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Identification and molecular characterization of miRNAs and their target genes associated with seed development through small RNA sequencing in chickpea

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Abstract

Multiple studies have attempted to dissect the molecular mechanism underlying seed development in chickpea (Cicer arietinum L.). These studies highlight the need to focus on the role of miRNAs in regulating storage protein accumulation in seeds. Therefore, a total of 8,856,691 short-read sequences were generated from a small RNA library of developing chickpea seeds and were analyzed using miRDeep-P to identify 74 known and 26 novel miRNA sequences. Known miRNAs were classified into 22 miRNA families with miRNA156 family being most abundant. Of the 26 putative novel miRNAs identified, only 22 could be experimentally validated using stem loop end point PCR. Differential expression analyses led to the identification of known as well as novel miRNAs that could regulate various stages of chickpea seed development. In silico target prediction revealed several important target genes and transcription factors like SPL, mediator of RNA Polymerase II transcription subunit 12, aspartic proteinase and NACs, which were further validated by real-time PCR analysis. A comparative expression analysis in chickpea genotypes with contrasting seed protein content revealed one known (Car-miR156h) and two novel miRNA (Car-novmiR7 and Car-novmiR23) candidates to be highly expressed in the LPC (low protein content) chickpea genotypes, targets of which are known to regulate seed storage protein accumulation. Therefore, this study provides a useful resource in the form of miRNA and their targets which can be further utilized to understand and manipulate various regulatory mechanisms involved in seed development with the overall aim of improving yield and nutrition attributes in chickpea.

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Data availability

All relevant supporting data can be found within the additional files accompanying this article. The RNA-Seq reads described in the article were deposited at the Sequence Read Archive (SRA) database; BioProject PRJNA298120; Accession number SRR3103025.

Abbreviations

RPM:

reads per million

TF:

transcription factor

LPC:

low protein content

HPC:

high protein content

GO:

gene ontology

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Acknowledgements

SP and SV acknowledge the award of research fellowship from the Department of Biotechnology, Govt. of India. AC acknowledges the award of a research fellowship from the CSIR, Govt. of India. The authors are thankful to DBT-eLibrary Consortium (DeLCON) for providing access to e-resources. The authors also thank Dr. Swarup Parida, NIPGR, New Delhi, India for providing the chickpea seeds for LPC and HPC genotypes.

Funding

This work was funded by the Department of Biotechnology, Government of India, under the Challenge Programme on Chickpea Functional Genomics (grant number: BT/AGR/CG-PhaseII/01/2014).

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  1. Subodh Verma and Anirban Chakraborty contributed equally to this work.

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  1. National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India

    Seema Pradhan, Subodh Verma, Anirban Chakraborty & Sabhyata Bhatia

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  1. Seema Pradhan
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SP, SV, AC, and SB were involved in the designing and execution of the work. SP, SV, and AC conducted all the experiments, analyzed data, and prepared the manuscript draft. SB corrected the manuscript and gave the final approval for the version to be published.

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Correspondence to Sabhyata Bhatia.

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Pradhan, S., Verma, S., Chakraborty, A. et al. Identification and molecular characterization of miRNAs and their target genes associated with seed development through small RNA sequencing in chickpea. Funct Integr Genomics 21, 283–298 (2021). https://doi.org/10.1007/s10142-021-00777-w

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