Genome-Wide Identification and Characterization of RNA/DNA Differences Associated with Drought Response in Wheat
RNA/DNA difference (RDD) is a post-transcriptional RNA modification to enrich genetic information, widely involved in regulating diverse biological processes in eukaryotes. RDDs in the wheat nuclear genome, especially those associated with drought response or tolerance, were not well studied up to n...
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MDPI AG
2022-01-01
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| Series: | International Journal of Molecular Sciences |
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| author | Yan Pan Mengqi Li Jiaqian Huang Wenqiu Pan Tingrui Shi Qifan Guo Guang Yang Xiaojun Nie |
| author_facet | Yan Pan Mengqi Li Jiaqian Huang Wenqiu Pan Tingrui Shi Qifan Guo Guang Yang Xiaojun Nie |
| author_sort | Yan Pan |
| collection | DOAJ |
| description | RNA/DNA difference (RDD) is a post-transcriptional RNA modification to enrich genetic information, widely involved in regulating diverse biological processes in eukaryotes. RDDs in the wheat nuclear genome, especially those associated with drought response or tolerance, were not well studied up to now. In this study, we investigated the RDDs related to drought response based on the RNA-seq data of drought-stressed and control samples in wheat. In total, 21,782 unique RDDs were identified, of which 265 were found to be drought-induced, representing the first drought-responsive RDD landscape in the wheat nuclear genome. The drought-responsive RDDs were located in 69 genes, of which 35 were differentially expressed under drought stress. Furthermore, the effects of RNA/DNA differences were investigated, showing that they could result in changes of RNA secondary structure, miRNA-target binding as well as protein conserved domains in the RDD-containing genes. In particular, the A to C mutation in TraesCS2A02G053100 (orthology to <i>OsRLCK</i>) led to the loss of tae-miR9657b-5p targeting, indicating that RNA/DNA difference might mediate miRNA to regulate the drought-response process. This study reported the first drought-responsive RDDs in the wheat nuclear genome. It sheds light on the roles of RDD in drought tolerance, and may also contribute to wheat genetic improvement based on epi-transcriptome methods. |
| first_indexed | 2024-03-09T23:47:20Z |
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| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-09T23:47:20Z |
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| series | International Journal of Molecular Sciences |
| spelling | doaj.art-0564da3051444dd6bc062eb813dab7062023-11-23T16:39:53ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672022-01-01233140510.3390/ijms23031405Genome-Wide Identification and Characterization of RNA/DNA Differences Associated with Drought Response in WheatYan Pan0Mengqi Li1Jiaqian Huang2Wenqiu Pan3Tingrui Shi4Qifan Guo5Guang Yang6Xiaojun Nie7State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, ChinaState Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, ChinaState Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, ChinaState Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, ChinaState Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, ChinaState Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, ChinaState Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, ChinaState Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, ChinaRNA/DNA difference (RDD) is a post-transcriptional RNA modification to enrich genetic information, widely involved in regulating diverse biological processes in eukaryotes. RDDs in the wheat nuclear genome, especially those associated with drought response or tolerance, were not well studied up to now. In this study, we investigated the RDDs related to drought response based on the RNA-seq data of drought-stressed and control samples in wheat. In total, 21,782 unique RDDs were identified, of which 265 were found to be drought-induced, representing the first drought-responsive RDD landscape in the wheat nuclear genome. The drought-responsive RDDs were located in 69 genes, of which 35 were differentially expressed under drought stress. Furthermore, the effects of RNA/DNA differences were investigated, showing that they could result in changes of RNA secondary structure, miRNA-target binding as well as protein conserved domains in the RDD-containing genes. In particular, the A to C mutation in TraesCS2A02G053100 (orthology to <i>OsRLCK</i>) led to the loss of tae-miR9657b-5p targeting, indicating that RNA/DNA difference might mediate miRNA to regulate the drought-response process. This study reported the first drought-responsive RDDs in the wheat nuclear genome. It sheds light on the roles of RDD in drought tolerance, and may also contribute to wheat genetic improvement based on epi-transcriptome methods.https://www.mdpi.com/1422-0067/23/3/1405droughtmiRNA targetingRNA secondary structureRNA/DNA differencewheat |
| spellingShingle | Yan Pan Mengqi Li Jiaqian Huang Wenqiu Pan Tingrui Shi Qifan Guo Guang Yang Xiaojun Nie Genome-Wide Identification and Characterization of RNA/DNA Differences Associated with Drought Response in Wheat International Journal of Molecular Sciences drought miRNA targeting RNA secondary structure RNA/DNA difference wheat |
| title | Genome-Wide Identification and Characterization of RNA/DNA Differences Associated with Drought Response in Wheat |
| title_full | Genome-Wide Identification and Characterization of RNA/DNA Differences Associated with Drought Response in Wheat |
| title_fullStr | Genome-Wide Identification and Characterization of RNA/DNA Differences Associated with Drought Response in Wheat |
| title_full_unstemmed | Genome-Wide Identification and Characterization of RNA/DNA Differences Associated with Drought Response in Wheat |
| title_short | Genome-Wide Identification and Characterization of RNA/DNA Differences Associated with Drought Response in Wheat |
| title_sort | genome wide identification and characterization of rna dna differences associated with drought response in wheat |
| topic | drought miRNA targeting RNA secondary structure RNA/DNA difference wheat |
| url | https://www.mdpi.com/1422-0067/23/3/1405 |
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