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

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