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Tomato Analyzer: A Useful Software Application to Collect Accurate and Detailed Morphological and Colorimetric Data from Two-dimensional Objects
Published on: March 16, 2010
Sequence diversity in three tomato species: SNPs, markers, and molecular evolution
José M Jiménez-Gómez1, Julin N Maloof
1Department of Plant Biology, College of Biological Sciences, University of California Davis, Davis, CA 95616, USA. jmjimenez@ucdavis.edu
BMC Plant Biology
|July 7, 2009
Summary
This study analyzed tomato expressed sequence tags (ESTs) to uncover nucleotide diversity between species. The findings reveal genes important for tomato evolution and domestication, particularly those related to environmental responses.
Area of Science:
- Genomics
- Evolutionary Biology
- Plant Science
Background:
- Tomato species, including cultivated and wild varieties, are agriculturally and ecologically significant.
- Wild tomatoes exhibit diverse traits valuable for crop improvement, but interspecies nucleotide diversity remains underexplored.
- Limited sequence data previously hindered genome-wide evolutionary studies in tomato.
Purpose of the Study:
- To conduct a comprehensive cross-species analysis of nucleotide diversity in tomato using available expressed sequence tag (EST) data.
- To leverage linked meta-information within ESTs for functional and evolutionary insights.
- To develop and validate molecular markers for polymorphism detection.
Main Methods:
- Mining of over 20,000 interspecific and 28,800 intraspecific polymorphisms from tomato ESTs.
- Classification of genes into functional categories and analysis of single nucleotide polymorphism (SNP) quality, position, and protein effects.
- Development of over 10,000 between-species molecular markers, optimized for sequence quality and intron position, with experimental validation.
Main Results:
- Identification of substantial interspecific and intraspecific polymorphisms within tomato species.
- Enabled evolutionary analyses by integrating SNP data with gene function and quality metrics.
- Validated 413 out of 491 developed molecular markers, confirming their utility.
Conclusions:
- Presents the most extensive survey of sequence diversity across Solanum species to date.
- Identified genes crucial for tomato evolution and domestication, enriched for environmental response pathways.
- Provides a valuable resource of SNPs and molecular markers for the scientific community via a website.
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