Generation and mapping of AFLP, SSRs and SNPs in Lycopersicon esculentum

Saskia Suliman-Pollatschek, Khalil Kashkush, Hadas Shats, Jossi Hillel, Uri Lavi

Research output: Contribution to journalArticlepeer-review

50 Scopus citations


Amplified Fragment Length Polymorphism (AFLP), Simple Sequence Repeat (SSR) and Single Nucleotide Polymorphism (SNP), were applied to the tomato genome for assessment of polymorphism and for mapping. The polymorphism of AFLP was studied in twenty-one commercial tomato (L. esculentum) varieties. Four AFLP primer combinations produced 298 clear bands; an average of 75 bands per combination. SSR markers were generated from two sources: (1) size-selected genomic libraries screened with (AT)n, (CT)n, (GT)n, (ATT)n and (CTT)n probes. (2) GeneBank database. Primers were designed for 114 loci and used for genotyping 13 tomato varieties and three Lycopersicon species. Eighteen markers were used to evaluate the polymorphism among the commercial cultivars and were found to be a useful tool for cultivar identification. In-silico Comparison of DNA sequences (ESTs and genes) of L. pennellii and L. esculentum, yielded 312 SNPs. Ten L. pennelli genomic fragments were sequenced and the comparison with L. esculentum yielded 22 SNPs: Another 19 SNPs were discovered by sequencing and comparing L. pennellii genomic DNA to L. esculentum DNA fragments containing SSRs. The average SNP frequency was found to be one in a few tens of base pairs. A total of 52 microsatellites, 159 polymorphic AFLP markers and six SNPs were mapped using the Introgression Lines generated by [1]. Map location and markers' distribution are presented.

Original languageEnglish
Pages (from-to)583-597
Number of pages15
JournalCellular and Molecular Biology Letters
Issue number2 A
StatePublished - 1 Jan 2002
Externally publishedYes


  • DNA markers
  • Genetic maps
  • Genetic variation
  • Polymorphism
  • Tomato

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Cell Biology


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