Abstract
SummaryHybrids 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.
Highlights
Pigeonpea is the sixth most important legume crop, cultivated on ~7.03 million ha (m ha), with a production of ~4.89 million tons, globally (FAO, 2017)
Epigenetic modifications (DMGs: methylated-hybrid-mid-parent value (MPV) differentially expressed genes (DEGs)) in the key genes associated with the identified regulatory pathways associated with heterosis were observed
We report that DNA methylation may play a potential role in heterosis and genome-wide re-modelling of gene expression in hybrids is expected to provide an opportunity to understand and exploit this complex trait for crop improvement programmes
Summary
Pigeonpea is the sixth most important legume crop, cultivated on ~7.03 million ha (m ha), with a production of ~4.89 million tons (mt), globally (FAO, 2017). The first commercial food legume pigeonpea hybrid, ICPH 2671, was released for cultivation (Saxena et al, 2013) followed by ICPH 3762 (Saxena and Tikle, 2015) and ICPH 2740 (Saxena, 2015). These hybrids have >30% higher yield over the local varieties in farmers’ fields showing that higher yields in pigeonpea can be achieved. The potential molecular mechanism of heterosis is associated with genomic and epigenetic modification in hybrids.
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