Cell-type-specific regulatory variation shapes maize heterosis

Abstract

Heterosis, the superior performance of hybrids over their parents, has been widely exploited to enhance crop productivity, but its underlying regulatory mechanisms remain incompletely understood. In particular, how cis-regulatory elements (CREs) vary between parents and hybrids, and how this variation is organized across cell types, remains largely unresolved. Here we profiled chromatin accessibility in 131,890 nuclei derived from seedlings of three Zea mays (maize) inbred lines and their reciprocal hybrids, resolving 14 major cell types. Parental haplotype comparisons showed that most accessible chromatin regions (ACRs) were sequence-conserved and have similar binarized chromatin accessibility status. At cellular resolution, hybridization broadly attenuated chromatin accessibility cell-type specificity, weakening parental cell-type bias and yielding a more even chromatin accessibility profile across cellular contexts. Chromatin inheritance was strongly cell-type dependent, with non-additive inheritance preferentially concentrated at cell-type-specific ACRs. Although cis effects were most prevalent overall, ACRs with attenuated cell-type specificity in hybrids were enriched for non-additive inheritance and trans effects. Attenuated ACRs were more prone to transcription factor (TF) footprint gains than loci retaining high cell-type specificity, with DNA-BINDING WITH ONE FINGER (DOF) and VASCULAR PLANT ONE ZINC FINGER (VOZ) among the motif families most enriched in high-confidence footprint-gaining events. ACRs with footprint gains were preferentially linked to genes involved in development, hormone responses and growth, including DOF-family gains at GOLDEN2-like (GLK2), where both the motif family and the locus have been implicated in bundle-sheath development and C4 photosynthetic specialization. Together, our findings reveal that parental chromatin accessibility patterns are reconfigured across cell types in maize hybrids, with attenuation of cell-type specificity offering a potential cellular mechanism underlying heterosis.