Spatial and single-nucleus transcriptomics reveal the complexity of genomic imprinting in maize

Genomic imprinting is a classic epigenetic phenomenon first discovered in maize, which occurs predominantly in the triploid endosperm and is thought to mediate parental influences on seed development. Previous studies based on bulk RNA sequencing of manually dissected endosperm have identified hundreds of putative imprinted genes; however, the extensive cellular heterogeneity of the endosperm has remained largely unexplored. Here, we combine 10x Visium spatial transcriptomics and single-nucleus RNA sequencing (snRNA-seq) to profile reciprocal maize kernels and characterize allele-specific expression and genomic imprinting at cellular resolution. We identify six major endosperm cell types and find that allele-specific expression exhibits strong cell-type specificity, with approximately two-thirds of allele-specific expression genes detected in only a single cell type. Spatial transcriptomics and snRNA-seq show high concordance, with nearly 70% of imprinted genes identified by spatial profiling being validated at the cell-type level. Less than half of the imprinted genes are shared among multiple endosperm cell types, revealing substantial spatial and cellular heterogeneity in imprinting. We find that paternally expressed genes outnumber maternally expressed genes by approximately twofold. In addition, we identify a maternally expressed long non-coding RNA located within a maternally hypomethylated region together with the canonical imprinted gene Mez1 , suggesting coordinated epigenetic regulation. Our findings demonstrate that post-fertilization endosperm differentiation shapes the spatial and cellular landscape of genomic imprinting in maize and provide a resource for investigating the functional roles of imprinting during kernel development.