Journal Article

A candidate gene survey of quantitative trait loci affecting chemical composition in tomato fruit

L. Bermúdez, U. Urias, D. Milstein, L. Kamenetzky, R. Asis, A. R. Fernie, M. A. Van Sluys, F. Carrari and M. Rossi

in Journal of Experimental Botany

Published on behalf of Society for Experimental Biology

Volume 59, issue 10, pages 2875-2890
Published in print July 2008 | ISSN: 0022-0957
Published online June 2008 | e-ISSN: 1460-2431 | DOI:

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In tomato, numerous wild-related species have been demonstrated to be untapped sources of valuable genetic variability, including pathogen-resistance genes, nutritional, and industrial quality traits. From a collection of S. pennellii introgressed lines, 889 fruit metabolic loci (QML) and 326 yield-associated loci (YAL), distributed across the tomato genome, had been identified previously. By using a combination of molecular marker sequence analysis, PCR amplification and sequencing, analysis of allelic variation, and evaluation of co-response between gene expression and metabolite composition traits, the present report, provides a comprehensive list of candidate genes co-localizing with a subset of 106 QML and 20 YAL associated either with important agronomic or nutritional characteristics. This combined strategy allowed the identification and analysis of 127 candidate genes located in 16 regions of the tomato genome. Eighty-five genes were cloned and partially sequenced, totalling 45 816 and 45 787 bases from S. lycopersicum and S. pennellii, respectively. Allelic variation at the amino acid level was confirmed for 37 of these candidates. Furthermore, out of the 127 gene-metabolite co-locations, some 56 were recovered following correlation of parallel transcript and metabolite profiling. Results obtained here represent the initial steps in the integration of genetic, genomic, and expressional patterns of genes co-localizing with chemical compositional traits of the tomato fruit.

Keywords: Candidate genes; introgressed lines; metabolite content; quantitative trait loci; Solanum lycopersicum; Solanum pennelli; tomato

Journal Article.  7758 words.  Illustrated.

Subjects: Plant Sciences and Forestry

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