Population genomics reveals association of transposable elements variants with climatic adaptation in wild Amur grape
Amur grape (Vitis amurensis Rupr.) is widely recognized for its cold tolerance traits and serves as a valuable genetic resource for breeding climate-resilient grape cultivars. 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 covering the species' distribution range. We discover a biased accumulation of SNPs around TEVs and identify 823 candidate adaptive genes associated with environmental 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% under future climate scenarios. Our study shows the power of a graph-based pangenome to resolve complex variation and 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.
Authors
- Zhongxin Jin
- Zhenya Liu
- Zhiyao Ma (ORCID: https://orcid.org/0000-0003-0666-8661)
- Wenrui Wang (ORCID: https://orcid.org/0000-0002-7918-3318)
- Ting Hou (ORCID: https://orcid.org/0009-0002-4325-5567)
- Yanmei Peng (ORCID: https://orcid.org/0000-0002-7801-8994)
- Jun Wen (ORCID: https://orcid.org/0000-0002-1926-6517)
- Mengya Zhang (ORCID: https://orcid.org/0000-0002-1055-3528)
- Hui Xue
- Shuo Cao
- Zhongjie Liu
- Yuting Liu (ORCID: https://orcid.org/0009-0008-7234-4570)
- Zhuyifu Chen
- Xiaodong Xu
- Yiwen Wang
- Hua Xiao
- Fan Zhang
- Wenjing Peng
- Brandon Gaut
- Qiming Long
- Yongfeng Zhou
- Tianhao Zhang
Institutions
- Smithsonian Institution (US)
- Chinese Academy of Tropical Agricultural Sciences (CN)
- National Museum of Natural History (US)
- The University of Melbourne (AU)
- University of California, Irvine (US)
- Xishuangbanna Tropical Botanical Garden (CN)
- Agricultural Genomics Institute at Shenzhen (CN)
- Tropical Crops Genetic Resources Institute (CN)
- Chinese Academy of Agricultural Sciences (CN)
- Ministry of Agriculture and Rural Affairs (CN)
- Melbourne Genomics Health Alliance (AU)
Publication Details
- Journal
- Nature Communications
- Published
- 2026-02-26
- DOI
- https://doi.org/10.1038/s41467-026-70026-w
- Primary Topic
- Horticultural and Viticultural Research
- Type
- article
- Field-Weighted Citation Impact
- 0.00