Transcriptome profiling reveals characteristics of hairy root and the role of AhGLK1 in response to drought stress and post-drought recovery in peanut
Abstract Background HR (hairy root) has emerged as a valuable tissue for the rapid characterization of plant gene function and enzyme activity in vivo. AhGLK1 (Arachis hypogaea L. golden2-like 1) is known to play a role in post-drought recovery. However, it is unclear (a) whether HR has properties t...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2023-03-01
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| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12864-023-09219-2 |
| _version_ | 1797865451901943808 |
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| author | Xing Liu Liangchen Su Limei Li Zhi Zhang Xiaoyun Li Qingjian Liang Ling Li |
| author_facet | Xing Liu Liangchen Su Limei Li Zhi Zhang Xiaoyun Li Qingjian Liang Ling Li |
| author_sort | Xing Liu |
| collection | DOAJ |
| description | Abstract Background HR (hairy root) has emerged as a valuable tissue for the rapid characterization of plant gene function and enzyme activity in vivo. AhGLK1 (Arachis hypogaea L. golden2-like 1) is known to play a role in post-drought recovery. However, it is unclear (a) whether HR has properties that are distinct from those of PR (primary root); and (b) which gene networks are regulated by AhGLK1 in response to drought stress and recovery in peanut. Results We found that cells of the root tip cortex were larger in HR than in PR, while a total of 850 differentially expressed genes (DEGs) were identified in HR compared to PR. Eighty-eight of these DEGs, relating to chlorophyll and photosynthesis, were upregulated in HR. In addition, AhGLK1-OX (AhGLK1-overexpressing) HR showed a green phenotype, and had a higher relative water content than 35 S::eGFP (control) HR during drought stress. RNA-seq analysis showed that 74 DEGs involved both in the drought response and the post-drought recovery process were significantly enriched in the galactose metabolism pathway. GO terms enrichment analysis revealed that 59.19%, 29.79% and 17.02% of the DEGs mapped to the ‘biological process’ (BP), ‘molecular function’ (MF) and ‘cellular component’ (CC) domains, respectively. Furthermore, 20 DEGs involved in post-drought recovery were uniquely expressed in AhGLK1-OX HR and were significantly enriched in the porphyrin metabolism pathway. GO analysis showed that 42.42%, 30.30% and 27.28% of DEGs could be assigned to the BP, MF and CC domains, respectively. Transcription factors including bHLH and MYB family members may play a key role during drought stress and recovery. Conclusion Our data reveal that HR has some of the characteristics of leaves, indicating that HR is suitable for studying genes that are mainly expressed in leaves. The RNA-seq results are consistent with previous studies that show chlorophyll synthesis and photosynthesis to be critical for the role of AhGLK1 in improving post-drought recovery growth in peanut. These findings provide in-depth insights that will be of great utility for the exploration of candidate gene functions in relation to drought tolerance and/or post-drought recovery ability in peanut. |
| first_indexed | 2024-04-09T23:09:22Z |
| format | Article |
| id | doaj.art-11405c57f6ac4ca3bb80a993d3564f0b |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-09T23:09:22Z |
| publishDate | 2023-03-01 |
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| series | BMC Genomics |
| spelling | doaj.art-11405c57f6ac4ca3bb80a993d3564f0b2023-03-22T10:30:37ZengBMCBMC Genomics1471-21642023-03-0124112010.1186/s12864-023-09219-2Transcriptome profiling reveals characteristics of hairy root and the role of AhGLK1 in response to drought stress and post-drought recovery in peanutXing Liu0Liangchen Su1Limei Li2Zhi Zhang3Xiaoyun Li4Qingjian Liang5Ling Li6Department of Bioengineering, Zhuhai Campus of Zunyi Medical UniversityDepartment of Bioengineering, Zhuhai Campus of Zunyi Medical UniversityGuangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal UniversityGuangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal UniversityGuangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal UniversitySchool of Fishery, Zhejiang Ocean UniversityGuangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal UniversityAbstract Background HR (hairy root) has emerged as a valuable tissue for the rapid characterization of plant gene function and enzyme activity in vivo. AhGLK1 (Arachis hypogaea L. golden2-like 1) is known to play a role in post-drought recovery. However, it is unclear (a) whether HR has properties that are distinct from those of PR (primary root); and (b) which gene networks are regulated by AhGLK1 in response to drought stress and recovery in peanut. Results We found that cells of the root tip cortex were larger in HR than in PR, while a total of 850 differentially expressed genes (DEGs) were identified in HR compared to PR. Eighty-eight of these DEGs, relating to chlorophyll and photosynthesis, were upregulated in HR. In addition, AhGLK1-OX (AhGLK1-overexpressing) HR showed a green phenotype, and had a higher relative water content than 35 S::eGFP (control) HR during drought stress. RNA-seq analysis showed that 74 DEGs involved both in the drought response and the post-drought recovery process were significantly enriched in the galactose metabolism pathway. GO terms enrichment analysis revealed that 59.19%, 29.79% and 17.02% of the DEGs mapped to the ‘biological process’ (BP), ‘molecular function’ (MF) and ‘cellular component’ (CC) domains, respectively. Furthermore, 20 DEGs involved in post-drought recovery were uniquely expressed in AhGLK1-OX HR and were significantly enriched in the porphyrin metabolism pathway. GO analysis showed that 42.42%, 30.30% and 27.28% of DEGs could be assigned to the BP, MF and CC domains, respectively. Transcription factors including bHLH and MYB family members may play a key role during drought stress and recovery. Conclusion Our data reveal that HR has some of the characteristics of leaves, indicating that HR is suitable for studying genes that are mainly expressed in leaves. The RNA-seq results are consistent with previous studies that show chlorophyll synthesis and photosynthesis to be critical for the role of AhGLK1 in improving post-drought recovery growth in peanut. These findings provide in-depth insights that will be of great utility for the exploration of candidate gene functions in relation to drought tolerance and/or post-drought recovery ability in peanut.https://doi.org/10.1186/s12864-023-09219-2Hairy rootAhGLK1TranscriptomeDrought stressPost-drought recovery |
| spellingShingle | Xing Liu Liangchen Su Limei Li Zhi Zhang Xiaoyun Li Qingjian Liang Ling Li Transcriptome profiling reveals characteristics of hairy root and the role of AhGLK1 in response to drought stress and post-drought recovery in peanut BMC Genomics Hairy root AhGLK1 Transcriptome Drought stress Post-drought recovery |
| title | Transcriptome profiling reveals characteristics of hairy root and the role of AhGLK1 in response to drought stress and post-drought recovery in peanut |
| title_full | Transcriptome profiling reveals characteristics of hairy root and the role of AhGLK1 in response to drought stress and post-drought recovery in peanut |
| title_fullStr | Transcriptome profiling reveals characteristics of hairy root and the role of AhGLK1 in response to drought stress and post-drought recovery in peanut |
| title_full_unstemmed | Transcriptome profiling reveals characteristics of hairy root and the role of AhGLK1 in response to drought stress and post-drought recovery in peanut |
| title_short | Transcriptome profiling reveals characteristics of hairy root and the role of AhGLK1 in response to drought stress and post-drought recovery in peanut |
| title_sort | transcriptome profiling reveals characteristics of hairy root and the role of ahglk1 in response to drought stress and post drought recovery in peanut |
| topic | Hairy root AhGLK1 Transcriptome Drought stress Post-drought recovery |
| url | https://doi.org/10.1186/s12864-023-09219-2 |
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