The Aquagenomics consortium has proven experience in the field of fish genomics, including the production and analysis of specific EST collections and the application of microarrays to study global gene expression. In the last 5 years an investment has been made in the construction of EST collections which are specifically enriched for genes which represent biological processes of interest with particular emphasis on the immune system in fish. This strategy has produced excellent results in both the rainbow trout and the gilthead sea bream and has identified a large number of previously unknown genes of which many have and are being studied on an individual basis. Furthermore many have been selected to contribute to the development of specific targeted microarrays. In salmonids, the consortium has actively participated in the design and development of a cDNA microarray platform, this platform is now at a 2nd generation which has been enriched with immune system relevant genes. The microarray platform and its use to study the biology of fish has produced in the past 2 years a wealth of transcriptomic information in trout and, as a result, several publications have been made and others are currently under preparation by consortium members. Current state of the art in the scientific literature shows that this microarray platform may be considered one of the most successful to date on an International scale in terms of scientific production(>8 ISI articles).
Due to the experience gained in the design and development of the salmonid microarray, a significant and crucial working experience has been obtained for the development of microarrays for new species in which selected annotated genes are identified and selected from EST collections. The Aquagenomics consortium is actively involved in the development of bioinformatic\biostatistic methodologies to characterise molecular signatures/gene circuits for specific biological processes in fish, to study temporal relationships between organs (tissue specific gene circuits) in whole animal studies, both laboratory and field studies. Preliminary analyses using this database, which contains >150 microarray expts has identified a molecular signature in trout which can be correlated to distinct behavioural profiles and the resultant response to immune challenge in cultured carp thus highlighting the potential of this approach.
Aquagenomics partners have already begun characterization of 10000 ESTs from lymphoid organs in response to pathogens with impact in turbot aquaculture which will be used as a basis for the study of immune response in turbot. Besides, 300 microsatellite loci have been characterized and included in the first genetic map of this species with anonymous markers. Thanks to the integration of different groups it has been possible to carry out the sequencing of the complete turbot genome. Available ESTs in the case of Sparus aurata is currently situated at around 3000 sequences deposited in GenBank. Aquagenomics partners integrated in the immunology and growth areas have developed sea bream cDNA libraries and a large number of ESTs have been sequenced from which the Consortium has direct access to construct dedicated microarray platforms.
Researchers in Aquagenomics cooperate with the “Pleurogene project”, funded by Genome Spain with the aim to create an important functional genomics knowledge base in the Senegalese sole (Solea senegalensis), a new species in Spanish aquaculture. This reinforces the experience of Aquagenomics consortium as a whole in the use and managing of genomic resources (cDNA libraries, ESTs, microarrays and data analysis).
Consequently, the use of microarrays and genetic maps constitute a strategy with promising possibilities in Aquaculture, particularly for analysis of gene expression patterns and for localization of genomic regions of interesting traits and therefore improving farmed fish. The development of high quality species-specific microarrays from which high performance oligoprobe sets are developed from extensive EST collections is key to identify candidate genes in relation to growth, sexual determination and resistance against pathogens.
As a conclusion the funding of the Aquagenomics proposed tasks allowed us to reach the following:
a) Production of specific technological platforms (microarrays) and genetic maps, that will allow us to deepen our knowledge in the proposed research areas with a central goal to improving the selection of varieties of interest in the selected species.
b) Establishment of an integrative database, EST and microarray data, that will facilitate analysis and allow interspecific analyses to identify target processes and gene networks.
c) Establishment and maintenance of a high quality scientific consortium at the national and international level addressing functional genomics, improving scientific production and the exploitation/transfer of results.
d) Development of genomic tools of potential commercial interest.
e) Creation of a training platform on Genomics Tools in Aquaculture at the postdoctoral level and the establishment of a PhD programme on Biotechnology in Aquaculture integrated into the consortium to provide high quality training and experience to young investigators.