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Genome-wide analysis of miRNAs and Tasi-RNAs in Zea mays in response to phosphate deficiency

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Abstract

Globally important cereal crop maize provides important nutritions and starch in dietary foods. Low phosphate (LPi) availability in the soil frequently limits the maize quality and yield across the world. Small non-coding RNAs (Snc-RNAs) play crucial roles in growth and adaptation of plants to the environment. Snc-RNAs like microRNAs (miRs) and trans-acting small interfering RNAs (Tasi-Rs) play important functions in posttranscriptional regulation of gene expression, which controls plant development, reproduction, and biotic/abiotic stress responses. In order to identify the miR and Tasi-R alterations in leaf and root of maize in response to sufficient phosphate and LPi at 3LS and 4LS, the snc-RNA population libraries for 0th, 1st, 2nd, 4th, and 8th day were constructed. These libraries were used for genome-wide alignment and RNA-fold analysis for possible prediction of potential miRs and Tasi-Rs. This study reported 174 known and conserved differentially expressed miRs of 27 miR families of maize plant. In addition, leaf and root specific potential novel miRs representing 155 new families were also discovered. Differentially expressed conserved as well as novel miR functions in root and leaf during early stage of Pi starvation were extensively discussed. Leaf and root specific miRs as well as common miRs with their target genes, participating in different biological, cellular, and metabolic processes were explored. Further, four miR390-directed Tasi-Rs which belong to TAS3 gene family along with other orthologs of Tasi-Rs were also identified. Finally, the study provides an insight into the composite regulatory mechanism of miRs in maize in response to Pi deficiency.

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Abbreviations

LPi:

Low phosphate

SPi:

Sufficient phosphate

LS:

Leaf stage

snc-RNAs:

Small non-coding RNAs

miRs:

MicroRNAs

Tasi-Rs:

Trans-acting small interfering RNAs

SnoRNAs:

Small nucleolar RNAs

SnRNAs:

Small nuclear RNAs

SiRNAs:

Small interfering RNAs

RISC-RNA:

Induced silencing complex

MFE:

Minimum free energy

PNRD:

Plant non-coding RNA databases

TPM:

Transcripts per million

GO:

Gene ontology

FC:

Fold change

REVGO:

Reduced visualize gene ontology

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Acknowledgements

The authors are grateful to Dr. Zhang J. and his group of Shandong University, China, providing their sequencing data (GEO Accession No. GSE70612) to carry out this study. Authors also acknowledge Mr. Rahul Semwal of Indian Institute of Information Technology, Allahabad, for his support to complete this work.

Author contributions

Performed the experiments and analysis: SG and MK; designed experiments: SG, MK, and PKV; wrote paper: SG, HK, and PKV.

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Authors and Affiliations

  1. Department of Bioinformatics, Indian Institute of Information Technology-Allahabad, Devghat, Jhalwa, Allahabad, Uttar Pradesh, 211012, India

    Saurabh Gupta, Manju Kumari & Pritish Kumar Varadwaj

  2. Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Pusa, New Delhi, 110012, Delhi, India

    Himansu Kumar

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  1. Saurabh Gupta
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  2. Manju Kumari
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  4. Pritish Kumar Varadwaj
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Correspondence to Pritish Kumar Varadwaj.

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This research does not perform any experiment on human and animals. All data used in this in silico work collected from the open sources. Hence, authors declare that there is no compliance with ethical standards.

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The authors declare that they have no conflict of interest.

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This study was not supported by any funding agency.

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This article forms part of a special issue of Functional & Integrative Genomics entitled “miRNA in model and complex organisms” (Issue Editors: Hikmet Budak and Baohong Zhang).

Saurabh Gupta and Manju Kumari contributed equally in this work.

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Gupta, S., Kumari, M., Kumar, H. et al. Genome-wide analysis of miRNAs and Tasi-RNAs in Zea mays in response to phosphate deficiency. Funct Integr Genomics 17, 335–351 (2017). https://doi.org/10.1007/s10142-016-0538-4

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