Genetic diversity analysis and DNA fingerprinting of elite genetic stocks of tomato using SSR markers

Abstract

Thirty genetic stocks of tomato (So/anum lycopersicum L.) were subjected to genetic diversity analysis and DNA fingerprinting using SSR markers. The stocks included male sterile lines (both pollen abortive and functional types); non-ripening mutants; disease (leaf curl virus, late blight and early blight) and nematode resistant lines; temperature stress (both low and high); and salt tolerant lines. Of the 25 primers used, 21 showed polymorphism and amplified 60 alleles with an average of 2.86 alleles per locus. Of these alleles, 21 were polymorphic and the rest were monomorphic. The PIC values for 21 primers obtained varied from 0.06 for SSR128 to 0.68 for SSR565, with an average PIC value to be 0.43. The greater number of repeat units and longer SSRs tend to have higher PIC values. Based on the PIC values and number of alleles amplified, the primer SSR565 was found to be more informative in the present set of genotypes. Similarity coefficient between any two genotypes estimated based on DNA amplification by SSR primers varied from 0.18 to 0.94. The lowest similarity coefficient (0.18) observed between genotypes belonging to the cultivated species lycopersicum and the wild species pimpinellifolium confirmed their differentiation at the species level. Many of the cultivated types were found to have fairly narrow genetic base. UPGMA revealed that SSR markers were helpful in differentiating the genotypes on the basis of horticultural and genetic factors. However, grouping of the 30 genetic stocks was independent of their geographic distribution. Based on the DNA fingerprints, it was possible to differentiate 23 of the 30 genotypes screened.