Open AccessGenome‐wide analysis of epigenetic and transcriptional changes associated with heterosis in pigeonpea
Author(s) -
Sinha Pallavi,
Singh Vikas K.,
Saxena Rachit K.,
Kale Sandip M.,
Li Yuqi,
Garg Vanika,
Meifang Tang,
Khan Aamir W.,
Kim Kyung Do,
Chitikineni Annapurna,
Saxena K. B.,
Sameer Kumar C. V.,
Liu Xin,
Xu Xun,
Jackson Scott,
Powell Wayne,
Nevo Eviatar,
Searle Iain R.,
Lodha Mukesh,
Varshney Rajeev K.
Publication year - 2020
Publication title -
plant biotechnology journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.525
H-Index - 115
eISSN - 1467-7652
pISSN - 1467-7644
DOI - 10.1111/pbi.13333
Subject(s) - biology , epigenetics , heterosis , dna methylation , transcriptome , hybrid , genetics , gene , gene expression , gene expression profiling , regulation of gene expression , methylation , botany
Summary 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.