摘要In plants,the genome structure of hybrids changes compared with their parents,but the effects of these changes in hybrids remain elusive.Comparing re-ciprocal crosses between Col×C24 and C24×Col in Arabidopsis using high-throughput chromosome conformation capture assay(Hi-C)analysis,we found that hybrid three-dimensional(3D)chromatin organ-ization had more long-distance interactions relative to parents,and this was mainly located in promoter regions and enriched in genes with heterosis-related pathways.The interactions between euchromatin and heterochromatin were increased,and the compartment strength decreased in hybrids.In compartment domain(CD)boundaries,the distal in-teractions were more in hybrids than their parents.In the hybrids of CURLY LEAF(clf)mutants clfCol×clfC24 and clfC24×clfCol,the heterosis phenotype was damaged,and the long-distance interactions in hy-brids were fewer than in their parents with lower H3K27me3.ChIP-seq data revealed higher levels of H3K27me3 in the region adjacent to the CD boun-dary and the same interactional homo-trans sites in the wild-type(WT)hybrids,which may have led to more long-distance interactions.In addition,the dif-ferentially expressed genes(DEGs)located in the boundaries of CDs and loop regions changed ob-viously in WT,and the functional enrichment for DEGs was different between WT and clf in the long-distance interactions and loop regions.Our findings may therefore propose a new epigenetic explanation of heterosis in the Arabidopsis hybrids and provide new insights into crop breeding and yield increase.