Transcriptomic Analysis Reveals the Role of Long Non-Coding RNAs in Response to Drought Stress in Tibetan Hulless Barley
LncRNAs, a type of RNAs exceeding 200 nucleotides (nt) and lacking representative open reading frames (ORFs), have emerged as crucial regulatory molecules that modulate numerous growth and development processes in plants. While substantial progress has been made in interpreting the functions and reg...
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2025-06-01
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| author | Zitao Wang Yue Fang Qinyue Min Kaifeng Zheng Yanrong Pang Jinyuan Chen Feng Qiao Shengcheng Han |
| author_facet | Zitao Wang Yue Fang Qinyue Min Kaifeng Zheng Yanrong Pang Jinyuan Chen Feng Qiao Shengcheng Han |
| author_sort | Zitao Wang |
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| description | LncRNAs, a type of RNAs exceeding 200 nucleotides (nt) and lacking representative open reading frames (ORFs), have emerged as crucial regulatory molecules that modulate numerous growth and development processes in plants. While substantial progress has been made in interpreting the functions and regulatory mechanisms of coding RNAs, the study of lncRNAs in Tibetan hulless barley remains incomplete. To elucidate the coordination of drought stress responses in Tibetan hulless barely by lncRNAs, we analyzed the previously published RNA-seq data from two cultivars of hulless barley, drought-tolerant (Z772) and drought-sensitive (Z013), subjected to varying durations of drought treatment (0, 1, and 5 h). Initially, we identified a total of 2877 lncRNAs through a strict pipeline, of which 2179 were co-expressed in both cultivars. Additionally, 331 and 367 lncRNAs showed cultivar-specific expression patterns in Z772 and Z013, respectively. Given the <i>trans</i>-regulatory functions of lncRNAs, we utilized WGCNA and uncovered 11 modules that were enriched in drought-responsive pathways. Within these modules, lncRNAs and neighboring PCGs were co-clustered in key control modules. The GO enrichment analysis of potential lncRNA-PCG pairs primarily involved processes related to the response to water deprivation, regulation of abiotic stress, and RNA metabolic processes. Notably, 12 high-confidence lncRNA-PCG pairs displayed concordant expression profiles, with some annotated as TFs. Two of these pairs were validated by qRT-PCR in the Tibetan hulless barley cultivar Kunlun 14. These findings suggested that lncRNAs may participate in regulatory networks involved in drought adaptation in Tibetan hulless barley, offering novel insights into the drought resistance mechanisms of Poaceae crops and potential targets for breeding drought-resistant varieties. |
| format | Article |
| id | doaj-art-c0d03c69ddca43cf8d09684a9a199145 |
| institution | Kabale University |
| issn | 2079-7737 |
| language | English |
| publishDate | 2025-06-01 |
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| record_format | Article |
| series | Biology |
| spelling | doaj-art-c0d03c69ddca43cf8d09684a9a1991452025-08-20T03:32:31ZengMDPI AGBiology2079-77372025-06-0114773710.3390/biology14070737Transcriptomic Analysis Reveals the Role of Long Non-Coding RNAs in Response to Drought Stress in Tibetan Hulless BarleyZitao Wang0Yue Fang1Qinyue Min2Kaifeng Zheng3Yanrong Pang4Jinyuan Chen5Feng Qiao6Shengcheng Han7Key Laboratory of Biodiversity Formation Mechanism and Comprehensive Utilization of the Qinghai-Tibet Plateau in Qinghai Province, School of Life Sciences, Qinghai Normal University, Xining 810008, ChinaKey Laboratory of Biodiversity Formation Mechanism and Comprehensive Utilization of the Qinghai-Tibet Plateau in Qinghai Province, School of Life Sciences, Qinghai Normal University, Xining 810008, ChinaKey Laboratory of Biodiversity Formation Mechanism and Comprehensive Utilization of the Qinghai-Tibet Plateau in Qinghai Province, School of Life Sciences, Qinghai Normal University, Xining 810008, ChinaCollege of Life