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


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.

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Figure 1: Overlay heat map of the metabolite profiles and other traits of the ILs in comparison to the parental control (S. lycopersicum).
Figure 2: Cartographic representation of the combined metabolic and morphological network of the tomato.
Figure 3: Morphologically associated and independent metabolites.
Figure 4: Fine evaluation of genomic regions containing morphologically associated and independent metabolite QTLs.


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This research was supported by a grant from the German-Israeli Cooperation Project (DIP).

Author information

Correspondence to Alisdair R Fernie.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Fig. 1

Heat maps of the metabolite profiles of the introgession lines from the individual data sets of A) 2001 and B) 2003. (PDF 645 kb)

Supplementary Fig. 2

Performance of module identification. (PDF 936 kb)

Supplementary Fig. 3

HI and BX levels in three different genotypes of the recessive self-pruning (SP) allele of tomato plants. (PDF 9 kb)

Supplementary Table 1

Metabolite QTL table (PDF 100 kb)

Supplementary Table 2

Yield associated QTL table. (PDF 42 kb)

Supplementary Table 3

Association analysis between pairs of traits. (PDF 3463 kb)

Supplementary Table 4

Dependence of metabolite QTLs in morphology traits. (PDF 761 kb)

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Schauer, N., Semel, Y., Roessner, U. et al. Comprehensive metabolic profiling and phenotyping of interspecific introgression lines for tomato improvement. Nat Biotechnol 24, 447–454 (2006).

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