Development of a core set of simple sequence repeat markers for dna fingerprinting of tomato germplasm

Distinctness, uniformity and stability (DUS) testing of varieties based on morphological, physiological and biological descriptors has raised many concerns i.e., these traits are influenced by environment hence non reproducible. Therefore, DNA fingerprinting has been proposed as a necessary part of DUS testing of a plant variety for protection of PBRs and registration of a variety in PBRs registry. Present study was conducted for DNA fingerprinting and genetic diversity assessment in recently developed 13 tomato genotypes including hybrids, OPVs and inbred lines. About 212 SSR markers were used for DNA fingerprinting and genetic diversity assessment. Out of these 199 markers were amplified whereas 13 were not amplified. A total of 1314 alleles were amplified by 199 SSR markers and among these 912 alleles (70%) were polymorphic which exhibited high genetic diversity among genotypes. Cluster and structure analysis was performed to study the genetic relationship of varieties with each other. Genetic similarity coefficient between genotypes ranged from 0.76 to 0.88. Cluster and structure analysis grouped genotypes to three distinct classes. Hybrids genotypes i.e. Salar-F1, Saandal-F1, Sundar-hybrid and Ahmar-hybrid were clustered with each other, two of the OPVs i.e. Nadir and Naqeeb shared same cluster and inbred lines 8502, 8505, 9108, 13195, 8504, 68543 and 17253 were shared the same cluster. Different markers for unique identification of genotypes were also proposed i.e. XM010323394 was most informative SSR marker as it amplified unique alleles for 8 genotypes i.e. Naqeeb, Nadir, 17253, 8502, 8504, 8505, 68543 and 9108. A set of 50 most informative SSR markers was proposed for future DNA fingerprinting studies based on number of alleles, polymorphic alleles and PIC contents. Results reported in this study would be useful for future DNA fingerprinting and genetic diversity studies and protection of varieties under Plant Breeders Rights Rules.