Identification of microRNAs That Provide a Low Light Stress Tolerance-Mediated Signaling Pathway during Vegetative Growth in Rice
Low light intensity affects several physiological parameters during the different growth stages in rice. Plants have various regulatory mechanisms to cope with stresses. One of them is the differential and temporal expression of genes, which is governed by post-transcriptional gene expression regula...
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| Format: | Article |
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MDPI AG
2022-09-01
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| Series: | Plants |
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| author | Sudhanshu Sekhar Swagatika Das Darshan Panda Soumya Mohanty Baneeta Mishra Awadhesh Kumar Devanna Basavantraya Navadagi Rameswar Prasad Sah Sharat Kumar Pradhan Sanghamitra Samantaray Mirza Jaynul Baig Lambodar Behera Trilochan Mohapatra |
| author_facet | Sudhanshu Sekhar Swagatika Das Darshan Panda Soumya Mohanty Baneeta Mishra Awadhesh Kumar Devanna Basavantraya Navadagi Rameswar Prasad Sah Sharat Kumar Pradhan Sanghamitra Samantaray Mirza Jaynul Baig Lambodar Behera Trilochan Mohapatra |
| author_sort | Sudhanshu Sekhar |
| collection | DOAJ |
| description | Low light intensity affects several physiological parameters during the different growth stages in rice. Plants have various regulatory mechanisms to cope with stresses. One of them is the differential and temporal expression of genes, which is governed by post-transcriptional gene expression regulation through endogenous miRNAs. To decipher low light stress-responsive miRNAs in rice, miRNA expression profiling was carried out using next-generation sequencing of low-light-tolerant (Swarnaprabha) and -sensitive (IR8) rice genotypes through Illumina sequencing. Swarnaprabha and IR8 were subjected to 25% low light treatment for one day, three days, and five days at the active tillering stage. More than 43 million raw reads and 9 million clean reads were identified in Swarnaprabha, while more than 41 million raw reads and 8.5 million clean reads were identified in IR8 after NGS. Importantly, 513 new miRNAs in rice were identified, whose targets were mostly regulated by the genes involved in photosynthesis and metabolic pathways. Additionally, 114 known miRNAs were also identified. Five novel (<i>osa-novmiR1</i>, <i>osa-novmiR2</i>, <i>osa-novmiR3</i>, <i>osa-novmiR4</i>, and <i>osa-novmiR5</i>) and three known (<i>osa-miR166c-3p</i>, <i>osa-miR2102-3p</i>, and <i>osa-miR530-3p</i>) miRNAs were selected for their expression validation through miRNA-specific <i>q</i>RT-PCR. The expression analyses of most of the predicted targets of corresponding miRNAs show negative regulation. Hence, miRNAs modulated the expression of genes providing tolerance/susceptibility to low light stress. This information might be useful in the improvement of crop productivity under low light stress. |
| first_indexed | 2024-03-09T21:17:49Z |
| format | Article |
| id | doaj.art-5742aca3b21545d89e120baa54cb8c26 |
| institution | Directory Open Access Journal |
| issn | 2223-7747 |
| language | English |
| last_indexed | 2024-03-09T21:17:49Z |
| publishDate | 2022-09-01 |
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| record_format | Article |
| series | Plants |
| spelling | doaj.art-5742aca3b21545d89e120baa54cb8c262023-11-23T21:29:28ZengMDPI AGPlants2223-77472022-09-011119255810.3390/plants11192558Identification of microRNAs That Provide a Low Light Stress Tolerance-Mediated Signaling Pathway during Vegetative Growth in RiceSudhanshu Sekhar0Swagatika Das1Darshan Panda2Soumya Mohanty3Baneeta Mishra4Awadhesh Kumar5Devanna Basavantraya Navadagi6Rameswar Prasad Sah7Sharat Kumar Pradhan8Sanghamitra Samantaray9Mirza Jaynul Baig10Lambodar Behera11Trilochan Mohapatra12Crop Improvement Division, ICAR-National Rice Research Institute (NRRI), Cuttack 753006, IndiaCrop Improvement Division, ICAR-National Rice Research Institute (NRRI), Cuttack 753006, IndiaCrop Improvement Division, ICAR-National Rice Research Institute (NRRI), Cuttack 753006, IndiaCrop Improvement Division, ICAR-National Rice