Unravelling Genotypic Divergence Among Tomato (Solanum lycopersicum L.) Genotypes Using Simple Sequence Repeat Marker Profiling

Tomato ( Solanum lycopersicum L.) is an economically important fruit vegetable crop valued for its nutritional and income generation. Its genetic improvement depends on the efficient use of diverse germplasm, yet molecular characterization of conserved genotypes remains limited, especially in developing regions. This study evaluated the population structure and genetic diversity among 43 tomato genotypes sourced from three distinct genetic resources in Taiwan, the United States of America, and Nigeria, using 12 polymorphic Simple Sequence Repeat markers out of 21 screened. A total of 39 alleles were detected, with an average of 3 alleles per locus, indicating substantial polymorphism. Major allele frequency ranged from 0.58 to 0.79, averaging 0.73, suggesting balanced allele distribution. The expected heterozygosity for the markers varied from 0.33 (SLM 6–12) to 0.40 (SLM 6–56). Gene diversity ranged from 0.33 to 0.59, indicating a moderately broad genetic base. The Polymorphic Information Content values ranging from 0.28 to 0.53 demonstrated the markers' effectiveness in detecting polymorphisms and suitability for distinguishing the genotypes. Particularly, TP 122 and SLM 6–56 were identified as highly informative markers with PIC values above 0.40. Cluster analysis grouped the 43 genotypes into four main clusters. However, the groupings were independent of their geographic distribution. Likewise, the population structure (K = 4) supported the clustering result. Principal coordinate analysis revealed that the genotypes were distributed across the two axes with 86% of cumulative variation. The findings underscore a wide genetic base among the genotypes, offering valuable insights for planned hybridization schemes. The polymorphic markers used in this study may also be useful in variety identification and screening for distinctiveness in tomato breeding programmes.