Development and characterization of simple sequence repeat (SSR) markers and their use in determining relationships among Lycopersicon esculentum cultivars

Abstract

The simple sequence repeat (SSR) or microsatellite marker is currently the preferred molecular marker due to its highly desirable properties. The aim of this study was to develop and characterize more SSR markers because the number of SSR markers currently available in tomato is very limited. Five hundred DNA sequences of tomato were searched for SSRs and analyzed for the design of PCR primers. Of the 158 pairs of SSR primers screened against a set of 19 diverse tomato cultivars, 129 pairs produced the expected DNA fragments in their PCR products, and 65 of them were polymorphic with the polymorphism information content (PIC) ranging from 0.09 to 0.67. Among the polymorphic loci, 2-6 SSR alleles were detected for each locus with an average of 2.7 alleles per locus; 49.2% of these loci had two alleles and 33.8% had three alleles. The vast majority (93.8%) of the microsatellite loci contained di- or tri-nucleotide repeats and only 6.2% had tetra- and penta-nucleotide repeats. It was also found that TA/AT was the most frequent type of repeat, and the polymorphism information content (PIC) was positively correlated with the number of repeats. The set of 19 tomato cultivars were clustered based on the banding patterns generated by the 65 polymorphic SSR loci. Since the markers developed in this study are primarily from expressed sequences, they can be used not only for molecular mapping, cultivar identification and marker-assisted selection, but for identifying gene-trait relations in tomato.

Genetic diversity and relationships among different tomato varieties revealed by EST-SSR markers

“…Fifty microsatellite markers were chosen on the basis of their repeat patterns (di-, tri-, tetra-, penta-, and hexanucleotide) among the highly polymorphic primers published by He et al (2003). These markers were originally screened from the Solanum genomics network (http://www.sgn.cornell.edu).…”

“…This narrow diversity makes it difficult to identify molecular markers that are polymorphic in modern breeding material. However, a number of polymorphic microsatellite markers generated from database sequences have been successfully used for genotyping tomato cultivars and accessions (He et al, 2003;Smulders et al, 1997;Bredemeijer et al, 1998).…”

“…For instance, Bredemeijer et al (2002) differentiated 468 of 521 European tomato varieties using only 20 SSR markers, while He et al (2003) and Garcia-Martinez et a1. (2006) both confirmed the applicability of SSR markers for analysis of genetic diversity and variability in tomato varieties.…”

“…It is widely accepted that SSR techniques are expensive if the sequence information for designing the primers has not yet been developed. However, for the tomato, the primer sets for SSR analysis have already been developed (Smulders et al, 1997;Bredemeijer et al, 1998;He et al, 2003). Besides, SSR has recently produced highly informative genotyping sets in other crops, such as leafy brassicas (Celucia et al, 2009), among others.…”

Multilocus sequence data reveal extensive departures from equilibrium in domesticated tomato (Solanum lycopersicum L.)

“…Genetic diversity within cultivated tomato is understood to be low (Nesbitt and Tanksley, 2002) and has never been extensively surveyed in these large assemblages of accessions. Cost-effective molecular markers such as simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) are increasingly available for S. lycopersicum (He et al, 2003;Yang et al, 2004;Labate and Baldo, 2005;Ruiz et al, 2005;Van Deynze et al, 2007).…”