Research Institute (NRRI), Cuttack 753006, IndiaCrop Improvement Division, ICAR-National Rice Research Institute (NRRI), Cuttack 753006, IndiaCrop Improvement Division, ICAR-National Rice Research Institute (NRRI), Cuttack 753006, IndiaCrop Improvement Division, ICAR-National Rice Research Institute (NRRI), Cuttack 753006, IndiaCrop Improvement Division, ICAR-National Rice Research Institute (NRRI), Cuttack 753006, IndiaCrop Improvement Division, ICAR-National Rice Research Institute (NRRI), Cuttack 753006, IndiaCrop Improvement Division, ICAR-National Rice Research Institute (NRRI), Cuttack 753006, IndiaCrop Improvement Division, ICAR-National Rice Research Institute (NRRI), Cuttack 753006, IndiaCrop Improvement Division, ICAR-National Rice Research Institute (NRRI), Cuttack 753006, IndiaFormer Secretary DARE, DG, ICAR, Government. of India, New Delhi 11001, IndiaLow light intensity affects several physiological parameters during the different growth stages in rice. Plants have various regulatory mechanisms to cope with stresses. One of them is the differential and temporal expression of genes, which is governed by post-transcriptional gene expression regulation through endogenous miRNAs. To decipher low light stress-responsive miRNAs in rice, miRNA expression profiling was carried out using next-generation sequencing of low-light-tolerant (Swarnaprabha) and -sensitive (IR8) rice genotypes through Illumina sequencing. Swarnaprabha and IR8 were subjected to 25% low light treatment for one day, three days, and five days at the active tillering stage. More than 43 million raw reads and 9 million clean reads were identified in Swarnaprabha, while more than 41 million raw reads and 8.5 million clean reads were identified in IR8 after NGS. Importantly, 513 new miRNAs in rice were identified, whose targets were mostly regulated by the genes involved in photosynthesis and metabolic pathways. Additionally, 114 known miRNAs were also identified. Five novel (<i>osa-novmiR1</i>, <i>osa-novmiR2</i>, <i>osa-novmiR3</i>, <i>osa-novmiR4</i>, and <i>osa-novmiR5</i>) and three known (<i>osa-miR166c-3p</i>, <i>osa-miR2102-3p</i>, and <i>osa-miR530-3p</i>) miRNAs were selected for their expression validation through miRNA-specific <i>q</i>RT-PCR. The expression analyses of most of the predicted targets of corresponding miRNAs show negative regulation. Hence, miRNAs modulated the expression of genes providing tolerance/susceptibility to low light stress. This information might be useful in the improvement of crop productivity under low light stress.https://www.mdpi.com/2223-7747/11/19/2558index: low lightmiRNAriceSwarnaprabhaIR8vegetative stage |
| spellingShingle | Sudhanshu Sekhar Swagatika Das Darshan Panda Soumya Mohanty Baneeta Mishra Awadhesh Kumar Devanna Basavantraya Navadagi Rameswar Prasad Sah Sharat Kumar Pradhan Sanghamitra Samantaray Mirza Jaynul Baig Lambodar Behera Trilochan Mohapatra Identification of microRNAs That Provide a Low Light Stress Tolerance-Mediated Signaling Pathway during Vegetative Growth in Rice Plants index: low light miRNA rice Swarnaprabha IR8 vegetative stage |
| title | Identification of microRNAs That Provide a Low Light Stress Tolerance-Mediated Signaling Pathway during Vegetative Growth in Rice |
| title_full | Identification of microRNAs That Provide a Low Light Stress Tolerance-Mediated Signaling Pathway during Vegetative Growth in Rice |
| title_fullStr | Identification of microRNAs That Provide a Low Light Stress Tolerance-Mediated Signaling Pathway during Vegetative Growth in Rice |
| title_full_unstemmed | Identification of microRNAs That Provide a Low Light Stress Tolerance-Mediated Signaling Pathway during Vegetative Growth in Rice |
| title_short | Identification of microRNAs That Provide a Low Light Stress Tolerance-Mediated Signaling Pathway during Vegetative Growth in Rice |
| title_sort | identification of micrornas that provide a low light stress tolerance mediated signaling pathway during vegetative growth in rice |
| topic | index: low light miRNA rice Swarnaprabha IR8 vegetative stage |
| url | https://www.mdpi.com/2223-7747/11/19/2558 |
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