Population Structure of Genotypes and Genome-Wide Association Studies of Cannabinoids and Terpenes Synthesis in Hemp (Cannabis sativa L.)

Hemp (<i>Cannabis sativa</i> L.) is one of the oldest cultivated plants in the world. It is a wind-pollinated and heterozygous species, and diverse phenotypes can occur within population varieties. In our study, three different hemp varieties-('Carmagnola Selected' (CS), 'Tiborszallasi' (TS) and 'Finola selection' (FS))-were grown. Based on visual characteristics, two, five and four phenotypes were identified within CS, TS and FS, respectively. According to <i>Cannabis sativa</i> L. transcriptome data from the Sequence Read Archive (SRA), 4631 single-nucleotide polymorphism (SNP) positions were identified to develop capture probes. DNA was isolated from 171 plants representing selected phenotypes of three cultivars. Next-generation sequencing (NGS) libraries were constructed and hybridized with capture probes for target enrichment. The population structure of the samples was analyzed using SNP data for each genotype. Based on genotype profiles, CS formed a single cluster, while TS and FS were each grouped into two clusters, with phenotypes randomly distributed among them. The GWAS results were visualized using Manhattan plots. Fourteen significant SNPs surpassing the false discovery rate (FDR) of 0.01 were identified for delta-9-tetrahydrocannabinol (delta-9-THC). For cannabigerol (CBG), 12 significant SNPs were detected, and for myrcene, one SNP exceeded the 0.01 FDR threshold. However, plausible genes located 1000 bp to the left and right of the SNP position were identified for all significant SNPs.