Genome-wide analysis of epigenetic and transcriptional changes associated with heterosis in pigeonpea

Pallavi Sinha, Vikas K. Singh, Rachit K. Saxena, Sandip M. Kale, Yuqi Li, Vanika Garg, Tang Meifang, Aamir W. Khan, Kyung Do Kim, Annapurna Chitikineni, K. B. Saxena, C. V. Sameer Kumar, Xin Liu, Xun Xu, Scott Jackson, Wayne Powell, Eviatar Nevo, Iain R. Searle, Mukesh Lodha, Rajeev K. Varshney*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

38 Citations (Scopus)
68 Downloads (Pure)


Hybrids are extensively used in agriculture to deliver an increase in yield, yet the molecular basis of heterosis is not well understood. Global DNA methylation analysis, transcriptome analysis and small RNA profiling were aimed to understand the epigenetic effect of the changes in gene expression level in the two hybrids and their parental lines. Increased DNA methylation was observed in both the hybrids as compared to their parents. This increased DNA methylation in hybrids showed that majority of the 24-nt siRNA clusters had higher expression in hybrids than the parents. Transcriptome analysis revealed that various phytohormones (auxin and salicylic acid) responsive hybrid-MPV DEGs were significantly altered in both the hybrids in comparison to MPV. DEGs associated with plant immunity and growth were overexpressed whereas DEGs associated with basal defence level were repressed. This antagonistic patterns of gene expression might contribute to the greater growth of the hybrids. It was also noticed that some common as well as unique changes in the regulatory pathways were associated with heterotic growth in both the hybrids. Approximately 70% and 67% of down-regulated hybrid-MPV DEGs were found to be differentially methylated in ICPH 2671 and ICPH 2740 hybrid, respectively. This reflected the association of epigenetic regulation in altered gene expressions. Our findings also revealed that miRNAs might play important roles in hybrid vigour in both the hybrids by regulating their target genes, especially in controlling plant growth and development, defence and stress response pathways. The above finding provides an insight into the molecular mechanism of pigeonpea heterosis.

Original languageEnglish
Pages (from-to)1697-1710
Number of pages14
JournalPlant Biotechnology Journal
Issue number8
Early online date3 Feb 2020
Publication statusPrint publication - Aug 2020

Bibliographical note

© 2020 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.


  • differentially expression gene
  • epigenomics
  • heterosis
  • miRNA
  • pigeonpea
  • small RNA


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