Integrated genetic and -omics analyses revealed Salvia officinalis genotypes high in carnosic acid content linked to distinct genetic backgrounds

Salvia officinalis is abundant in the bioactive carnosic acid (CA) and carnosol (CO), phenolic diterpenes highly regarded their potent antioxidant, anti-inflammatory and anticancer, properties. The increasing global demand for CA in the food and cosmetic industry demands the identification and characterization of high-producing genotypes. This study employed multi- omics approaches to assess 50 S. officinalis genotypes in terms of their genetic variability, CA/CO content, and antioxidant activity. Genetic analysis using ISSR and SCoT markers revealed high intra-population variation, with the Elafotopos population showing the highest genetic differentiation. HPLC-PDA-MS analysis displayed significant variations in CA/CO content among genotypes, with Kalyvia and Mesobouni producing the highest levels, whereas a significant association was observed between CA content and antioxidant activity. A comparative transcriptomic analysis of contrasting genotypes (M1 high-CA, I1 low-CA) revealed that all genes involved in CA biosynthesis were upregulated in M1, which was additionally confirmed by qPCR. Furthermore, analysis of promoter regions identified cis -acting elements linked to MeJA, SA, and abiotic responses, whereas variant analysis disclosed a high-impact insertion in KSL2 ( Saoff1g02122 ) in the M1 genotype, and several missense SNPs in CA pathway genes in I1. Lastly, correlation analyses between transcription factors-CA related genes and transcription factors-CA content linked the transcription factor WD40 ( Saoff1g01558 ) with both CA content and canrosic acid synthase ( CAS; Saoff6g03569 ) expression, suggesting its key role in regulating CA biosynthesis in S. officinalis. • Genetic analysis disclosed intra-population variance and moderate structure. • CA accumulation is driven by upregulation of DXS , CPS2, KSL2 , FS , and CAS genes. • MeJA responsiveness is overrepresent in DXS CPS2 and CAS promoters. • Saoff1g01558 (WD40), may regulate the expression of CAS ( Saoff6g03569 ) gene.