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Dehydration-responsive miRNAs in foxtail millet: genome-wide identification, characterization and expression profiling

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Abstract

Main Conclusion

A set of novel and known dehydration-responsive miRNAs have been identified in foxtail millet. These findings provide new insights into understanding the functional role of miRNAs and their respective targets in regulating plant response to dehydration stress.

MicroRNAs perform significant regulatory roles in growth, development and stress response of plants. Though the miRNA-mediated gene regulatory networks under dehydration stress remain largely unexplored in plant including foxtail millet (Setaria italica), which is a natural abiotic stress tolerant crop. To find out the dehydration-responsive miRNAs at the global level, four small RNA libraries were constructed from control and dehydration stress treated seedlings of two foxtail millet cultivars showing contrasting tolerance behavior towards dehydration stress. Using Illumina sequencing technology, 55 known and 136 novel miRNAs were identified, representing 22 and 48 miRNA families, respectively. Eighteen known and 33 novel miRNAs were differentially expressed during dehydration stress. After the stress treatment, 32 dehydration-responsive miRNAs were up-regulated in tolerant cultivar and 22 miRNAs were down-regulated in sensitive cultivar, suggesting that miRNA-mediated molecular regulation might play important roles in providing contrasting characteristics to these cultivars. Predicted targets of identified miRNAs were found to encode various transcription factors and functional enzymes, indicating their involvement in broad spectrum regulatory functions and biological processes. Further, differential expression patterns of seven known miRNAs were validated by northern blot and expression of ten novel dehydration-responsive miRNAs were confirmed by SL-qRT PCR. Differential expression behavior of five miRNA-target genes was verified under dehydration stress treatment and two of them also validated by RLM RACE. Overall, the present study highlights the importance of dehydration stress-associated post-transcriptional regulation governed by miRNAs and their targets in a naturally stress-tolerant model crop.

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Abbreviations

GRF:

Growth regulating factor

MFE:

Minimum fold energy

miRNA*:

MicroRNA star

RLM-5′ Race:

RNA ligase mediated 5′ rapid amplification of cDNA ends

RPM:

Reads per million

SBP:

Squamosa promoter-binding protein

SL-qRT:

Stem loop quantitative real time PCR

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Acknowledgments

Authors’ work in the area of foxtail millet genomics is supported by the Core Grant of National Institute of Plant Genome Research, New Delhi, India. Ms. Amita Yadav acknowledges the Research Fellowship received from Council of Scientific and Industrial Research (CSIR), New Delhi, India.

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  1. National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110 067, India

    Amita Yadav, Yusuf Khan & Manoj Prasad

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  1. Amita Yadav
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Correspondence to Manoj Prasad.

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Yadav, A., Khan, Y. & Prasad, M. Dehydration-responsive miRNAs in foxtail millet: genome-wide identification, characterization and expression profiling. Planta 243, 749–766 (2016). https://doi.org/10.1007/s00425-015-2437-7

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