Role of omics in crop improvement
Authors: Shiv Lal, D.B. Singh, O.C. Sharma

It is true that green revolution of 60’s and 70’s enabled India to achieve self sufficiency in terms of food production, but still there is a continuous challenge before agriculture scientists to further increase agricultural production to feed the growing population of India. Crop productivity must be enhanced with increase in nutritive value of crops to solve the problem of malnutrition prevalent among large number of children and women. Recent developments in the field of ‘OMICS’ technologies hold immense potential to reshape Indian agriculture through ‘Gene Revolution’.

The term ‘omics’ refers to the comprehensive analysis of the biological system. An omics approach can be considered to be large-scale data rich biology consisting of a heavy data mining or bioinformatics component. The modern concept of omics was initiated by Human Genome Project, which was launched in 1986. Genomics, proteomics and metabolomics are the three core omics technologies, which respectively deal with the analysis of genome, proteome and metabolome of cells and tissues of an organism.

The plant genomics provides a platform for analyzing and understanding the genetic and molecular basis of all biological processes in plants that are relevant to the species and these are given as below:


  1. Genomics allow efficient exploitation of plants as biological resources in the development of new cultivars with improved quality and reduced economic and environmental costs.
  2. It allows the scientists to analyze thousands of genes in parallel and to understand the complex crop traits, such as yield and yield stability.
  3. It reduces the gap between phenotype and genotype and helps to comprehend not only the isolated effect of a gene, but also the way its genetic content and genetic networks it interacts with can modulate its activity.
  4. It helps in assaying genetic make up of the individual plants rapidly, so as to select desirable genotypes in breeding populations, and to design the superior genotypes for ‘breeding by design’ approach.
  5. With genomic approaches, the marker-assisted breeding or marker-assisted selection will gradually evolve into ‘genomics-assisted breeding’ for crop improvement.
  6. The knowledge of genomics is valid for development of new plant diagnostic tools.
  7. It will help to find new solutions for improved germplasm in crop plants and for chemical protection of crops. Thus, a genome programme can be envisioned as a highly important tool for crop improvement


  1. Screening target genes
  2. Predict gene function
  3. Discovery of cis regulatory motifs
  4. Comparative transcriptomics helps in pattern of selection
  5. Role of comparative safety assessment of plant products (GMO)
  6. Helps in optimizing phytoremediation activities
  7. Identification of gene involving in stress
  8. Understanding symbiotics association
  9. Determination,of pathogenecity function
  10. Host pathogen interactions
  11. Dissection of food quality traits
  12. Expression of QTL isolation.

  1. In Arabidopsis , while studying the role of GAs during initial stages of seed germination, and the impact of scarification on seed germination, application of proteome analysis resulted in better understanding of the complex cellular events.
  2. Similarly, in barley, the proteome analysis revealed new insights into cellular mechanisms under lying seed development during grain filling and seed maturation phases.
  3. In rice, proteome studies have helped in detecting novel traits useful for breeding. Mutants are generally subjected to proteome analysis to compare their responses to different hormonal treatments, nutritional factors, and photosynthetic traits.
  4. In maize, a number of previously unknown novel genes coding for enzymes in metabolic pathways were identified during grain development following proteome analysis.
  5. Proteomics has been widely used to assess genetic variability at the level of expressed proteins.
  6. Both abiotic and biotic stresses can bring about dramatic changes to the plant proteome, and these are manifested as the up- or down- regulation of proteins, or their post translation modification.
  7. Salinity stress results in change in the proteome, as the plant attempts to restore homeostasis in osmolarity to resume growth and development. Detailed analysis indicated that during salt stress, plant diverts carbon to glycolysis to provide the energy required to return the plant to homeostasis.
  8. In case of pathogen attack (biotic stress), the proteome analyses have indicated involvement of defense and stress related proteins, metabolic enzymes, translocation and protein turnover proteins, and proteins of unknown functions in the defense response
  9. The application of proteomics has also been used to decipher the highly complex genetic interactions involved in plant-microbe interactions and for studying symbioses (nitrogen symbiosis, ecto- and endo-mycorrhizal symbiosis) in plants.

  1. Monitoring crop quality characteristics
  2. Identifying potential biochemical markers to detect product contamination and adulteration optimizing trait development in agricultural products and in biorefining
  3. Metabolomics offers the unbiased ability to characterize and differentiate genotypes and phenotypes based on metabolic levels.
  4. Differentiating various genotypes and understanding plant responses to biotic and abiotic stresses,
  5. characterization of the novel plant products,
  6. Breeding of crops based on specific biochemical composition and assessing the substantial equivalence i.e., comparison between transgenic and wild-type plants.
  7. Application in efficient engineering of crops that combine an attractive appearance and taste with improved levels of phytonutrients such as flavonoids and carotensids.
  8. Plant properties can be improved in various ways, such as by increasing metabolic fluxes into valuable biochemical pathways using metabolic engineering (e.g., enhancing the nutritional value of foods, decreasing the need for pesticide or fertilizer application etc.), or into pathways needed for the production of pharmaceuticals in plants
  9. Similarly, metabolic shortcuts can be created by introducing foreign set of enzymes(s) that lead to the production of desired end products from other or more upstream precursores, and the foreign enzymes can also lead to the production of new metabolites

  1. The integration of knowledge from bioinformatic tools, databases and other different fields enables the identification of genes and gene products, and helps in elucidating the functional relationships between genotypes and phenotypes
  2. Using bioinformatics tools, scientists can search genomic data and identify a region important for a desired trait.
  3. The computational approaches facilitate the understanding of various biological processes by providing a more global perspective in experimental design, and ability to capitalize on the emerging technology of database mining.
Considerable progress has been made building infrastructure for applying knowledge and tools of genomics (and other ‘omics’) to allow the characteristics of crop plant to be altered for improved actual and potential yields, increased resource use efficiency and enhanced crop system health.

About Author / Additional Info:
Scientist working on fruit biotechnology and improvement.