Szymański, J. - aDepartment of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel;iDepartment of Molecular Genetics, The Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) in Gatersleben, Seeland, OT Gatersleben, Germany. 

Bocobza, S. - Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel; Institute of Plant Sciences, Agricultural Research Organization, Rishon LeZion, Israel.

Panda, S. - Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel; Gilat Research Center, Agricultural Research Organization, Negev, Israel.

Sonawane, P. - Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel

Cárdenas, P.D. - Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark. 
Lashbrooke, J. - Institute for Wine Biotechnology, Faculty of AgriSciences, Stellenbosch University, Stellenbosch, South Africa. 
Kamble, A. - Department of Botany, Savitribai Phule Pune University, Pune, India. 
Shahaf, N. - Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel

Meir, S. - Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel

Bovy, A. - Department of Plant Breeding, Wageningen Plant Research, Wageningen, Netherlands. 
Beekwilder, J. - BU Bioscience, Wageningen Plant Research, Wageningen, Netherlands. 
Tikunov, Y. - Department of Plant Breeding, Wageningen Plant Research, Wageningen, Netherlands.
 Romero de la Fuente, I. - Department of Plant Breeding, Wageningen Plant Research, Wageningen, Netherlands; Institute of Food Science, Technology and Nutrition, Madrid, Spain.
Zamir, D. - Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel 
Rogachev, I. -  Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
 Aharoni, A. - Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel

Wild tomato species represent a rich gene pool for numerous desirable traits lost during domestication. Here, we exploited an introgression population representing wild desert-adapted species and a domesticated cultivar to establish the genetic basis of gene expression and chemical variation accompanying the transfer of wild-species-associated fruit traits. Transcriptome and metabolome analysis of 580 lines coupled to pathogen sensitivity assays resulted in the identification of genomic loci associated with levels of hundreds of transcripts and metabolites. These associations occurred in hotspots representing coordinated perturbation of metabolic pathways and ripening-related processes. Here, we identify components of the Solanum alkaloid pathway, as well as genes and metabolites involved in pathogen defense and linking fungal resistance with changes in the fruit ripening regulatory network. Our results outline a framework for understanding metabolism and pathogen resistance during tomato fruit ripening and provide insights into key fruit quality traits.