Single-cell transcriptomics reveals cellular and genetic mechanisms of alpine adaptation in Rosa sericea

Hengning Deng^1,2Jian Ru³Zhenlong Liang⁴Tang Zhongyu⁴Yang Wang⁴Wenqin Yuan⁴Liangying Li⁴Yu Feng⁴Xinfen Gao^4*

• ¹Chengdu Institute of Biology, Chinese Academy of Sciences (CAS), Chengdu, China
• ²University of the Chinese Academy of Sciences, Beijing, China
• ³Shangrao Normal University, Shangrao, China
• ⁴Chinese Academy of Science Chengdu Institute of Biology, Chengdu, China

Plant development is shaped by environmental conditions, and its adaptation to climate change is crucial for biodiversity conservation. The extreme climate of the Qinghai-Tibet Plateau makes it an ideal system for studying plant adaptive strategies. Rosa sericea, a dominant alpine shrub, exhibits remarkable morphological plasticity, but its molecular and cellular adaptation mechanisms are still unclear. In this study, we integrated single-nucleus RNA sequencing (snRNA-seq) with high-dimensional weighted gene co-expression network analysis (hdWGCNA), gene ontology (GO) enrichment, gene set enrichment analysis (GSEA), pseudotime trajectory inference, and gene overexpression techniques to profile 31,796 cells from R. sericea leaves. We constructed a draft single-cell transcriptional atlas with putative annotation of 11 leaf cell types and identified eight co-expression gene modules linked to key cell types. The leaf development spatiotemporal dynamics uncovered a developmental continuum from cell proliferation to photosynthetically specialized maturation. Furthermore, we identified several developmental and physiological features potentially associated with high-altitude adaptation, including presence of transcriptionally active nuclear-encoded genes involved in chloroplast function in epidermal pavement cells, the potential role of SPL7-mediated copper homeostasis, and a putative RO6G37307–TTG2–TCP4 regulatory module associated with trichome development. Together, this study provides the first single-cell–resolved transcriptional framework for R. sericea leaves and suggests adaptive developmental mechanisms at the cellular and genetic levels, enhancing our understanding of how alpine plants respond to climate change.