Comparative transcriptome analysis revealed genes commonly responsive to varied nitrate stress in leaves of Tibetan hulless barley
Nitrogen (N) deprivation or excess can lead to dramatic phenotype change, disrupt important biological processes, and ultimately limit plant productivity. To explore genes in Tibetan hulless barley responsive to varied N stress, we utilized a comparative transcriptomics method to investigate gene ex...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2016-07-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | http://journal.frontiersin.org/Journal/10.3389/fpls.2016.01067/full |
| _version_ | 1828486852024205312 |
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| author | Cheng Qin Zexiu Wei Xingquan Zeng Yulin Wang Lijun Bai Qijun Xu Hongjun Yuan Yawei Tang Tashi Nyima |
| author_facet | Cheng Qin Zexiu Wei Xingquan Zeng Yulin Wang Lijun Bai Qijun Xu Hongjun Yuan Yawei Tang Tashi Nyima |
| author_sort | Cheng Qin |
| collection | DOAJ |
| description | Nitrogen (N) deprivation or excess can lead to dramatic phenotype change, disrupt important biological processes, and ultimately limit plant productivity. To explore genes in Tibetan hulless barley responsive to varied N stress, we utilized a comparative transcriptomics method to investigate gene expression patterns under three nitrate treatments. The transcriptome of the control (optimal-nitrate, ON) sample was compared with that of free-nitrate (FN), low-nitrate (LN) and high-nitrate (HN) treatment samples, identifying 2,428, 1,274, and 1,861 genes, respectively, that exhibited significant differences in transcript abundance. Among these, 9 genes encoding ribulose bisphosphate carboxylases exhibited up-regulated expression under varied N stress. We further compared FN versus ON and LN versus ON to investigate the impact of stress degree on gene expression. With the aggravation of stress, more genes were differentially expressed and thus possibly involved in the response to nitrogen deficiency. Cluster and functional enrichment analysis indicated that the differentially expressed genes (DEGs) in FN were highly enriched in response to stress, defense response, and gene expression regulation. Comprehensive comparison analysis further suggested that Tibetan hulless barley could respond to varied N stress by regulating multiple common biological processes and pathways such as nitrogen metabolism, carbon metabolism, and photosynthesis. A large number of specific DEGs involved in diverse biological processes were also detected, implying differences in the potential regulatory patterns of low- and high-N stress response. Notably, we also identified some NIN-like proteins and other transcription factors significantly modulated by these stresses, suggesting the involvement of these transcription factors in N stress response. To our knowledge, this study is the first investigation of the Tibetan hulless barley transcriptome under N stress. The identified N-stress-related genes may provide resources for genetic improvement and promote N use efficiency. |
| first_indexed | 2024-12-11T09:40:27Z |
| format | Article |
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| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-11T09:40:27Z |
| publishDate | 2016-07-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-ecd2c62e891b48c98104b250ff4de8b22022-12-22T01:12:42ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2016-07-01710.3389/fpls.2016.01067208041Comparative transcriptome analysis revealed genes commonly responsive to varied nitrate stress in leaves of Tibetan hulless barleyCheng Qin0Zexiu Wei1Xingquan Zeng2Yulin Wang3Lijun Bai4Qijun Xu5Hongjun Yuan6Yawei Tang7Tashi Nyima8Zunyi Academy of Agricultural SciencesTibet Academy of Agricultural and Animal Husbandry SciencesTibet Academy of Agricultural and Animal Husbandry SciencesTibet Academy of Agricultural and Animal Husbandry SciencesBest Biological Technology Co., LTDTibet Academy of Agricultural and Animal Husbandry SciencesTibet Academy of Agricultural and Animal Husbandry SciencesTibet Academy of Agricultural and Animal Husbandry SciencesTibet Academy of Agricultural and Animal Husbandry SciencesNitrogen (N) deprivation or excess can lead to dramatic phenotype change, disrupt important biological processes, and ultimately limit plant productivity. To explore genes in Tibetan hulless barley responsive to varied N stress, we utilized a comparative transcriptomics method to investigate gene expression patterns under three nitrate treatments. The transcriptome of the control (optimal-nitrate, ON) sample was compared with that of free-nitrate (FN), low-nitrate (LN) and high-nitrate (HN) treatment samples, identifying 2,428, 1,274, and 1,861 genes, respectively, that exhibited significant differences in transcript abundance. Among these, 9 genes encoding ribulose bisphosphate carboxylases exhibited up-regulated expression under varied N stress. We further compared FN versus ON and LN versus ON to investigate the impact of stress degree on gene expression. With the aggravation of stress, more genes were differentially expressed and thus possibly involved in the response to nitrogen deficiency. Cluster and functional enrichment analysis indicated that the differentially expressed genes (DEGs) in FN were highly enriched in response to stress, defense response, and gene expression regulation. Comprehensive comparison analysis further suggested that Tibetan hulless barley could respond to varied N stress by regulating multiple common biological processes and pathways such as nitrogen metabolism, carbon metabolism, and photosynthesis. A large number of specific DEGs involved in diverse biological processes were also detected, implying differences in the potential regulatory patterns of low- and high-N stress response. Notably, we also identified some NIN-like proteins and other transcription factors significantly modulated by these stresses, suggesting the involvement of these transcription factors in N stress response. To our knowledge, this study is the first investigation of the Tibetan hulless barley transcriptome under N stress. The identified N-stress-related genes may provide resources for genetic improvement and promote N use efficiency.http://journal.frontiersin.org/Journal/10.3389/fpls.2016.01067/fullTranscription Factorsnitrogen stressTibetan hulless barleyDifferential expression genescomparative transcriptome |
| spellingShingle | Cheng Qin Zexiu Wei Xingquan Zeng Yulin Wang Lijun Bai Qijun Xu Hongjun Yuan Yawei Tang Tashi Nyima Comparative transcriptome analysis revealed genes commonly responsive to varied nitrate stress in leaves of Tibetan hulless barley Frontiers in Plant Science Transcription Factors nitrogen stress Tibetan hulless barley Differential expression genes comparative transcriptome |
| title | Comparative transcriptome analysis revealed genes commonly responsive to varied nitrate stress in leaves of Tibetan hulless barley |
| title_full | Comparative transcriptome analysis revealed genes commonly responsive to varied nitrate stress in leaves of Tibetan hulless barley |
| title_fullStr | Comparative transcriptome analysis revealed genes commonly responsive to varied nitrate stress in leaves of Tibetan hulless barley |
| title_full_unstemmed | Comparative transcriptome analysis revealed genes commonly responsive to varied nitrate stress in leaves of Tibetan hulless barley |
| title_short | Comparative transcriptome analysis revealed genes commonly responsive to varied nitrate stress in leaves of Tibetan hulless barley |
| title_sort | comparative transcriptome analysis revealed genes commonly responsive to varied nitrate stress in leaves of tibetan hulless barley |
| topic | Transcription Factors nitrogen stress Tibetan hulless barley Differential expression genes comparative transcriptome |
| url | http://journal.frontiersin.org/Journal/10.3389/fpls.2016.01067/full |
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