Assessing Somaclonal Variation in Micro-Propagated Plants: A Comparative Review of Molecular Marker Systems

Micro-propagation has expanded globally and has revolutionized the mass production of elite true-to-type plant varieties as a solution for the rising demands of agriculture and forestry. However, there lies an inherent risk of somaclonal variation induced during the in vitro process. Ensuring the regenerants are “true-to-type” is now not only a laboratory requirement but also a critical safeguard for biodiversity and agricultural stability. This review synthesizes the current landscape of molecular marker technologies used for the assessment of clonal fidelity. A comparative analysis is provided for the most widely used marker systems, including Random Amplified Polymorphic DNA (RAPD), Inter-Simple Sequence Repeats (ISSR), Simple Sequence Repeats (SSR), and Amplified Fragment Length Polymorphism (AFLP). Furthermore, the review highlights the emerging role of Start Codon Targeted (SCoT) markers and the shift toward Single Nucleotide Polymorphism (SNP) genotyping via Next-Generation Sequencing (NGS) for high-throughput validation. The paper emphasizes the relative strengths, limitations and cost effectiveness of these systems and provides a roadmap for commercial breeders and researchers to select the most reliable diagnostic tools for maintaining the genetic blueprint of the plants.