Understanding the molecular basis of phytonutrient composition differences in organic tomatoes via quantitative transcriptome analysis

In an ongoing BIOAg supported study, it has been shown that tomatoes grown with organic nitrogen sources had higher phytonutrient contents than those fertilized with readily available nitrogen. It is hypothesized that improved nitrogen cycling may be the underlying cause of these observed differences. In addition, defense compounds are enhanced in tomatoes grown with organic fertilizers, whereas herbivory may enhance them in tomatoes grown with inorganic fertilizers. Fruit and leaf samples from tomatoes grown with organic and readily available nitrogen sources and phenotyped in the preceding study were used to generate comprehensive transcriptome data. This project addresses the priority area of breeding, varietal selection, management practices, processing, or marketing practices to increase food quality, nutrition, safety or access. In this project we will perform comprehensive data analysis of the available transcriptome information and establish correlations between changes in global gene expression and observed phenotypes. This will enable the identification of metabolic mechanisms that alter phytonutrient content under organic vs. inorganic fertilization. Gene-based knowledge generated in this project is expected to enable varietal selection in breeding approaches aimed at identifying genotypes that are able to utilize organic fertilizer efficiently.


Grant Information

  • Project ID: 118
  • Project Status: Complete


  • Principal Investigator(s): Dhingra, A.
  • Investigator(s): Andrews, P.
  • Grant Amount: $7,000


Additional Funds Leveraged

Inability to perform timely and comprehensive data analysis due to reduced levels of funding delayed completion of the work and a resulting manuscript which would have formed the basis of additional funding. We are attempting to complete the analysis as resources permit so that a USDA OREI can be submitted in 2015.


  • SHORT-TERM: Currently no definitive molecular evidence exists to support that organic soil treatment results in production of compounds that can impact human health. Data presented here is the first semblance of such evidence. We plan to disseminate this information via a manuscript. The project will increase our knowledge of the relationship between observed phytonutrient changes and underlying gene expression changes in plants when grown under organic soil fertility management and plant herbivory in a model crop plant (tomato). Such an interdisciplinary and comprehensive analysis remains to be done in the field of crop production. Once the analysis is completed, results of this study will be used to apply for grant funding in USDA’s AFRI program in order to conduct a more comprehensive study, which includes field research.
  • INTERMEDIATE-TERM: The knowledge generated from this BIOAg and subsequent federal projects will assist organic and sustainable producers to develop management plans for soil fertility and pest control that help them optimize the nutritional quality and yields of their products. The understanding of gene function and of markers associated with those genes will help plant breeders in the breeding and selection of more efficient crop cultivars that optimize both nutritional quality and yields of crops grown using more sustainable farming practices.
  • LONG-TERM: Increased consumption of foods with better nutritional quality should contribute to the health of American children and adults and reduce health care costs. Using more sustainable farming practices, especially of soil fertility and pest management, will enhance the quality of U.S. agroecosystems. Besides improving agricultural sustainability and public health, this project could also contribute to the long-term economic viability of American farmers.