KEGG) revealed that NGY1 uniquely mobilized a broader repertoire of stress-responsive genes within shorter timeframes than its parents lines, particularly those associated with redox homeostasis, phytohormone signaling, and MAPK cascades. Meanwhile, NGY1 can rapidly upregulate genes related to salt tolerance compared to its parent during the initial stress phase. Additionally, differences in salt tolerance between NGY1 and its parents were linked to variations in alternative splicing and the high expression of certain NBS-LRR protein genes early in salt stress exposure. These findings not only provide new insights into the molecular mechanisms of salt tolerance, but also provide a theoretical basis for genetic improvement of salt tolerance in rice.https://doi.org/10.1186/s12284-025-00802-7RiceSalt-stressTranscriptomicAlternative splicingMechanism |
| spellingShingle | Cheng Li Kai Lu Wen-Hua Liang Tao Chen Shu Yao Lei He Xiao-Dong Wei Ling Zhao Li-Hui Zhou Chun-Fang Zhao Qing-Yong Zhao Zhen Zhu Cai-Lin Wang Ya-Dong Zhang Transcriptome Analysis Between Parents and Offspring Revealed the Early Salt Tolerance Mechanism of Rice NGY1 Rice Rice Salt-stress Transcriptomic Alternative splicing Mechanism |
| title | Transcriptome Analysis Between Parents and Offspring Revealed the Early Salt Tolerance Mechanism of Rice NGY1 |
| title_full | Transcriptome Analysis Between Parents and Offspring Revealed the Early Salt Tolerance Mechanism of Rice NGY1 |
| title_fullStr | Transcriptome Analysis Between Parents and Offspring Revealed the Early Salt Tolerance Mechanism of Rice NGY1 |
| title_full_unstemmed | Transcriptome Analysis Between Parents and Offspring Revealed the Early Salt Tolerance Mechanism of Rice NGY1 |
| title_short | Transcriptome Analysis Between Parents and Offspring Revealed the Early Salt Tolerance Mechanism of Rice NGY1 |
| title_sort | transcriptome analysis between parents and offspring revealed the early salt tolerance mechanism of rice ngy1 |
| topic | Rice Salt-stress Transcriptomic Alternative splicing Mechanism |
| url | https://doi.org/10.1186/s12284-025-00802-7 |
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