Comprehensive metabolic profiling and phenotyping of interspecific introgression lines for tomato improvement

Nat Biotechnol. 2006 Apr;24(4):447-54. doi: 10.1038/nbt1192. Epub 2006 Mar 12.


Tomato represents an important source of fiber and nutrients in the human diet and is a central model for the study of fruit biology. To identify components of fruit metabolic composition, here we have phenotyped tomato introgression lines (ILs) containing chromosome segments of a wild species in the genetic background of a cultivated variety. Using this high-diversity population, we identify 889 quantitative fruit metabolic loci and 326 loci that modify yield-associated traits. The mapping analysis indicates that at least 50% of the metabolic loci are associated with quantitative trait loci (QTLs) that modify whole-plant yield-associated traits. We generate a cartographic network based on correlation analysis that reveals whole-plant phenotype associated and independent metabolic associations, including links with metabolites of nutritional and organoleptic importance. The results of our genomic survey illustrate the power of genome-wide metabolic profiling and detailed morphological analysis for uncovering traits with potential for crop breeding.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computer Simulation
  • Gene Expression Profiling / methods
  • Genetic Enhancement / methods*
  • Models, Biological*
  • Phenotype
  • Plant Proteins / genetics*
  • Plant Proteins / metabolism*
  • Plants, Genetically Modified / physiology*
  • Protein Engineering / methods
  • Solanum lycopersicum / genetics*
  • Solanum lycopersicum / metabolism*


  • Plant Proteins