Understanding the Molecular Basis of Plant Response to Organic Versus Conventional Fertilizer Using A Metatranscriptomic Approach

Project Overview

Project Type: Graduate Student
Funds awarded in 2018: $25,000.00
Projected End Date: 07/31/2020
Grant Recipient: Washington State University
Region: Western
State: Washington
Graduate Student:
Principal Investigator:
Amit Dhingra
Washington State University


Not commodity specific


  • Crop Production: crop improvement and selection, fertilizers, nutrient cycling
  • Education and Training: mentoring

    Proposal abstract:

    The goal of this project is to determine the physiological and genetic basis underlying the potential production of more nutrient  dense  crops  in  farming  systems.  This  will  enable  farmers interested  in  organic  or  conventional  practices  to  integrate  soil  fertility systems  that  favor  more sustainable  production.  It  will  allow  plant  breeders  to  develop  crop  cultivars  suited  for  organic production.

    Previously, we demonstrated that tomato fruit grown under an organic fertilizer regime had elevated  phytonutrient  content  compared  to  tomato  fruit  grown  under  a  conventional  fertilizer regime.  Using  a  comprehensive  transcriptome  analysis,  we  tested  the  following  hypotheses:  1.) Growth under organic fertilizer regime will result in differential expression of the tomato genome and 2.) Genes and pathways associated with phytonutrients that were observed to be significantly higher under organic fertilizer regime will demonstrate higher expression. Both hypotheses tested true, indicating an adjustment of the plants' genomic activity in response to a different nitrogen regime. We identified genes and associated pathways --among them, lycopene, ascorbate, soluble solids, and salvage pathways --which are expressed at higher levels under organic conditions.

    The  next  logical step is  to  investigate  the  genomic  response  of  roots  after  exposure  to organic   vs   conventional   fertilizer,   to   provide   further   understanding   of   how   organic   and conventional nitrogen are metabolized. We propose to test the following hypotheses: 1.) Different fertilizer  regimes  will  elicit  differential  expression  of  nitrogen  metabolism  genes,  and  2.)  A different root/soil microbiome will be fostered under the two nitrogen conditions. This research includes  a  time  course  root/microbiome-targeted  transcriptome  analysis,  focusing  on  genes  and pathways  associated  with  nitrogen  metabolism  and  on  the  microbial  symbionts  activity  favored under   the   different   fertilizer   conditions.   Gene-based   knowledge   generated   will   facilitate identification of genotypes that utilize organic fertilizer more efficiently.

    Project objectives from proposal:

    Short-term:  We  aim  to  increase  knowledge  of  the  relationship  between  phytonutrient content  and  underlying  gene  expression  changes  in  plants  when  grown  under  organic  or conventional soil fertility  management systems in a model  crop plant (tomato). We clarify here that promoting organic over conventional is not the goal of this study; rather, we hope to provide a basis for understanding of gene expression and metabolic differences, which may in turn result in nutritional differences, between the organic and conventional treatments. We aim to develop a model for comprehensive analysis in the field of crop production. We seek to use our study results to apply for grant funding in the USDA's AFRI program in order to conduct a more comprehensive study, which will include field research.

    Intermediate-term:  Knowledge  generated  from  the  project,  particularly  with  regards  to organic  vs.  conventional  nitrogen  uptake  and  utilization  as  well  as  corresponding  phytonutrient profiles in the different fertilizer regimes, will assist organic and sustainable producers to develop management plans for soil fertility. Understanding of gene function and of markers associated with genes expressed differentially under organic or conventional conditions will help plant breeders in the  crossing  and  selection  of  more  efficient  crop  cultivars  that  optimize  both  nutritional  quality and yields of crops grown using more sustainable farming practices.

    Long-term: Increase  consumption  of  foods  with  improved  nutritional  quality,  thereby contributing  to  the  health  of  American  children  and  adults and  reducing  health  care  costs. Implement  more  sustainable  farming  practices,  particularly  related  to  soil  fertility  and  pest management,  will  enhance  the  quality  of  U.S.  agro ecosystems. Contribute to the  long-term economic viability of American farmers.

    Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the view of the U.S. Department of Agriculture or SARE.