Comprehensive analysis of the chloroplast genome in Cannabis sativa L. reveals variations in simple sequence repeats among cultivars

Due to the psychotropic substances contained in the cannabis plant, its cultivation is restricted in many countries around the world. Identifying specific cannabis genotypes can be of great importance in genetic studies, breeding programs, and particularly cannabis trafficking across borders and forensic casework. Although chloroplast DNA in cannabis holds significant importance in distinguishing genotypes, it has not been comprehensively investigated for SSRs yet. This study aimed to analyze the CP genome of cannabis for its complete cpSSR profile. Bioinformatics and genetic analyses were performed to identify SSRs in six different cpDNA sequences. According to the results, 30-46 SSRs were identified in the entire chloroplast genome of the studied accessions. The most common cpSSRs were mononucleotide repeats, followed by tetra-, tri-, penta-, hexa-, and dinucleotide repeats. Both genotype-based distributions and genomic locations of cpSSR motifs were unveiled. Comparative evaluations revealed the cpSSRs that were shared across all genotypes as well as genotype-specific cpSSRs. Based on the mapping data, the majority of the cpSSRs were distributed in the intergenic regions. Several SSR hotspot regions were identified, and among these, the atpH-atpI and ndhF-rpl32 regions are reported here for the first time as potential genetic markers in Cannabis.