Landscape and population genomic analysis reveal climate adaptation strategies in Chinese wild grapes (Vitis spp.)

Abstract

Global climate change threatens grape production, while wild germplasm provides valuable genetic resources for climate resilience. To systematically understand the genetic diversity and climate adaptation of Chinese wild grapes, we integrated population and landscape genomics analyses of 61 accessions. The Northeastern group formed a distinct genetic cluster, whereas most other groups exhibited high genetic diversity, moderate genetic differentiation, and substantial admixture. The temperature‐related variables, particularly annual mean temperature and maximum temperatures in June and July, were associated with patterns of adaptive genetic variation in Chinese wild grape populations. Genotype‐environment association (GEA) analysis identified 346 SNPs significantly associated with temperature‐related climatic factors. Among the corresponding candidate genes, transcriptomic, RT‐qPCR, and biochemical evidence further supported VdCAT1 (Vitvi18g00095) as a heat‐responsive candidate, while promoter analysis identified a SNP difference between Vitis davidii and Vitis vinifera that may affect a CTCC cis‐regulatory element and thereby influence VdCAT1 expression under heat stress. Meanwhile, we found that the population vulnerability of Chinese wild grapes would markedly increase due to climate warming, particularly in Northeastern China and the Yunnan‐Guizhou region. These findings advanced the understanding of climate-associated variation to local adaptation in Chinese wild grapes, provided a basis for conserving wild grape germplasm and breeding climate‐adaptive cultivars.