Haplotype-Resolved 3D Genomic Landscapes and Their Impacts on Agronomic Traits in Grapevine

In clonally propagated crops, extensive divergence between haplotypes complicates transcriptional regulation. However, the contribution of the three dimensional (3D) genome organization to these allelic differences and agronomic traits remains unclear. Here, we generated haplotype-resolved 3D genome landscapes for grapevine cultivars with contrasting berry colors and seed traits, integrating them with genomic, epigenomic, and transcriptomic profiles. We found profound 3D architectural divergence between haplotypes, spanning from large-scale A/B compartments down to a level of topologically associated domain (TAD) boundary variation (18.53%∼23.01%) that approached inter-cultivar differences (18.74~21.62%) (p > 0.05). A key mechanism driving these effects involves large-scale, haplotype-specific transitions between distinct TAD states (Active, Inactive, Heterochromatic), which asymmetrically regulate transcription and alter local DNA methylation patterns. Importantly, these structural rearrangements, including TAD boundary shifts, are strongly associated with underlying structural variants (SVs). Critically, this regulatory cascade impacts key agronomic loci, genes controlling berry color (e.g. VvMYBA) and seedlessness determination (e.g. VvSUS2) were positioned at cultivar-specific TAD boundaries, exhibiting presence/absence variations and differential expression patterns. Our findings support a mechanistic model wherein phased 3D chromatin architecture and heterozygous SVs are strongly associated with the regulation of key agronomic traits, paving the way for accelerating the genetic improvement of clonal crops.