Project Synopsis

Changes in environmental conditions and need for increased agricultural production and quality require plant varieties tolerant to various abiotic stresses. Traditional barley breeding has generated varieties adapted to dramatically different environments, however, the process of creating varieties has been rather slow.

Understanding of the molecular mechanisms of adaptation and tolerance to abiotic stress could facilitate targeted design of improved barley varieties. As a first step towards this goal we want to identify the genes differentially expressed in response to abiotic stress and to develop sequence-based markers that could be used for linkage and association mapping.Several EST sequencing projects have generated close to 400,000 barley EST sequences (see NCBI EST summary).

Considering the wide variety of analyzed tissues, developmental stages and various biotic and abiotic stress treatments (see HarvEST for more details), it can be expected that the information about significant proportion of barley genes has been obtained. The EST sequence information enabled design of an Affymetrix GeneChip Barley1 (see Close et al. 2004 for details).

Availability of EST sequences and barley microarray provides a robust and straightforward way to analyze abiotic stress response in barley. First, it is possible to conduct genome-wide transcription profiling of barley genes differentially expressed during various abiotic stresses. Second, EST sequences allow to develop sequence- based markers, such as SNPs, for genetic mapping and association studies.

We have identified barley genes associated with response to abiotic stresses by using the Barley1 microarray and by homology to such genes in other plant species. Fragments of approximately 1400 of these genes were resequenced from 8 diverse barley genotypes to identify sequence polymorphisms. SNP markers were used for linkage mapping to facilitate the association of genes with known abiotic stress QTL (see Rostoks et al. 2005). SNP information was also used to study sequence diversity and haplotype structure in barley.


  • Bioinformatics Group Mail
  • Robbie Waugh
  • David Marshall

  • Project Details and Funding

    Title:   A comparative SNP map-based approach to identify and mine wheat and barley genes, with emphasis on genes controlling root traits.

    Funding:   Scottish Executive Environment and Rural Affairs Department (SEERAD) and Biotechnology and Biological Sciences Research Council (BBSRC)

  • Principal Investigator:
  • Robbie Waugh
  • Co-Principal Investigator:
  • David Marshall
  • Staff:
  • Nils Rostoks, Sharon Mudie
  • Bioinformatics support:
  • Linda Cardle, David Marshall
  • Project Duration:
  • May 2003 - May 2006