Tissue culture-somaclonal variation can generate desirable phenotypes in clonally propagated crops. In our previous study, inducing two horn banana (Musa spp.) mutants (Torpedo 1/TM1 and Torpedo 2/TM2) used benzyl aminopurine (BAP) that produced substantially enhanced fruit weight compared with their parental wild-type cultivars (Agung Semeru/PAS and Local Bogor/PLB). In this study, the employment of RAPD and SCoT markers with the sequencing of polymorphic amplicons sought to determine the genetic distinctiveness of these two mutants. RAPD analysis produced 68 loci up to 83% polymorphism, while SCoT markers generated 39 alleles with lower polymorphism (8%–14%). Sequencing of the 750 bp OPC-07 RAPD and SCoT-2 revealed SNPs and indels with extensive nucleotide variations. Although OPC-07 had a nearly identical band size, a mutation hotspot at positions 116–123 uniquely distinguished TM2 from others. Similarly, sequencing of SCoT-2 amplicons revealed numerous A–T, C–G, and A–G substitutions, several triallelic polymorphic sites, and small indels. The TM2 mutants were notable with point mutations, which revealed somaclonal variations, differentiating mutants from their wild types. The results disclosed RAPD and SCoT markers effectively distinguish the improved banana genotypes. Further characterization of these genetic differences will help in planning more precise and targeted banana breeding programs.

Keywords: Banana (Musa spp.), induced mutation, benzyl aminopurine (BAP), genetic characterization, plant tissue culture, mutants, Torpedo bananas

Key findings: RAPD and SCoT markers distinguished the superior banana (Musa spp.) mutants Torpedo 1 and 2 from their wild type. Beyond detecting polymorphic bands, sequencing of selected amplicons revealed nucleotide variations in genes associated with organ formation and growth. Cluster analysis supported these findings by clearly separating the mutants Torpedo 1 and 2 from the wild type.