A Multimodal Study of Wild Tomato Species Introgressions Unravels the Genetic Basis of Transcriptome and Metabolome Variation in Important Fruit Traits

  • Jędrzej Szymański (Creator)
  • S.E. Bocobza (Creator)
  • Sayantan Panda (Creator)
  • Prashant Sonawane (Creator)
  • P.D. Cardenas (Creator)
  • Justin Lashbrooke (Creator)
  • Avinash Kamble (Creator)
  • Nir Shahaf (Creator)
  • Sagit Meir (Creator)
  • Arnaud Bovy (Creator)
  • Jules Beekwilder (Creator)
  • Yury Tikunov (Creator)
  • Irene Romero de la Fuente (Creator)
  • Dani Zamir (Creator)
  • Ilana Rogachev (Creator)
  • Asaph Aharoni (Creator)



Here, we report RNAseq data from a Solanum lycopersicum-pennellii introgression population (IL) and a backcross introgression population (BIL), to establish the genetic basis of gene expression and chemical variation accompanying transfer of wild species-associated fruit traits. Transcriptome analysis of these lines resulted in the identification of genomic loci significantly linked with levels of hundreds of transcripts and metabolites. These associations occurred in functionally coherent hotspots that represent coordinated perturbation of metabolic pathways and ripening-related processes. We demonstrated the efficacy of our approach by discovering yet undisclosed components of the renowned Solanum alkaloids pathway and moreover, showing that fruit fungal resistance is associated with changes in the ripening regulatory network.
Date made available28 Jul 2020


  • Solanum lycopersicum
  • Solanum pennellii
  • Expression profiling by high throughput sequencing
  • introgression

Accession numbers

  • GSE151451
  • PRJNA635884

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