Comparative miRomics of Salt-Tolerant and Salt-Sensitive Rice
Increase in soil salt causes osmotic and ionic stress to plants, which inhibits their growth and productivity. Rice production is also hampered by salinity and the effect of salt is most severe at the seedling and reproductive stages. Salainity tolerance is a quantitative property controlled by mult...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
| Published: |
De Gruyter
2017-06-01
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| Series: | Journal of Integrative Bioinformatics |
| Subjects: | |
| Online Access: | https://doi.org/10.1515/jib-2017-0002 |
| _version_ | 1819020426990321664 |
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| author | Goswami Kavita Tripathi Anita Sanan-Mishra Neeti |
| author_facet | Goswami Kavita Tripathi Anita Sanan-Mishra Neeti |
| author_sort | Goswami Kavita |
| collection | DOAJ |
| description | Increase in soil salt causes osmotic and ionic stress to plants, which inhibits their growth and productivity. Rice production is also hampered by salinity and the effect of salt is most severe at the seedling and reproductive stages. Salainity tolerance is a quantitative property controlled by multiple genes coding for signaling molecules, ion transporters, metabolic enzymes and transcription regulators. MicroRNAs are key modulators of gene-expression that act at the post-transcriptional level by translation repression or transcript cleavage. They also play an important role in regulating plant’s response to salt-stress. In this work we adopted the approach of comparative and integrated data-mining to understand the miRNA-mediated regulation of salt-stress in rice. We profiled and compared the miRNA regulations using natural varieties and transgenic lines with contrasting behaviors in response to salt-stress. The information obtained from sRNAseq, RNAseq and degradome datasets was integrated to identify the salt-deregulated miRNAs, their targets and the associated metabolic pathways. The analysis revealed the modulation of many biological pathways, which are involved in salt-tolerance and play an important role in plant phenotype and physiology. The end modifications of the miRNAs were also studied in our analysis and isomiRs having a dynamic role in salt-tolerance mechanism were identified. |
| first_indexed | 2024-12-21T03:51:02Z |
| format | Article |
| id | doaj.art-07dc6edc3c084a329986abfdc425e967 |
| institution | Directory Open Access Journal |
| issn | 1613-4516 |
| language | English |
| last_indexed | 2024-12-21T03:51:02Z |
| publishDate | 2017-06-01 |
| publisher | De Gruyter |
| record_format | Article |
| series | Journal of Integrative Bioinformatics |
| spelling | doaj.art-07dc6edc3c084a329986abfdc425e9672022-12-21T19:16:58ZengDe GruyterJournal of Integrative Bioinformatics1613-45162017-06-011411899710.1515/jib-2017-0002jib-2017-0002Comparative miRomics of Salt-Tolerant and Salt-Sensitive RiceGoswami Kavita0Tripathi Anita1Sanan-Mishra Neeti2Plant RNAi Biology Group, International Center for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, IndiaPlant RNAi Biology Group, International Center for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, IndiaPlant RNAi Biology Group, International Center for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, IndiaIncrease in soil salt causes osmotic and ionic stress to plants, which inhibits their growth and productivity. Rice production is also hampered by salinity and the effect of salt is most severe at the seedling and reproductive stages. Salainity tolerance is a quantitative property controlled by multiple genes coding for signaling molecules, ion transporters, metabolic enzymes and transcription regulators. MicroRNAs are key modulators of gene-expression that act at the post-transcriptional level by translation repression or transcript cleavage. They also play an important role in regulating plant’s response to salt-stress. In this work we adopted the approach of comparative and integrated data-mining to understand the miRNA-mediated regulation of salt-stress in rice. We profiled and compared the miRNA regulations using natural varieties and transgenic lines with contrasting behaviors in response to salt-stress. The information obtained from sRNAseq, RNAseq and degradome datasets was integrated to identify the salt-deregulated miRNAs, their targets and the associated metabolic pathways. The analysis revealed the modulation of many biological pathways, which are involved in salt-tolerance and play an important role in plant phenotype and physiology. The end modifications of the miRNAs were also studied in our analysis and isomiRs having a dynamic role in salt-tolerance mechanism were identified.https://doi.org/10.1515/jib-2017-0002mirnaend modificationssalt-stressisomirsworkflowdata integration |
| spellingShingle | Goswami Kavita Tripathi Anita Sanan-Mishra Neeti Comparative miRomics of Salt-Tolerant and Salt-Sensitive Rice Journal of Integrative Bioinformatics mirna end modifications salt-stress isomirs workflow data integration |
| title | Comparative miRomics of Salt-Tolerant and Salt-Sensitive Rice |
| title_full | Comparative miRomics of Salt-Tolerant and Salt-Sensitive Rice |
| title_fullStr | Comparative miRomics of Salt-Tolerant and Salt-Sensitive Rice |
| title_full_unstemmed | Comparative miRomics of Salt-Tolerant and Salt-Sensitive Rice |
| title_short | Comparative miRomics of Salt-Tolerant and Salt-Sensitive Rice |
| title_sort | comparative miromics of salt tolerant and salt sensitive rice |
| topic | mirna end modifications salt-stress isomirs workflow data integration |
| url | https://doi.org/10.1515/jib-2017-0002 |
| work_keys_str_mv | AT goswamikavita comparativemiromicsofsalttolerantandsaltsensitiverice AT tripathianita comparativemiromicsofsalttolerantandsaltsensitiverice AT sananmishraneeti comparativemiromicsofsalttolerantandsaltsensitiverice |