Genome-wide identification and characterization of the CCT gene family in Chinese cabbage (Brassica rapa) response to abiotic stress
Abstract Background The CCT (CONSTANS, CONSTANS-LIKE and TOC1) gene family plays a crucial role in regulating diurnal rhythms and responding to abiotic stress, which significantly impacts crop growth, development, and yield. However, comprehensive information on the CCT gene family in Chinese cabbag...
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| Language: | English |
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BMC
2025-07-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-025-11768-7 |
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| author | Haoqi Liu Zhiyuan Yin Mengping Qiu Yan Yang Ye Xu Han Wang Min Yan Guohua Xu |
| author_facet | Haoqi Liu Zhiyuan Yin Mengping Qiu Yan Yang Ye Xu Han Wang Min Yan Guohua Xu |
| author_sort | Haoqi Liu |
| collection | DOAJ |
| description | Abstract Background The CCT (CONSTANS, CONSTANS-LIKE and TOC1) gene family plays a crucial role in regulating diurnal rhythms and responding to abiotic stress, which significantly impacts crop growth, development, and yield. However, comprehensive information on the CCT gene family in Chinese cabbage (Brassica rapa) is currently unavailable. Results In this study, we conducted a genome-wide identification and analysis ofCCT genes in Chinese cabbage. In total, we identified 66 CCT genes in the Chinese cabbage genome, and we elucidated the physicochemical properties and subcellular locations of the corresponding CCT proteins. Phylogenetic analysis, examination of conserved motifs, and gene structure analysis revealed that the BraCCT gene family could be classified into three well-conserved subfamilies: COL, PRR, and CMF. The BraCCT gene family has close relationships with Arabidopsis thaliana. Sixty-three pairs of BraCCTs exhibited collinear relationships through interchromosomal synteny analysis in Brassica rapa, indicating that segmental duplication played a vital role in the expansion of the BraCCT gene family. Cis-acting elements of the CCT promoters have been identified to play a role in plant development, hormonal responses, and stress responses. Expression profile analysis showed that CCT genes were extensively expressed in various tissues of Chinese cabbage, exhibiting diverse expression patterns appeared to be diverse. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis of ten CCT genes confirmed their response to heat stress, cold stress, drought stress, and abscisic acid stress. The full-length coding sequence of BraCCT24 was obtained using homologous cloning technology, and further investigation revealed that the BraCCT24 protein is located in the nucleus. Conclusions In this study, 66 CCT genes were identified in Brassica rapa, and their phylogenetic relationships, gene structural features, duplication events, gene expression, and potential roles in Brassica rapa development were investigated. Overall, this study offers a theoretical foundation for further investigating the significant role of the CCT gene family in the functional genome of Chinese cabbage. |
| format | Article |
| id | doaj-art-7a15638d9f2e4b7787be0b1fb0979f6f |
| institution | Kabale University |
| issn | 1471-2164 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj-art-7a15638d9f2e4b7787be0b1fb0979f6f2025-08-20T04:01:24ZengBMCBMC Genomics1471-21642025-07-0126112110.1186/s12864-025-11768-7Genome-wide identification and characterization of the CCT gene family in Chinese cabbage (Brassica rapa) response to abiotic stressHaoqi Liu0Zhiyuan Yin1Mengping Qiu2Yan Yang3Ye Xu4Han Wang5Min Yan6Guohua Xu7Jiangsu Key Laboratory for Innovative Applications of Bioresources and Biofunctional Molecules, Jiangsu Second Normal UniversityJiangsu Key Laboratory for Innovative Applications of Bioresources and Biofunctional Molecules, Jiangsu Second Normal UniversityJiangsu Key Laboratory for Innovative Applications of Bioresources and Biofunctional Molecules, Jiangsu Second Normal UniversityJiangsu Key Laboratory for Innovative Applications of Bioresources and Biofunctional Molecules, Jiangsu Second Normal UniversityJiangsu Key Laboratory for Innovative