Journal Article

SNP Discovery and Linkage Map Construction in Cultivated Tomato

Kenta Shirasawa, Sachiko Isobe, Hideki Hirakawa, Erika Asamizu, Hiroyuki Fukuoka, Daniel Just, Christophe Rothan, Shigemi Sasamoto, Tsunakazu Fujishiro, Yoshie Kishida, Mitsuyo Kohara, Hisano Tsuruoka, Tsuyuko Wada, Yasukazu Nakamura, Shusei Sato and Satoshi Tabata

in DNA Research

Published on behalf of Kazusa DNA Research Institute

Volume 17, issue 6, pages 381-391
Published in print December 2010 | ISSN: 1340-2838
Published online November 2010 | e-ISSN: 1756-1663 | DOI:

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Few intraspecific genetic linkage maps have been reported for cultivated tomato, mainly because genetic diversity within Solanum lycopersicum is much less than that between tomato species. Single nucleotide polymorphisms (SNPs), the most abundant source of genomic variation, are the most promising source of polymorphisms for the construction of linkage maps for closely related intraspecific lines. In this study, we developed SNP markers based on expressed sequence tags for the construction of intraspecific linkage maps in tomato. Out of the 5607 SNP positions detected through in silico analysis, 1536 were selected for high-throughput genotyping of two mapping populations derived from crosses between ‘Micro-Tom’ and either ‘Ailsa Craig’ or ‘M82’. A total of 1137 markers, including 793 out of the 1338 successfully genotyped SNPs, along with 344 simple sequence repeat and intronic polymorphism markers, were mapped onto two linkage maps, which covered 1467.8 and 1422.7 cM, respectively. The SNP markers developed were then screened against cultivated tomato lines in order to estimate the transferability of these SNPs to other breeding materials. The molecular markers and linkage maps represent a milestone in the genomics and genetics, and are the first step toward molecular breeding of cultivated tomato. Information on the DNA markers, linkage maps, and SNP genotypes for these tomato lines is available at

Keywords: DNA marker; linkage map; single nucleotide polymorphism; Solanum lycopersicum; tomato

Journal Article.  5323 words.  Illustrated.

Subjects: Genetics and Genomics

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