Mapping structural variants in Populus tomentosa reveals adaptive signatures and improves prediction of wood properties

Structural variants (SVs) are key drivers of genome plasticity and adaptation in plants, yet their roles in woody perennials remain understudied. Here, we build a comprehensive SV landscape based on a haplotype-resolved chromosomal genome assembly and population resequencing of 302 Populus tomentosa accessions. We reconstruct the evolutionary trajectories of SVs, revealing that they shape subpopulation differentiation through both independent and joint genomic variations. Integrating transcriptomics, we demonstrate that SVs exert broad dosage and cis-acting regulatory effects. Furthermore, segmental duplications drive SV hotspot formation, and these regions are significantly enriched for adaptive signals. SV-based GWAS reveals 61 candidate genes influencing wood-related traits under adaptive selection. Functionally, a causal 54-bp insertion in the PtoERD3 promoter balances lignin-mediated growth and drought adaptation. Additionally, we implement an optimized genomic prediction method with an accuracy of 0.94 for wood-related traits. Finally, we propose an SV-based breeding navigation map to improve the accuracy of multi-trait selection. This study provides a comprehensive genome-wide landscape of structural variations (SVs) in Populus tomentosa. The authors reveal how SVs influence adaptation and wood performance, offering new insights for tree molecular breeding.