Genomic insights into adaptive divergence and genetic vulnerability to climate change of the medicinal plant Isodon rubescens (Hemsl.) H. Hara in central China

Background Global climate change is rapidly impacting biodiversity and threatening the sustainable use of medicinal plant species by reducing their availability and increasing harvest uncertainty. Understanding the adaptive genetic variation and genetic vulnerability of medicinal plants under climate change is crucial for effective germplasm management, cultivation, and breeding efforts. In this study, we assessed the genetic differentiation, local adaptation, and genomic vulnerability of the medicinal plant Isodon rubescens (Hemsl.) H. Hara, with the goals of elucidating the impacts of geographic and environmental factors on its genetic structure and identifying at-risk populations for informed conservation and breeding under climate change. Results We applied restriction site-associated DNA sequencing (RAD-seq) to 17 populations of I. rubescens spanning its central and peripheral ranges, including the Taihang and Qinling-Funiu Mountains. The analysis revealed two distinct genetic groups: one in the Taihang Mountains and the other in the Qinling-Funiu Mountains. Significant patterns of isolation by distance (IBD), environment (IBE), and resistance (IBR) were detected, alongside high niche differentiation. We identified 456 candidate adaptive SNPs, some linked to genes involved in stress responses and biosynthesis. Precipitation was a key environmental driver of local adaptation. Populations in the northern Taihang Mountains and southern Funiu Mountains showed higher genomic vulnerability, indicating a greater risk of maladaptation. Conclusion Our findings demonstrate that geographic isolation and environmental factors, particularly precipitation, are key drivers of genetic differentiation and local adaptation in I. rubescens . The identified genomic vulnerability pinpoints specific populations at high risk under climate change. These insights provide a crucial genetic basis for formulating targeted conservation strategies and developing climate-resilient breeding programs for this medicinal species.