Integrative Phytochemical and Transcriptomic Analysis Reveals Genes Regulating 14-Deoxyandrographolide in Thai <i>Andrographis paniculata</i>

<i>Andrographis paniculata</i> (Burm.f.) Nees is a medicinal plant widely cited in the Thai Herbal Pharmacopoeia, primarily due to its bioactive diterpenoid lactones, particularly andrographolide (AP1), which exhibits anti-inflammatory and antiviral properties. However, regional cultivation across Thailand has led to considerable variability in plant morphology, flowering time, and phytochemical profile, resulting in inconsistent raw material quality. We hypothesized that variation in 14-deoxyandrographolide (AP6) content is genetically regulated. The objectives of this study were to comprehensively profile the diterpenoid lactones and flavonoids across 40 Thai accessions, identify accessions with contrasting AP6 content, and provide preliminary insights into candidate genes involved in AP6 biosynthesis through comparative transcriptomic analyses. Forty <i>A. paniculata</i> accessions from different regions of Thailand were cultivated under identically natural environmental conditions and harvested at the early flowering stage. Chemical profiling using high-performance thin-layer chromatography (HPTLC) and quantitative analysis by high-performance liquid chromatography (HPLC) (mean ± SD, <i>n</i> = 3) identified four major diterpenoid lactones composed of andrographolide (AP1), dehydroandrographolide (AP2), neoandrographolide (AP4), and 14-deoxyandrographolide (AP6). Among the identified compounds, AP1 was the most abundant, whereas AP6 showed the greatest variability across accessions and was therefore selected for further transcriptomic investigation. Based on AP6 content, the accessions were subjected to cluster analysis using the UPGMA clustering, which classified them into high- and low-AP6 groups for comparative transcriptomic analysis. RNA sequencing (RNA-seq) of these groups identified 255 differentially expressed genes (DEGs) (TMM normalized, negative binomial distribution, |log₂(Fold change) | ≥1, <i>P</i>-value ≤0.05, including CYP94C1-like (LOC127251729), CYP84A1-like (LOC127250079)), and β-amyrin 28-monooxygenase-like (LOC127264669), which may be involved in AP6 biosynthesis. This study is the first to integrate phytochemical and transcriptomic analyses to investigate the genetic basis of AP6 accumulation in <i>A. paniculata</i>. It addresses a critical knowledge gap in the molecular regulation of diterpenoid lactones and identifies novel candidate genes for future functional validation. The findings offer key insights into the biosynthesis of bioactive compounds and have practical implications for phytochemical standardization, precise cultivar selection, and the development of value-added herbal products.