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However, how viral infection rewires and shapes chromatin\u2010based epigenetic regulatory networks in crops with contrasting resistance remains unclear. To this end, we investigated the consequences of epigenetic variations in resistant and susceptible soybean cultivars following soybean mosaic virus (SMV) infection. SMV infection mediates the depletion of 24\u2010nucleotide small interfering RNAs (24\u2010nt siRNAs) in susceptible cultivars and induces the accumulation of 24\u2010nt siRNAs in resistant cultivars. Twenty\u2010four\u2013nucleotide siRNA\u2010dependent DNA methylation variable regions are preferentially enriched in euchromatic CHH contexts, and highly variable DNA methylation regions in heterochromatic long terminal repeat (LTR) retrotransposons are independent of 24\u2010nt siRNAs. Moreover, SMV infection triggers extensive chromatin remodelling in susceptible cultivar, where the depletion of 24\u2010nt siRNAs is related to reduced chromatin accessibility. Conversely, SMV infection mildly remodels chromatin accessibility at heterochromatic LTR retrotransposons in the resistant cultivar. Variations in 24\u2010nt siRNA levels and DNA methylation in upstream regions of autophagy\u2010related genes in susceptible cultivars may influence their expression. Our work provides insights into SMV\u2010triggered divergent epigenetic regulatory networks in soybeans with contrasting resistance and provides a valuable foundation for investigating gene regulatory programmes based on epigenetic variations.<\/jats:p>","DOI":"10.1111\/pce.70446","type":"journal-article","created":{"date-parts":[[2026,2,19]],"date-time":"2026-02-19T05:45:10Z","timestamp":1771479910000},"page":"3115-3133","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Epigenetic Rewiring Shapes Divergent Genome Plasticity in Virus Response Circuitry in Soybean"],"prefix":"10.1111","volume":"49","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0101-5354","authenticated-orcid":false,"given":"Ting","family":"Fang","sequence":"first","affiliation":[{"name":"State Key Laboratory of Plant Environmental Resilience, College of Agronomy and Biotechnology China Agricultural University Beijing 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