Abstract: Aims The rapid fluctuations of climate are increasingly altering the fate of species, exacerbating their vulnerability, leading to the loss of genetic diversity in many species, and even pushing some to the brink of extinction. Relict plants, having survived extreme climate changes since the Cenozoic era, carry a wealth of genetic information related to environmental adaptation. Investigating the genetic basis of their population-level environmental adaptation and their potential to cope with future climate change can provide valuable insights for biodiversity conservation. Methods In this study, restriction site-associated DNA sequencing (RAD-seq) was performed on 122 individuals from 18 populations of Pterocarya hupehensis, which is a Cenozoic relict plant distributed around the Sichuan Basin in China. Then, the ecological adaptation and genetic vulnerability of P. hupehensis were studied by landscape genomics. First, we use a latent factor mixed model (LFMM) and Pcadapt to detect selected sites. Second, a Mantel test based on linear models, redundancy analysis (RDA), gradient forest (GF), and generalized dissimilarity modelling (GDM) were used to investigate the response patterns of genetic variation to environmental gradients. Finally, based on the risk of non-adaptedness (RONA), the vulnerability of the P. hupehensis was predicted for the SSP 245 and SSP585 scenarios in 2090. Important findings A total of 398 single nucleotide polymorphism loci (SNPs) were significantly associated with the six climatic factors (Isothermality, Minimum Temperature of Coldest Month, Temperature Annual Range, Mean Temperature of Wettest Quarter, Precipitation of Wettest Month, and Precipitation Seasonality). In addition, 177 of them were detected as selected SNPs. We found that Precipitation Seasonality was an important climatic factor affecting the genetic variation of P. hupehensis. A significant signal of isolation by environment (IBE) was detected, indicating that environmental factors account for more genetic variation than geographical factors. Under the SSP585 scenario in 2090, the genetic vulnerability of P. hupehensis was higher than that under SSP126 scenario. The Precipitation Seasonality has an important effect on the adaptative ability of the population in the northwest range of P. hupehensis. This study not only provides a theoretical foundation for the management and conservation strategies of vulnerable species in the face of future climate change, but also offers a new case study on how relict plants around Sichuan Basin may respond to future climate change.

Key words: relict plants, landscape genomics, ecological adaptation, genetic vulnerability, RAD-seq