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


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.


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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Apetala 2


Auxin response factor


Base pair


Coding sequence


Cytoplasmic male sterility




Genome-wide mapping of uncapped transcripts


Gene ontology


Growth-regulating factor


Homeodomain-leucine zipper


Micro RNA






Next generation sequencing




Open reading frame


Parallel analysis of RNA ends


Plant Non-coding RNA Database


Precursor miRNA


Primary miRNA




RNA-induced silencing complex


RNA ligase-mediated rapid amplification of cDNA ends


Ribosomal RNA


Squamosa promoter binding protein


Small nuclear RNA

Sno RNA:

Small nucleolar RNA


Small RNA


Teosinte branched 1 cycloidea and PCF


Transcription factor


Transfer RNA


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

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Correspondence to Abhishek Bohra.

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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).

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  • Male sterility
  • microRNA
  • Degradome
  • Sequencing
  • Gene expression