Co-expression analysis identifies organ-specific gene regulatory networks responsive to phosphate limitation in hemp (Cannabis sativa L.).

backgroundCannabis sativa L. is a compelling model species for studying how human selection has shaped plant traits through domestication. Cannabis hemp-type varieties are grown for fibre and seed, whereas drug-types are cultivated for high cannabinoid content in pharmaceutical and recreational use. These contrasting selection criteria have led to divergent physiological and morphological traits, providing a valuable model to investigate underlying molecular and physiological mechanisms. Cultivation of hemp on more marginal soils has favoured a greater capacity to acclimate to nutrient limitations, particularly phosphorus deficiency. However, the mechanisms underlying enhanced phosphorus acclimation in hemp remain poorly understood.

resultsUsing Weighted Gene Co-expression Network Analysis (WGCNA) of RNA-seq data from multiple organs of hemp-type Cannabis grown under contrasting phosphate supplies, we performed a global transcriptome analysis to capture organ-specific and phosphate-responsive gene expression dynamics. This analysis identified twelve co-expression modules capturing coordinated gene expression across organs and phosphate conditions, reflecting processes related to organ function (e.g. root development, fibre production, and flower development) and metabolism (including photosynthesis, nutrient transport, and lipid remodelling), as well as their relationships to physiological traits. Two modules, representing leaf- and root-specific responses, were strongly associated with plant phosphorus status, and cross-comparison with genes under selection during Cannabis domestication showed significant overlap with these modules. Gene regulatory network analysis revealed how gene expression supports prioritisation of resource allocation towards reproductive organs, with the Cannabis homolog of SPX DOMAIN GENE3 (SPX3) identified as a central hub in leaf tissues coordinating the shoot phosphate starvation response. In the root-specific module, root system architecture remodelling was mediated by transcription factors including SCARECROW-LIKE (SCL) family members and a homolog of the C2H2-type transcription factor SENSITIVE TO PROTON RHIZOTOXICITY (STOP). Strigolactones emerged as key hormonal regulators of the root-specific PSR, highlighting their role in phosphate deficiency tolerance in hemp.

conclusionThese findings provide an integrated, organ-specific view of gene networks underlying the phosphate starvation response in hemp and reveal distinct features of nutrient adaptation following domestication. They identify targets for improving nutrient use efficiency in hemp and support comparative studies across Cannabis germplasm.