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Identification of microRNA-target modules from rice variety Pusa Basmati-1 under high temperature and salt stress

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Abstract

High temperature and salinity stress are major factors limiting the growth and productivity of rice crop on a global scale. It is therefore an essential prerequisite to understand the molecular genetic regulation of plant responses to dual stresses. MicroRNAs (miRs) are recognized as key controllers of gene expression which act mainly at the post-transcriptional level to regulate various aspects of plant development. The present study attempts to investigate the miR circuits that are modulated in response to high temperature and salinity stress in rice. To gain insights into the pathway, preliminary miR profiles were generated using the next-generation sequencing (NGS) datasets. The identified molecules were filtered on the basis of fold differential regulation under high temperature, and time kinetics of their expression under the two individual stresses was followed to capture the regulatory windows. The analysis revealed the involvement of common miR regulatory nodes in response to two different abiotic stresses, thereby broadening our perspective about the stress-mediated regulatory mechanisms operative in rice.

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Abbreviations

PB-1:

Pusa Basmati-1

NGS:

Next Generation Sequencing

miR:

microRNA

miR*:

miR star sequence

nt:

nucleotides

HTS:

High Temperature Stress

SS:

Salt Stress

UTR:

Untranslated Region

sRNA:

small RNA

N-L-PB:

15-day-old PB-1 seedling leaves grown under normal conditions

N-R-PB:

15-day-old PB-1 seedling roots grown under normal conditions

N-FL-PB:

Flag Leaf from PB-1 plants grown under normal conditions

HT-L-PB:

15-day-old PB-1 seedling leaves grown under HTS conditions

HT-R-PB:

15-day-old PB-1 seedling roots grown under HTS conditions

HT-FL-PB:

Flag Leaf from PB-1 plants grown under HTS conditions

NL-Salt:

15-day-old PB-1 seedling leaves grown under SS conditions

NR-Salt:

15-day-old PB-1 seedling roots grown under SS conditions

GO:

Gene Ontology

SPL2:

Squamosa Promoter binding protein Like 2

TOE1:

Target Of EAT1

GRF6:

Growth-Regulating Factor 6

MFEI:

Minimal Folding free Energy Index

DE:

Differentially Expressed

TPM:

Transcript Per Million

AGO:

Argonaute

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Acknowledgements

The authors thank Dr. M. Aslam and Dr. S.K. Mukherjee for generation of the sRNA libraries.

Funding

This research was supported by financial grants received from the Department of Biotechnology, Government of India.

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Authors and Affiliations

  1. Discipline of Biochemistry, SOS, Indira Gandhi National Open University, New Delhi, 110068, India

    Shikha Goel & Maneesha Pandey

  2. Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India

    Shikha Goel, Kavita Goswami, Vimal K. Pandey & Neeti Sanan-Mishra

Authors
  1. Shikha Goel
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  2. Kavita Goswami
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  3. Vimal K. Pandey
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  4. Maneesha Pandey
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  5. Neeti Sanan-Mishra
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Contributions

SG and NSM conceptualized and designed the study. SG, VP and KG performed the experiments. SG, MP and NSM drafted and revised the manuscript. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Neeti Sanan-Mishra.

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ESM 1

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Table S2

List of primers (XLSX 11 kb)

Table S3

List of known miR distribution across libraries (XLSX 182 kb)

Table S4

Venn distribution analysis of known miRs (XLS 48 kb)

Table S5

List of novel miR and miR* distribution (XLS 34 kb)

Table S6

Targets of miR star sequences (XLS 395 kb)

Table S7

Targets of validated known and novel miRs (XLSX 31 kb)

Table S8

List of known and novel miR clusters by k-means clustering analysis (XLSX 63 kb)

Table S9

List of degradome libraries and validated targets (XLSX 14 kb)

Table S10

NGS data for salt stress (XLSX 40 kb)

Table S11

List of QTLs (XLSX 122 kb)

Table S12

Gene ontology analysis (XLSX 117 kb)

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Goel, S., Goswami, K., Pandey, V.K. et al. Identification of microRNA-target modules from rice variety Pusa Basmati-1 under high temperature and salt stress. Funct Integr Genomics 19, 867–888 (2019). https://doi.org/10.1007/s10142-019-00673-4

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