Comparative transcriptome analysis of the mechanism difference in heat stress response between indica rice cultivar “IR64” and japonica cultivar “Koshihikari” at the seedling stage
Heat stress (HS) has become a major abiotic stress in rice, considering the frequency and intensity of extreme hot weather. There is an urgent need to explore the differences in molecular mechanisms of HS tolerance in different cultivars, especially in indica and japonica. In this study, we investig...
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Frontiers Media S.A.
2023-04-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2023.1135577/full |
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| author | Yingfeng Wang Yubo Wang Wenjuan Chen Yating Dong Guilian Zhang Huabing Deng Xiong Liu Xuedan Lu Feng Wang Guihua Chen Yunhua Xiao Wenbang Tang Wenbang Tang |
| author_facet | Yingfeng Wang Yubo Wang Wenjuan Chen Yating Dong Guilian Zhang Huabing Deng Xiong Liu Xuedan Lu Feng Wang Guihua Chen Yunhua Xiao Wenbang Tang Wenbang Tang |
| author_sort | Yingfeng Wang |
| collection | DOAJ |
| description | Heat stress (HS) has become a major abiotic stress in rice, considering the frequency and intensity of extreme hot weather. There is an urgent need to explore the differences in molecular mechanisms of HS tolerance in different cultivars, especially in indica and japonica. In this study, we investigated the transcriptome information of IR64 (indica, IR) and Koshihikari (japonica, Kos) in response to HS at the seedling stage. From the differentially expressed genes (DEGs) consistently expressed at six time points, 599 DEGs were identified that were co-expressed in both cultivars, as well as 945 and 1,180 DEGs that were specifically expressed in IR and Kos, respectively. The results of GO and KEGG analysis showed two different HS response pathways for IR and Kos. IR specifically expressed DEGs were mainly enriched in chloroplast-related pathways, whereas Kos specifically expressed DEGs were mainly enriched in endoplasmic reticulum and mitochondria-related pathways. Meanwhile, we highlighted the importance of NO biosynthesis genes, especially nitrate reductase genes, in the HS response of IR based on protein-protein interaction networks. In addition, we found that heat shock proteins and heat shock factors play very important roles in both cultivars. This study not only provides new insights into the differences in HS responses between different subspecies of rice, but also lays the foundation for future research on molecular mechanisms and breeding of heat-tolerant cultivars. |
| first_indexed | 2024-04-09T13:09:56Z |
| format | Article |
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| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-04-09T13:09:56Z |
| publishDate | 2023-04-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-2e8e607357954fd1830681089530d42a2023-05-12T08:28:31ZengFrontiers Media S.A.Frontiers in Genetics1664-80212023-04-011410.3389/fgene.2023.11355771135577Comparative transcriptome analysis of the mechanism difference in heat stress response between indica rice cultivar “IR64” and japonica cultivar “Koshihikari” at the seedling stageYingfeng Wang0Yubo Wang1Wenjuan Chen2Yating Dong3Guilian Zhang4Huabing Deng5Xiong Liu6Xuedan Lu7Feng Wang8Guihua Chen9Yunhua Xiao10Wenbang Tang11Wenbang Tang12Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, College of Agronomy, Hunan Agricultural University, Changsha, ChinaHunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, College of Agronomy, Hunan Agricultural University, Changsha, ChinaHunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, College of Agronomy, Hunan Agricultural University, Changsha, ChinaHunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, College of Agronomy, Hunan Agricultural University, Changsha, ChinaHunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, College of Agronomy, Hunan Agricultural University, Changsha, ChinaHunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, College of Agronomy, Hunan Agricultural University, Changsha, ChinaHunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, College of Agronomy, Hunan Agricultural University, Changsha, ChinaHunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, College of Agronomy, Hunan Agricultural University, Changsha, ChinaHunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, College of Agronomy, Hunan Agricultural University, Changsha, ChinaHunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, College of Agronomy, Hunan Agricultural University, Changsha, ChinaHunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, College of Agronomy, Hunan Agricultural University, Changsha, ChinaHunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, College of Agronomy, Hunan Agricultural University, Changsha, ChinaState Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, ChinaHeat stress (HS) has become a major abiotic stress in rice, considering the frequency and intensity of extreme hot weather. There is an urgent need to explore the differences in molecular mechanisms of HS tolerance in different cultivars, especially in indica and japonica. In this study, we investigated the transcriptome information of IR64 (indica, IR) and Koshihikari (japonica, Kos) in response to HS at the seedling stage. From the differentially expressed genes (DEGs) consistently expressed at six time points, 599 DEGs were identified that were co-expressed in both cultivars, as well as 945 and 1,180 DEGs that were specifically expressed in IR and Kos, respectively. The results of GO and KEGG analysis showed two different HS response pathways for IR and Kos. IR specifically expressed DEGs were mainly enriched in chloroplast-related pathways, whereas Kos specifically expressed DEGs were mainly enriched in endoplasmic reticulum and mitochondria-related pathways. Meanwhile, we highlighted the importance of NO biosynthesis genes, especially nitrate reductase genes, in the HS response of IR based on protein-protein interaction networks. In addition, we found that heat shock proteins and heat shock factors play very important roles in both cultivars. This study not only provides new insights into the differences in HS responses between different subspecies of rice, but also lays the foundation for future research on molecular mechanisms and breeding of heat-tolerant cultivars.https://www.frontiersin.org/articles/10.3389/fgene.2023.1135577/fullrice (Oryza sativa L.)indicajaponicaheat stressRNA-seqDEGs |
| spellingShingle | Yingfeng Wang Yubo Wang Wenjuan Chen Yating Dong Guilian Zhang Huabing Deng Xiong Liu Xuedan Lu Feng Wang Guihua Chen Yunhua Xiao Wenbang Tang Wenbang Tang Comparative transcriptome analysis of the mechanism difference in heat stress response between indica rice cultivar “IR64” and japonica cultivar “Koshihikari” at the seedling stage Frontiers in Genetics rice (Oryza sativa L.) indica japonica heat stress RNA-seq DEGs |
| title | Comparative transcriptome analysis of the mechanism difference in heat stress response between indica rice cultivar “IR64” and japonica cultivar “Koshihikari” at the seedling stage |
| title_full | Comparative transcriptome analysis of the mechanism difference in heat stress response between indica rice cultivar “IR64” and japonica cultivar “Koshihikari” at the seedling stage |
| title_fullStr | Comparative transcriptome analysis of the mechanism difference in heat stress response between indica rice cultivar “IR64” and japonica cultivar “Koshihikari” at the seedling stage |
| title_full_unstemmed | Comparative transcriptome analysis of the mechanism difference in heat stress response between indica rice cultivar “IR64” and japonica cultivar “Koshihikari” at the seedling stage |
| title_short | Comparative transcriptome analysis of the mechanism difference in heat stress response between indica rice cultivar “IR64” and japonica cultivar “Koshihikari” at the seedling stage |
| title_sort | comparative transcriptome analysis of the mechanism difference in heat stress response between indica rice cultivar ir64 and japonica cultivar koshihikari at the seedling stage |
| topic | rice (Oryza sativa L.) indica japonica heat stress RNA-seq DEGs |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2023.1135577/full |
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