Start codon targeted (SCoT) based molecular diversity and population structure analysis in black turmeric (Curcuma caesia Roxb.)

Black turmeric (Curcuma caesia Roxb.) is an endangered perennial herb of the Zingiberaceae family. It is widely recognized for its rich phytochemical profile and therapeutic uses. Despite its significance, this crop is underexplored due to limited genomic research. To address this, we assessed the genetic variation and population structure of 54 black turmeric accessions collected from 16 districts of central India covering six agro-climatic zones using SCoT marker system. Out of 36 markers screened, 20 markers showed polymorphic and reproducible bands. These primers amplified 179 distinct fragments (150 –1300 bp; average 8.8 bands per primer) and revealed a high polymorphism rate (avg. 91.13%). The mean Polymorphism Information Content (PIC), Marker Index (MI), and Resolving Power (RP) were 0.234, 1.74 and 6.42, respectively, indicating a high level of marker informativeness. UPGMA clustering grouped the accession into six different clusters. Analysis of molecular variance (AMOVA) revealed that 94% of the genetic variation was present within populations. Bayesian clustering identified five genetic groups (K = 5). This study is the first comprehensive use of SCoT markers in Curcuma caesia for demonstrating their robustness and reliability for evaluating genetic diversity. These findings provide insights for germplasm conservation, management strategies and future breeding programs aimed at enhancing the agronomic and medicinal value of black turmeric.