Application of Expressed Sequence Tag and Genomic Simple Sequence Repeat Markers for Molecular Profiling and Population Structure of Underutilized Potato Germplasm With Unexplored Genetic Diversity

To understand the genetic potential of available potato ( Solanum tuberosum L.) germplasm, we characterized 34 potato genotypes from four populations, including local strains, local cultivars, breeding lines from the National Agricultural Research Centre (NARC), and exotic cultivars grown in the Potato Research Institute, Sahiwal, Pakistan. We used twenty simple sequence repeat (SSR) markers derived from both expressed sequence tag (EST) and genomic sequences to assess the genetic structure and molecular variation of 34 potato genotypes. Analysis of Molecular Variance (AMOVA) showed the highest genetic variation within genotypes rather than between populations, indicating that local potato genotypes have unexplored genetic potential for breeding programs in Pakistan. Phylogenetic analysis and Principal coordinate analysis (PCoA) consistently separated the 34 potato genotypes into two distinct groups, with certain genotypes, FSD Red and Cosmo, showing the highest genetic distance. These findings were further supported by STRUCTURE analysis, which confirmed the presence of two main clusters. Our results highlighted the significant variation present in Pakistani potato germplasm and validated that SSR‐based methods are a reliable and authentic approach for genetic diversity studies of potato. This data gives direction for selecting genetically diverse parents for breeding programs aimed at developing more resilient, adaptable, and productive potato cultivars.