Somaclonal variation, arising from genetic and epigenetic modifications during clonal propagation, was once regarded as a drawback of clonality but is now recognized as a valuable source of phenotypic innovation for plant breeding. This chapter explores the transcriptomic imprints of somaclonal variation and their implications for crop improvement. Such variation may result from single-nucleotide polymorphisms (SNPs), DNA methylation, transposable element activation, and chromosomal rearrangements, all of which can reshape gene expression and influence metabolic pathways, development, and stress responses. Advances in RNA sequencing (RNA-Seq) enable the identification of differentially expressed genes (DEGs) linked to pathogen resistance, oxidative stress, and hormonal regulation, thereby providing candidate traits for breeding throughout controlled propagation. Case studies in oil palm and cucumber highlight how floral abnormalities are associated with DNA methylation changes, and how auxin signaling and oxidative stress-related genes contribute to phenotypic diversity. In addition, RNA-based markers offer a powerful approach to tracing clonal diversity by capturing dynamic gene expression changes, as exemplified in mint species. These markers, combined with marker-assisted selection (MAS), can accelerate the identification of elite clones with improved resilience, yield, and secondary metabolite production. Looking forward, the integration of omics technologies with machine learning, big data analytics, single-cell transcriptomics, long-read sequencing, and CRISPR-based tools promises new opportunities to harness somaclonal variation for precision breeding. Ultimately, transcriptomic approaches will transform this once-undesired phenomenon into a driver of agricultural resilience, sustainability, food security, and agrobiodiversity conservation.