SSR Marker-Assisted Selection and Monitoring of High-Metabolite Cell Lines in Plant Tissue Culture: Protocols and Somaclonal Variation Assessment.

Simple Sequence Repeat (SSR) marker-assisted selection has proven to be the most powerful tool for genetic monitoring and selection in in vitro culture systems. It is widely used in detecting somaclonal variation and producing true-to-type in vitro plantlets with superior quality. Genetic fidelity is the critical point in plant tissue culture, and SSR markers act as a supporter to pass this critical point through locus specificity, codominancy and high polymorphism. SSR markers allow the precise detection of genetic changes during callus formation, organogenesis, somatic embryogenesis, and long-term subculturing. Secondary metabolite production can be enhanced through an in vitro culture system, and SSR markers enable the identification and continuous monitoring of genetic stability and high metabolite production in cell lines. Their co-dominant nature allows differentiation between homozygous and heterozygous alleles with deeper insights into allelic stability across successive culture cycles. Moreover, SSR markers exhibit high reproducibility and genome-wide distribution, making them reliable for long-term genetic monitoring. Overall, SSR marker-based analysis strengthens the reliability, efficiency, and commercial applicability of plant tissue culture by ensuring genetic uniformity and supporting the selection of elite in vitro materials. This chapter aims to review all the aspects related to the overview of SSR markers, real-world applications, somaclonal variations, phytochemical production, genetic fidelity, challenges, and future prospects.