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ESP-SOL | PROJECT

ESP-SOL | PROJECT

The genetic, molecular and biochemical variability of tomato accessions available in the consortium germoplasm collection, newly developed breeding lines and defined transgenic materials will be investigated to identify the molecular mechanisms underlying important traits such as pathogen resistance and fruit quality. In short the project aims at using both natural and generated variability as source of genes and molecules to identify via a number of genomic and bioinformatics tools, which ones are part of the processes leading to quality traits and regulating the plant-virus interaction.

BitLAB tasks are focused on providing the tools for genomics and genetic data management and analysis by means of application and development of bioinformatics tools.

PROJECT DETAILS

Identification of genes associated to tomato fruit quality

A consortium of Spanish Scientists from 6 universities, 4 Research Institutes of the Spanish Research Council, 2 Autonomous Government Research Institutes and two Biotechnology Companies have been assembled to take advantage of their respective expertises to conduct a genomics project on tomato, a crop of high economic importance in Spain.

The genetic, molecular and biochemical variability of tomato accessions available in the consortium germoplasm collection, newly developed breeding lines and defined transgenic materials will be investigated to identify the molecular mechanisms underlying important traits such as pathogen resistance and fruit quality.

The Project objectives are:

  • Identify tomato genes or gene regions associated to fruit quality traits.
  • Assessment of the mechanisms determining fruit quality traits by generating, identifying and characterizing tomato plants affected in those traits / genes.
  • Identify tomato genes and proteins to be used as targets for modified (increased) tomato resistance to viral infection.
  • Generate, identify and characterize tomato plants affected in genes involved in the plant-virus interaction.
  • Contribute to the International Sequencing Initiative by participating in the sequencing of euchromatic regions of Chr9.

In summary the project aims at using both natural and generated variability as source of genes and molecules to identify via a number of genomic and bioinformatics tools, which ones are part of the processes leading to quality traits and regulating the plant-virus interaction.

As a reference about 200 independent microarray (14000 elements) hybridizations with 4 replicates will be analyzed. Metabolic profiling of a similar number of samples (carotenoids, sugars, organic acids, volatiles – a total of 60 metabolites).

BitLAB tasks are focused on transcriptomics profiling, data management and analysis by means of application and development of bioinformatics tools.

  • Storage and organization of transcriptomic data and integration with related data bases.
  • Storage and organization of Marker/Mapping database and display tools.
  • Microarray data (Transcriptomics) database.
  • Gene expression data quality assessment (normalisation and error removing procedures).
  • Processing gene-expression data: classical clustering and classification procedures to produce transcriptome profiling and to elucidate the temporal expression patterns of genes associated with fruit-quality and virus resistance.
  • Intensive and intelligent automatic knowledge extraction to: ombreprovide a better understanding of genes involved in related biological processes ombreprovide substantial information towards deducing (by association) the potential function of unknown genes ombreidentify specific discriminants (in general, small informative components or markers) of specific biological functions shared by the group.
  • Co-ordination for the integration of data management and processing.
  • Training users in the efficient use of the tools and developed databases.

ADITIONAL INFORMATION

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