Sciences, Beijing Normal University, Beijing 100875, ChinaCollege of Life Sciences, Beijing Normal University, Beijing 100875, ChinaKey Laboratory of Biodiversity Formation Mechanism and Comprehensive Utilization of the Qinghai-Tibet Plateau in Qinghai Province, School of Life Sciences, Qinghai Normal University, Xining 810008, ChinaKey Laboratory of Biodiversity Formation Mechanism and Comprehensive Utilization of the Qinghai-Tibet Plateau in Qinghai Province, School of Life Sciences, Qinghai Normal University, Xining 810008, ChinaCollege of Life Sciences, Beijing Normal University, Beijing 100875, ChinaLncRNAs, a type of RNAs exceeding 200 nucleotides (nt) and lacking representative open reading frames (ORFs), have emerged as crucial regulatory molecules that modulate numerous growth and development processes in plants. While substantial progress has been made in interpreting the functions and regulatory mechanisms of coding RNAs, the study of lncRNAs in Tibetan hulless barley remains incomplete. To elucidate the coordination of drought stress responses in Tibetan hulless barely by lncRNAs, we analyzed the previously published RNA-seq data from two cultivars of hulless barley, drought-tolerant (Z772) and drought-sensitive (Z013), subjected to varying durations of drought treatment (0, 1, and 5 h). Initially, we identified a total of 2877 lncRNAs through a strict pipeline, of which 2179 were co-expressed in both cultivars. Additionally, 331 and 367 lncRNAs showed cultivar-specific expression patterns in Z772 and Z013, respectively. Given the <i>trans</i>-regulatory functions of lncRNAs, we utilized WGCNA and uncovered 11 modules that were enriched in drought-responsive pathways. Within these modules, lncRNAs and neighboring PCGs were co-clustered in key control modules. The GO enrichment analysis of potential lncRNA-PCG pairs primarily involved processes related to the response to water deprivation, regulation of abiotic stress, and RNA metabolic processes. Notably, 12 high-confidence lncRNA-PCG pairs displayed concordant expression profiles, with some annotated as TFs. Two of these pairs were validated by qRT-PCR in the Tibetan hulless barley cultivar Kunlun 14. These findings suggested that lncRNAs may participate in regulatory networks involved in drought adaptation in Tibetan hulless barley, offering novel insights into the drought resistance mechanisms of Poaceae crops and potential targets for breeding drought-resistant varieties.https://www.mdpi.com/2079-7737/14/7/737long noncoding RNAsprotein-coding genestranscriptomedrought toleranceTibetan hulless barley |
| spellingShingle | Zitao Wang Yue Fang Qinyue Min Kaifeng Zheng Yanrong Pang Jinyuan Chen Feng Qiao Shengcheng Han Transcriptomic Analysis Reveals the Role of Long Non-Coding RNAs in Response to Drought Stress in Tibetan Hulless Barley Biology long noncoding RNAs protein-coding genes transcriptome drought tolerance Tibetan hulless barley |
| title | Transcriptomic Analysis Reveals the Role of Long Non-Coding RNAs in Response to Drought Stress in Tibetan Hulless Barley |
| title_full | Transcriptomic Analysis Reveals the Role of Long Non-Coding RNAs in Response to Drought Stress in Tibetan Hulless Barley |
| title_fullStr | Transcriptomic Analysis Reveals the Role of Long Non-Coding RNAs in Response to Drought Stress in Tibetan Hulless Barley |
| title_full_unstemmed | Transcriptomic Analysis Reveals the Role of Long Non-Coding RNAs in Response to Drought Stress in Tibetan Hulless Barley |
| title_short | Transcriptomic Analysis Reveals the Role of Long Non-Coding RNAs in Response to Drought Stress in Tibetan Hulless Barley |
| title_sort | transcriptomic analysis reveals the role of long non coding rnas in response to drought stress in tibetan hulless barley |
| topic | long noncoding RNAs protein-coding genes transcriptome drought tolerance Tibetan hulless barley |
| url | https://www.mdpi.com/2079-7737/14/7/737 |
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