Chromatin accessibility landscape and its association with heterosis in maize hybrids

Accessible chromatin regions (ACRs) encompass diverse cis-regulatory elements (CREs) crucial for gene regulation, but their variations from parents to hybrids and their contribution to heterosis remain poorly understood. Here, using MNase hypersensitivity sequencing (MH-seq) across the maize B73-Mo17 pan-genome, we analyze chromatin accessibility in inbreds and their hybrids. Approximately 81% of ACRs are syntenic in parents, while ~20% show parent-specific accessibility driven by motif divergence. Chromatin accessibility is more stably inherited than transcriptomic profiles, yet ~3.5% of ACRs exhibit non-additive inheritance in hybrid. Among these, transgressively up-regulated ACRs are evolutionarily constrained, enhanced for chromatin modifications and interactions, and localized within enhancers and CRE-clusters serving as regulatory hubs, regulating complex traits including photoperiod and metabolite levels. Overexpression of a candidate rhamnosyl transferase gene under hybrid chromatin context increases plant height, suggesting a potential contribution to heterosis. Our study provides an insightful perspective on the role of chromatin accessibility in driving heterosis.