Population genomics of de novo domestication in wild Amur grape

Backgrounds: Extreme weather and diminished genetic diversity threaten global agriculture. De novo domestication offers an urgent, rapid pathway to develop climate-resilient crops directly from wild relatives. Yet, this essential strategy remains widely overlooked in corps research, particularly regarding highly resilient wild grape species. Results: We propose a population genomics framework to comprehensively investigate de novo domestication. By integrating resequencing data from 130 accessions and genomes from eight grape accessions, we identify an independent origin of rapid independent de novo domestication of wild Amur grape ( Vitis amurensis ) in Northeast China, accompanied by transposable element (TE)-mediated genome shrinkage. In the de novo domesticated Amur grape population, we detect 155 high-confidence selection signatures associated with fruit quality ( UFGT6 ), development (YABBY5), and cold tolerance ( LEA18 ). Structural variants (SVs) underpin key MYB gene clusters and PGG disease resistance clusters in both ancient and de novo domestication. Rapid de novo domestication also involved a bottleneck, leading to relaxed purifying selection and slower linkage disequilibrium (LD) decay, with deleterious variants accumulated in a heterozygous state but to a lesser extent than in ancient domestication. Conclusions: Our study demonstrates that de novo domestication can rapidly reshape the genomic landscape through TEs and SVs, and targeted selection on both conserved and species-specific traits. These findings establish the Amur grape as a paradigm for rapid crop improvement and provide a genomic roadmap for future molecular breeding.