Genotyping-by-sequencing (GBS) reveals greater somatic mutations than simple sequence repeats (SSRs) in micropropagated cannabis plants

Micropropagation is widely used in horticulture to provide large numbers of genetically similar, disease-free plants. The intent is to produce high-quality genetically identical planting material to ensure uniformity. However, this method can result in somaclonal variation, which refers to the increased rate of unusual phenotypic developments that result from genetic mutations or epigenetic alterations. While some mutations can be visually identified due to morphological or physiological defects, many are difficult to assess based on observation alone. Various DNA markers have been employed to assess the genetic fidelity of plants. However, these techniques have limited genome coverage, which makes it challenging to determine the overall genetic fidelity of the clones. Despite this, markers have widely been employed to assess genetic fidelity and to make claims that the process produces true-to-type plants. Genotyping-by-sequencing (GBS) can sequence and genotype thousands of markers from multiple individuals simultaneously and is now a common and low-cost technique. In this study, the efficacy of GBS versus simple sequence repeats (SSRs) in evaluating genetic fidelity in a clonal population of micropropagated cannabis plants was compared. The SSR analysis resulted in eight readable markers indicating negligible genetic diversity. In contrast, the GBS analysis identified over 9000 variants in cannabis clones, revealing genetic diversity within clonal lines across multiple subcultures. This study demonstrated the increased precision of sequencing-based technologies for detecting somaclonal mutations and highlighted the limitations of using SSRs or similar markers to evaluate genetic fidelity in these systems.