Transposable elements contribute to climate change adaptation in the wild Amur grape (Vitis amurensis)

Transposable elements (TEs), discovered as “jumping genes” by Barbara McClintock in 1948, are increasingly recognized as key contributors of plant evolution. However, their potential roles in climatic adaptation remain unclear. Here, we construct a graph pangenome reference (Vampan_V1.0) and generate a variant map comprising 48,308,434 short variants and 127,094 TE-associated structural variants (TEVs) using deep resequencing data from 330 samples across 31 natural populations in the distributional range of the Amur grape (Vitis amurensis Rupr.). We discover a biased accumulation of SNPs around TEVs and identify 823 candidate adaptive genes associated with climate variables. Using machine learning-based genetic offset models, we further show that putative adaptive TEVs significantly reduce genetic offsets by 7.3% to 8.2%. Our study highlights the impact of TEVs on genetic diversity, local adaptation, and resilience to future climate change, providing insights into utilizing crop wild relatives in climate-resilient crop breeding.