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Unique miRNome during anthesis in drought-tolerant indica rice var. Nagina 22

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An Erratum to this article was published on 16 May 2015

Abstract

Main conclusion

Drought-tolerant rice variety, Nagina 22 (N22), has a unique spikelet miRNome during anthesis stage drought as well as transition from heading to anthesis.

Molecular characterization of genetic diversity of rice is essential to understand the evolution and molecular basis of various agronomically important traits such as drought tolerance. miRNAs play an important role in regulating plant development as well as stress response such as drought. In this study, we characterized the yet unexplored dynamics of the spikelet miRNA population during developmental transition from ‘heading’ to ‘anthesis’ as well as anthesis stage drought stress in a drought-tolerant indica rice variety, N22. A significant proportion of miRNA population (~20 %) in N22 spikelets is modulated during transition from heading to anthesis indicating a unique miRNome at anthesis, a developmental stage highly sensitive to stress (drought/heat). Based on the analysis of degradome data, majority of differentially regulated miRNAs appear to regulate transcription factors, some of which are implicated in regulation of development and fertilization. Similarly, drought during anthesis leads to a global change in miRNA expression pattern including those which regulate ROS homeostasis. It was possible to identify several miRNAs that were not reported to be drought responsive in earlier studies. Interestingly, a significant proportion of the drought-regulated miRNAs co-localize within QTLs related to drought tolerance and associated traits. Comparison of the expression profiles between N22 and Pusa Basmati 1 (drought sensitive) identified miRNAs with variety-specific expression patterns during phase transition (miR164, miR396, miR812, and miR1881) as well as drought stress (miR1881) indicating an evolution of a distinct and variety-specific regulatory mechanism. The promoters of these miRNAs contain LREs (light-responsive elements) and are induced by dark treatment. It was also possible to identify 4 novel miRNAs including an intronic miRNA that was conserved in both rice varieties.

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Abbreviations

N22:

Nagina 22

PB1:

Pusa Basmati 1

DAF:

Days after fertilization

QTL:

Quantitative trait loci

ROS:

Reactive oxygen species

SNP:

Single nucleotide polymorphism

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Acknowledgments

This work was partially supported by the funds from Department of Biotechnology, Government of India and the ‘Scheme to strengthen R&D Doctoral Research program’ of Univ. of Delhi, New Delhi, India. For fellowship, SK acknowledges CSIR (Council of Scientific and Industrial Research), MRD acknowledges UGC (University Grants Commission), and SCB acknowledges University of Delhi.

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Authors and Affiliations

  1. Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Marg, New Delhi, 110021, India

    Shivani Kansal, Roseeta M. Devi, Sonia C. Balyan, Mukesh K. Arora & Saurabh Raghuvanshi

  2. Division of Genetics, Indian Agricultural Research Institute, Pusa New Delhi, 110012, India

    Anil K. Singh

  3. National Institute of Plant Genome Research, Aruna Asaf Ali Road, New Delhi, 110067, India

    Saloni Mathur

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  1. Shivani Kansal
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  2. Roseeta M. Devi
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  3. Sonia C. Balyan
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  4. Mukesh K. Arora
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  7. Saurabh Raghuvanshi
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Correspondence to Saurabh Raghuvanshi.

Electronic supplementary material

Below is the link to the electronic supplementary material.

425_2015_2279_MOESM1_ESM.pdf

Supplementary Fig. S1 Pictorial representation of the miRNA dynamics in the spikelets at heading, and anthesis stage of N22 (PDF 42 kb)

425_2015_2279_MOESM2_ESM.pdf

Supplementary Fig. S2 K-means clustering of miRNAs known during the male gametophytic development stages (UNM: Uninucleate microspore; BCP: Bicellular Pollen; TCP: Tricellular pollen), heading, anthesis and grain filling stages (5DAF: 5 days after fertilization, 7DAF: 7 days after fertilization, 12DAF: 12 days after fertilization, 17DAF: 17 days after fertilization) (PDF 1032 kb)

425_2015_2279_MOESM3_ESM.pdf

Supplementary Fig. S3 Alignment of promoter miR164a,b,f; miR396a,b; miR1881 and miR812f in 4 different indica varieties, i.e. Nagina-22, Vandana, Pusa Basmati-1 and IR64 with respect to Japonica variety Nipponbare. The identical sequence is depicted as dots while SNPs at specific positions have been shown (PDF 2395 kb)

425_2015_2279_MOESM4_ESM.pdf

Supplementary Fig. S4 Line representation of the promoters (2 kb upstream of precursor start site) of the representative members of the miRNA families under study. The scale represents position in base-pair with respect to precursor start site (PDF 135 kb)

Supplementary Table S1 Names and sequences of primers used for real-time profiling and cDNA synthesis (XLSX 10 kb)

425_2015_2279_MOESM6_ESM.xlsx

Supplementary Table S2 Normalized tag density of miRNAs identified in the different small RNA libraries of N22 (XLSX 57 kb)

425_2015_2279_MOESM7_ESM.xlsx

Supplementary Table S3 Analysis of targets of all the miRNAs (of heading and anthesis) identified as per the degradome data analysis (XLSX 117 kb)

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Supplementary Table S4 Compilation of the Gene Ontology IDs of all the targets listed in Table. S3 collected from RGAP database (XLSX 68 kb)

425_2015_2279_MOESM9_ESM.xlsx

Supplementary Table S5 Summarization of data of novel miRNAs. The data includes normalized tag densities in different small RNA libraries as well as target genes based on the degradome tags. The significant targets discussed in text have been highlighted in green (XLSX 51 kb)

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Kansal, S., Devi, R.M., Balyan, S.C. et al. Unique miRNome during anthesis in drought-tolerant indica rice var. Nagina 22. Planta 241, 1543–1559 (2015). https://doi.org/10.1007/s00425-015-2279-3

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