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. The contribution of variations within accessible chromatin regions (ACRs) to heterosis is not well understood. This study profiles chromatin accessibility in maize inbreds and their reciprocal F1 hybrids, showing that overexpressing a candidate rhamnosyl transferase gene in a hybrid chromatin context increases plant height.