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Molecular biology reports
Mar, 2021;48 (3): 2261-2271.

Identification and functional prediction of long non-coding RNAs of rice (Oryza sativa L.) at reproductive stage under salinity stress.

Priyanka Jain, Samreen Hussian, Jyoti Nishad, Himanshu Dubey, Deepak Singh Bisht, Tilak Raj Sharma, Tapan Kumar Mondal
Author Information
  1. Priyanka Jain: ICAR- National Institute for Plant Biotechnology, LBS Centre, IARI Campus, Pusa, New Delhi, 110012, India.
  2. Samreen Hussian: ICAR- National Institute for Plant Biotechnology, LBS Centre, IARI Campus, Pusa, New Delhi, 110012, India.
  3. Jyoti Nishad: ICAR- National Institute for Plant Biotechnology, LBS Centre, IARI Campus, Pusa, New Delhi, 110012, India.
  4. Himanshu Dubey: ICAR- National Institute for Plant Biotechnology, LBS Centre, IARI Campus, Pusa, New Delhi, 110012, India.
  5. Deepak Singh Bisht: ICAR- National Institute for Plant Biotechnology, LBS Centre, IARI Campus, Pusa, New Delhi, 110012, India.
  6. Tilak Raj Sharma: ICAR- National Institute for Plant Biotechnology, LBS Centre, IARI Campus, Pusa, New Delhi, 110012, India.
  7. Tapan Kumar Mondal: ICAR- National Institute for Plant Biotechnology, LBS Centre, IARI Campus, Pusa, New Delhi, 110012, India. mondaltk@rediffmail.com.
PMID: 33742326 DOI: 10.1007/s11033-021-06246-8

Abstract

Salinity adversely affects the yield and growth of rice (Oryza sativa L.) plants severely, particularly at reproductive stage. Long non-coding RNAs (lncRNAs) are key regulators of diverse molecular and cellular processes in plants. Till now, no systematic study has been reported for regulatory roles of lncRNAs in rice under salinity at reproductive stage. In this study, total 80 RNA-seq data of Horkuch (salt-tolerant) and IR-29 (salt-sensitive) genotypes of rice were used and found 1626 and 2208 transcripts as putative high confidence lncRNAs, among which 1529 and 2103 were found to be novel putative lncRNAs in root and leaf tissue respectively. In Horkuch and IR-29, 14 and 16 lncRNAs were differentially expressed in root tissue while 18 and 63 lncRNAs were differentially expressed in leaf tissue. Interaction analysis among the lncRNAs, miRNAs and corresponding mRNAs indicated that these modules are involved in different biochemical pathways e.g. phenyl propanoid pathway during salinity stress in rice. Interestingly, two differentially expressed lncRNAs such as TCONS_00008914 and TCONS_00008749 were found as putative target mimics of known rice miRNAs. This study indicates that lncRNAs are involved in salinity adaptation of rice at reproductive stage through certain biochemical pathways.

Keywords

Gene expression Long non-coding RNA Reproductive stage Rice Salinity stress

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MeSH Term

Exons
Gene Expression Profiling
Gene Expression Regulation, Plant
Genome, Plant
MicroRNAs
Oryza
Plant Leaves
Plant Roots
Propanols
RNA, Long Noncoding
RNA, Messenger
RNA, Small Interfering
Reproduction
Salt Stress

Chemicals

MicroRNAs
Propanols
RNA, Long Noncoding
RNA, Messenger
RNA, Small Interfering
1-phenylpropanol
Journal Article

Word Cloud

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