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

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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.

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Acknowledgements

The authors are grateful to Indian Council of Agricultural Research, New Delhi for financial Assistance and Director, ICAR-National Institute for Plant Biotechnology, New Delhi for providing the facility.

Funding

The research was funded by ICAR, New Delhi through in-house funding.

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Authors and Affiliations

  1. ICAR- National Institute for Plant Biotechnology, LBS Centre, IARI Campus, Pusa, New Delhi, 110012, India

    Priyanka Jain, Samreen Hussian, Jyoti Nishad, Himanshu Dubey, Deepak Singh Bisht, Tilak Raj Sharma & Tapan Kumar Mondal

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  1. Priyanka Jain
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  2. Samreen Hussian
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  3. Jyoti Nishad
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  4. Himanshu Dubey
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Contributions

TKM: conceived and designed the experiment, PJ did major data analysis and wrote paper, SH performed raw data analysis, HD helped in data analysis. JN performed wet lab validation of data and DSB, TKM and TRS helped in paper writing.

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Correspondence to Tapan Kumar Mondal.

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Supplementary Information

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11033_2021_6246_MOESM1_ESM.tif

Supplementary information 1 Fig. S1 Sample correlation matrix of lncRNAs, A) Horkuch root, B) IR-29 root, C) Horkuch leaf, D) IR-29 leaf. (TIF 41541 kb)

11033_2021_6246_MOESM2_ESM.tif

Supplementary information 2 Fig S2 Principal component analysis of lncRNA in control and stress conditions, A) Horkuch root, B) Horkuch leaf, C) IR-29 root, D) IR-29 leaf. (TIF 101178 kb)

11033_2021_6246_MOESM3_ESM.tif

Supplementary information 3 Fig. S3: The heat maps of differentially expressed lncRNAs A) Horkuch root B) IR-29 root tissue, C) Horkuch leaf, D) IR-29 leaf tissue. (TIF 36136 kb)

11033_2021_6246_MOESM4_ESM.tif

Supplementary information 4 Fig. S4: Volcano plot showing Pairwise comparisons of transcript abundance in A) IR-29 root, B) IR-29 leaf, C) Horkuch leaf, D) Horkuch root. Differentially expressed lncRNAs with FDR <0.05 are red coloured dots while black coloured dot represents non-significant differentially expressed lncRNA (TIF 18037 kb)

11033_2021_6246_MOESM5_ESM.tif

Supplementary information 5 Fig.S5: MA plot of differentially expressed lncRNAs in leaf tissue of Horkuch A), IR-29 B) and root tissue of Horkuch C), IR-29 D). Differentially expressed lncRNAs with FDR <0.05 are coloured red. (TIF 18645 kb)

11033_2021_6246_MOESM6_ESM.tif

Supplementary information 6 Fig. S6 Distribution patterns of identified lncRNAs on chromosomes, A) Leaf tissue, B) Root tissue. (TIF 30594 kb)

Supplementary information 7 Fig. S7 Length distribution of lncRNAs of A) leaf and B) root. (TIF 39392 kb)

Supplementary information 8 Fig. S8 Alignment of the miRNAs and their target lncRNAs as decoy. (TIF 64504 kb)

11033_2021_6246_MOESM9_ESM.tif

Supplementary information 9 Fig. S9 Gene ontology annotation of mRNA present in lncRNA- miRNA-mRNA interaction module. (TIF 21930 kb)

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Jain, P., Hussian, S., Nishad, J. et al. Identification and functional prediction of long non-coding RNAs of rice (Oryza sativa L.) at reproductive stage under salinity stress. Mol Biol Rep 48, 2261–2271 (2021). https://doi.org/10.1007/s11033-021-06246-8

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