Integrating 3D Genomics, Chromatin Architecture, and Multi-omics to Decipher Complex Agronomic Traits in Crops

Plant 3D genomics has emerged as an important framework for understanding how the spatial organization of chromosomes influences gene regulation and phenotypic variation. Although linear genome sequence, transcriptomics, and quantitative genetics have substantially advanced the dissection of complex agronomic traits, the mechanisms connecting regulatory loci to context-dependent gene expression remain incompletely understood. This challenge is particularly pronounced in polyploid crops, where genome duplication, structural rearrangements, subgenome asymmetry, and transposable-element activity contribute to highly complex regulatory landscapes. Recent applications of Hi-C, chromatin accessibility profiling, epigenomics, transcriptomics, and related multi-omics technologies in wheat, cotton, Brassica napus, soybean, and other crops have revealed chromatin loops, topologically associating domains, compartment changes, KNOT-like interactions, and other higher-order features. However, the extent to which these structures causally regulate trait-associated transcription and phenotypic diversity remains unresolved. Integrative computational analyses, quantitative genetic approaches, and functional perturbation studies are therefore needed to distinguish causal regulatory architecture from structural correlations and to establish general principles governing 3D genome function in crops.This Research Topic aims to advance a mechanistic understanding of how 3D genome organization, chromatin state, structural variation, and regulatory interactions contribute to complex agronomic traits. It will examine how the integration of 3D genomics with epigenomics, transcriptomics, quantitative genetics, pangenomics, and functional genomics can identify trait-associated regulatory elements and causal genes. Contributions may address how chromatin architecture varies across tissues, developmental stages, environments, genotypes, and subgenomes; how structural variants remodel regulatory interactions; and how 3D genomic information can be translated into molecular breeding, genome-enabled prediction, and precision crop improvement.To gather further insights into the contribution of genome architecture to complex trait regulation in crops, this Research Topic welcomes studies spanning model and cultivated plant species, with particular interest in polyploid and structurally complex genomes. Research may include experimental, computational, methodological, comparative, or translational approaches addressing, but not limited to, the following themes:o 3D genome architecture and the regulation of complex agronomic traitso Chromatin loops, topologically associating domains, compartments, and KNOT-like interactionso Structural variation, pangenomes, and phenotypic diversityo Integration of Hi-C and related 3D genomics data with epigenomics, transcriptomics, and quantitative geneticso Chromatin accessibility and the discovery of regulatory elementso Subgenome coordination and genome organization in allopolyploid cropso Tissue-, developmental stage-, environment-, and genotype-specific chromatin architectureo Functional validation of 3D genome-associated candidate genes and regulatory regionso Computational methods, artificial intelligence, and data resources for plant 3D genomicso Translational applications of 3D genome information in molecular breeding and crop improvement Topic editors: Libin Zhang, Xiangjia Min, Yin Li, Fabio Andres Gomez-Cano Source: https://www.frontiersin.org/research-topics/85519/integrating-3d-genomics-chromatin-architecture-and-multi-omics-to-decipher-complex-agronomic-traits-in-crops