Plant genomes are not arranged as simple linear strings. They fold into compartments, domains, and loops that can influence whether genes remain active, silent, or ready to respond. Although three-dimensional (3D) genome research has advanced rapidly in model plants and annual crops, perennial fruit crops remain less explored, partly because of their long life cycles and complex developmental programs. Kiwifruit is especially valuable for studying how genome structure relates to fruit development and agricultural traits. Because of these challenges, in-depth research is needed into how chromatin architecture, epigenomic signals, and gene expression are connected in kiwifruit and other perennial crops.
Researchers from the State Key Laboratory of Forest Food Resources Development and Utilization and the College of Horticulture Science at Zhejiang A&F University, together with collaborators from Zhejiang University, published (DOI: 10.1093/hr/uhag076) the study on March 5, 2026, in Horticulture Research. The article presents an integrated 3D genome atlas of Actinidia chinensis leaf and fruit tissues and connects genome folding with chromatin state and gene expression.
The team generated in situ high-throughput chromosome conformation capture (Hi-C) maps from leaf and fruit tissues, with three biological replicates for each tissue, producing about 6.51 billion paired-end reads. They then integrated these maps with assay for transposase-accessible chromatin using sequencing (ATAC-seq), whole-genome bisulfite sequencing (WGBS), seven histone modification profiles, and ribonucleic acid sequencing (RNA-seq) data across tissues and fruit developmental stages. The atlas resolved multiple layers of genome organization, including A/B compartments, hierarchical subcompartments, topologically associating domain (TAD)-like domains, and chromatin loops. Leaf and fruit shared broadly similar global genome organization, but differed at finer scales: fruit showed more short-range chromatin contacts, while leaf had relatively more long-range contacts. B-type subcompartments accounted for about 55%–60% of the genome and were linked with transposable elements, DNA methylation, and repressive chromatin marks. The study also identified 68 fruit-specific genes, most of which were located within TAD-like domains, suggesting that domain-scale chromatin context may be important for fruit-associated transcription.
The authors said the atlas offers a way to read the kiwifruit genome as a living structure rather than a static sequence. They said the findings show that fruit development is not controlled by single genes alone, but by genes working within organized chromatin neighborhoods. In their view, the most important message is that stable genome architecture can provide a regulatory framework, while local changes in chromatin state and domain insulation may help shape tissue-specific gene activity during fruit development.
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References
DOI
10.1093/hr/uhag076
Original Source URL
https://doi.org/10.1093/hr/uhag076
Funding information
This research was supported by the Zhejiang Province 'SanNongJiuFang'project (2025SNJF034) and Zhejiang Provincial Natural Science Foundation of China (LR23C150001).
About Horticulture Research
Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2023. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.