The need for agriculture phenotyping: "moving from genotype to phenotype"

J Proteomics. 2013 Nov 20;93:20-39. doi: 10.1016/j.jprot.2013.03.021. Epub 2013 Apr 2.


Increase in the world population has called for the increased demand for agricultural productivity. Traditional methods to augment crop and animal production are facing exacerbating pressures in keeping up with population growth. This challenge has in turn led to the transformational change in the use of biotechnology tools to meet increased productivity for both plant and animal systems. Although many challenges exist, the use of proteomic techniques to understand agricultural problems is steadily increasing. This review discusses the impact of genomics, proteomics, metabolomics and phenotypes on plant, animal and bacterial systems to achieve global food security and safety and we highlight examples of intra and extra mural research work that is currently being done to increase agricultural productivity.

Biological significance: This review focuses on the global demand for increased agricultural productivity arising from population growth and how we can address this challenge using biotechnology. With a population well above seven billion humans, in a very unbalanced nutritional state (20% overweight, 20% risking starvation) drastic measures have to be taken at the political, infrastructure and scientific levels. While we cannot influence politics, it is our duty as scientists to see what can be done to feed humanity. Hence we highlight the transformational change in the use of biotechnology tools over traditional methods to increase agricultural productivity (plant and animal). Specifically, this review deals at length on how a three-pronged attack, namely combined genomics, proteomics and metabolomics, can help to ensure global food security and safety. This article is part of a Special Issue entitled: Translational Plant Proteomics.

Keywords: ARS; Agricultural Research Services; Agricultural proteomics; Animal proteomics; CPLL; Combinatorial Peptide Ligand Library; Combinatorial peptide ligand libraries; Food proteomics; NIFA; National Institute of Food and Agriculture; Plant proteomics; USDA; United States Department of Agriculture.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.
  • Review

MeSH terms

  • Agriculture / economics
  • Agriculture / methods*
  • Animals
  • Biotechnology / methods
  • Cattle
  • Cattle Diseases / prevention & control
  • Computational Biology
  • Crops, Agricultural / genetics*
  • Dairying / methods
  • Databases, Protein / standards
  • Electrophoresis, Gel, Two-Dimensional
  • Escherichia coli O157 / pathogenicity
  • Food Safety / methods
  • Food Supply
  • Foodborne Diseases / prevention & control
  • Genotype
  • Humans
  • Metabolomics / methods
  • Milk Proteins / chemistry
  • Phenotype*
  • Plants / genetics
  • Proteomics / methods*
  • Shiga Toxin 2 / chemistry
  • Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
  • Triticum / genetics
  • Whey Proteins


  • Milk Proteins
  • Shiga Toxin 2
  • Whey Proteins