Comparative transcriptomics reveals potential regulators of climate adaptation in Santalum album L. (Indian Sandalwood).

Santalum album L. (Indian Sandalwood), a valued tree species known for its fragrant heartwood and essential oil is facing increasing threat due to severe anthropogenic pressures compounded by climate change which has resulted in depletion of its adaptive gene pool. The present study investigates the transcriptome-level responses of nine sandalwood genotypes sourced from diverse climatic zones to identify adaptive genes in the species. Comparative transcriptomics predicted 727, 1141 and 479 differentially expressed transcripts (DETs) across wet vs. dry; monsoon vs. dry and wet vs. monsoon conditions, respectively, and majority of DETs were up-regulated in samples sourced from high rainfall areas. Transcripts including heat shock proteins, Zinc finger binding protein, ribosomal proteins, transcription factors and protein kinase were identified as probable regulators of climate adaptation in S. album. The expression changes of eight selected transcripts were further validated by real-time quantitative PCR. Protein-protein interaction analysis revealed key hub transcripts involved in climate response, while alternative splicing events in transcripts such as SURP and G-patch domain-containing protein 1-like protein, G-type lectin S-receptor-like serine/threonine protein kinase B120, Tetraspanin-3 and ARM repeat superfamily protein indicated the probable role of alternate splicing in increasing the transcript diversity during adaptation. This study presents the first insight into the molecular mechanisms of climate adaptation in the species and can form the basis for specific interventions such as selective breeding, genetic manipulation, and habitat management for conservation and long-term survival of sandalwood.

Supplementary information: The online version contains supplementary material available at 10.1007/s13205-025-04218-4.