Applications of Bioresources and Biofunctional Molecules, Jiangsu Second Normal UniversityJiangsu Key Laboratory for Innovative Applications of Bioresources and Biofunctional Molecules, Jiangsu Second Normal UniversityJiangsu Key Laboratory for Innovative Applications of Bioresources and Biofunctional Molecules, Jiangsu Second Normal UniversityJiangsu Key Laboratory for Innovative Applications of Bioresources and Biofunctional Molecules, Jiangsu Second Normal UniversityAbstract Background The CCT (CONSTANS, CONSTANS-LIKE and TOC1) gene family plays a crucial role in regulating diurnal rhythms and responding to abiotic stress, which significantly impacts crop growth, development, and yield. However, comprehensive information on the CCT gene family in Chinese cabbage (Brassica rapa) is currently unavailable. Results In this study, we conducted a genome-wide identification and analysis ofCCT genes in Chinese cabbage. In total, we identified 66 CCT genes in the Chinese cabbage genome, and we elucidated the physicochemical properties and subcellular locations of the corresponding CCT proteins. Phylogenetic analysis, examination of conserved motifs, and gene structure analysis revealed that the BraCCT gene family could be classified into three well-conserved subfamilies: COL, PRR, and CMF. The BraCCT gene family has close relationships with Arabidopsis thaliana. Sixty-three pairs of BraCCTs exhibited collinear relationships through interchromosomal synteny analysis in Brassica rapa, indicating that segmental duplication played a vital role in the expansion of the BraCCT gene family. Cis-acting elements of the CCT promoters have been identified to play a role in plant development, hormonal responses, and stress responses. Expression profile analysis showed that CCT genes were extensively expressed in various tissues of Chinese cabbage, exhibiting diverse expression patterns appeared to be diverse. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis of ten CCT genes confirmed their response to heat stress, cold stress, drought stress, and abscisic acid stress. The full-length coding sequence of BraCCT24 was obtained using homologous cloning technology, and further investigation revealed that the BraCCT24 protein is located in the nucleus. Conclusions In this study, 66 CCT genes were identified in Brassica rapa, and their phylogenetic relationships, gene structural features, duplication events, gene expression, and potential roles in Brassica rapa development were investigated. Overall, this study offers a theoretical foundation for further investigating the significant role of the CCT gene family in the functional genome of Chinese cabbage.https://doi.org/10.1186/s12864-025-11768-7CCT gene familyChinese cabbageSegmental duplicationAbiotic stressBraCCT24 |
| spellingShingle | Haoqi Liu Zhiyuan Yin Mengping Qiu Yan Yang Ye Xu Han Wang Min Yan Guohua Xu Genome-wide identification and characterization of the CCT gene family in Chinese cabbage (Brassica rapa) response to abiotic stress BMC Genomics CCT gene family Chinese cabbage Segmental duplication Abiotic stress BraCCT24 |
| title | Genome-wide identification and characterization of the CCT gene family in Chinese cabbage (Brassica rapa) response to abiotic stress |
| title_full | Genome-wide identification and characterization of the CCT gene family in Chinese cabbage (Brassica rapa) response to abiotic stress |
| title_fullStr | Genome-wide identification and characterization of the CCT gene family in Chinese cabbage (Brassica rapa) response to abiotic stress |
| title_full_unstemmed | Genome-wide identification and characterization of the CCT gene family in Chinese cabbage (Brassica rapa) response to abiotic stress |
| title_short | Genome-wide identification and characterization of the CCT gene family in Chinese cabbage (Brassica rapa) response to abiotic stress |
| title_sort | genome wide identification and characterization of the cct gene family in chinese cabbage brassica rapa response to abiotic stress |
| topic | CCT gene family Chinese cabbage Segmental duplication Abiotic stress BraCCT24 |
| url | https://doi.org/10.1186/s12864-025-11768-7 |
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