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Identification of microRNAs and their gene targets in cytoplasmic male sterile and fertile maintainer lines of pigeonpea

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Abstract

Main conclusion

Comparative analysis of genome-wide miRNAs and their gene targets between cytoplasmic male sterile (CMS) and fertile lines of pigeonpea suggests a possible role of miRNA-regulated pathways in reproductive development.

Abstract

Exploitation of hybrid vigor using CMS technology has delivered nearly 50% yield gain in pigeonpea. Among various sterility-inducing cytoplasms (A1–A9) reported so far in pigeonpea, A2 and A4 are the two major sources that facilitate hybrid seed production. Recent evidence suggests involvement of micro RNA in vast array of biological processes including plant reproductive development. In pigeonpea, information about the miRNAs is insufficient. In view of this, we sequenced six small RNA libraries of CMS line UPAS 120A and isogenic fertile line UPAS 120B using Illumina technology. Results revealed 316 miRNAs including 248 known and 68 novel types. A total of 637 gene targets were predicted for known miRNAs, while 324 genes were associated with novel miRNAs. Degradome analysis revealed 77 gene targets of predicted miRNAs, which included a variety of transcription factors playing key roles in plant reproduction such as F-box family proteins, apetala 2, auxin response factors, ethylene-responsive factors, homeodomain-leucine zipper proteins etc. Differential expression of both known and novel miRNAs implied roles for both conserved as well as species-specific players. We also obtained several miRNA families such as miR156, miR159, miR167 that are known to influence crucial aspects of plant fertility. Gene ontology and pathway level analyses of the target genes showed their possible implications for crucial events during male reproductive development such as tapetal degeneration, pollen wall formation, retrograde signaling etc. To the best of our knowledge, present study is first to combine deep sequencing of small RNA and degradome for elucidating the role of miRNAs in flower and male reproductive development in pigeonpea.

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Abbreviations

AGO:

Argonaute

AP2:

Apetala 2

ARF:

Auxin response factor

Bp:

Base pair

CDS:

Coding sequence

CMS:

Cytoplasmic male sterility

DCL:

Dicer-like

GMUCT:

Genome-wide mapping of uncapped transcripts

GO:

Gene ontology

GRF:

Growth-regulating factor

HD-Zip:

Homeodomain-leucine zipper

miRNA:

Micro RNA

MYB:

Myeloblastosis

nc:

Non-coding

NGS:

Next generation sequencing

nt:

Nucleotide

ORF:

Open reading frame

PARE:

Parallel analysis of RNA ends

PNRD:

Plant Non-coding RNA Database

Pre-miRNA:

Precursor miRNA

Pri-miRNA:

Primary miRNA

Rf:

Fertility-restoring

RISC:

RNA-induced silencing complex

RLM-RACE:

RNA ligase-mediated rapid amplification of cDNA ends

rRNA:

Ribosomal RNA

SBP:

Squamosa promoter binding protein

Sn RNA:

Small nuclear RNA

Sno RNA:

Small nucleolar RNA

sRNA:

Small RNA

TCP:

Teosinte branched 1 cycloidea and PCF

TF:

Transcription factor

tRNA:

Transfer RNA

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Acknowledgements

AB acknowledges financial support from Indian Council of Agricultural Research (ICAR), New Delhi (Grant no.: AGENIASRICOP201501000047).

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Authors and Affiliations

  1. ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, India

    Abhishek Bohra, S. J. Satheesh Naik & Narendra P. Singh

  2. International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India

    Prasad Gandham, Abhishek Rathore, Rachit K. Saxena & Rajeev K. Varshney

  3. Hyderabad Central University (HCU), Hyderabad, India

    Vivek Thakur

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  1. Abhishek Bohra
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  2. Prasad Gandham
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  3. Abhishek Rathore
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  5. Rachit K. Saxena
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  6. S. J. Satheesh Naik
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  7. Rajeev K. Varshney
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Correspondence to Abhishek Bohra.

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425_2021_3568_MOESM7_ESM.png

Supplementary Fig 1 Gene ontology-Biological processes of genes (psRNATarget) targeted by known miRNAs. Color intensity represents the relative significance of the corresponding GO term (PNG 1184 KB)

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Bohra, A., Gandham, P., Rathore, A. et al. Identification of microRNAs and their gene targets in cytoplasmic male sterile and fertile maintainer lines of pigeonpea. Planta 253, 59 (2021). https://doi.org/10.1007/s00425-021-03568-6

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