Community Research and Development Information Service - CORDIS

DNA-microarrays carrying selected 70mer oligonucleotides covering approx. 1000 relevant structural and regulatory genes involved in primary and secondary metabolism of tomato

A dedicated tomato microarray was constructed containing 1000 oligonucleotides, each representing a gene putatively involved in regulatory and metabolic pathways important for fruit quality. These genes were selected from the existing public TIGR tomato database (LEGI) through a bioinformatics approach. In collaboration with all partners of the consortium a set of 608 unigenes were selected, representing metabolic and regulatory pathways which have relevance to aspects such as health and quality: Aromatic amino acids, sugar metabolism, flavonoid, stilbene and lignin, phenylpropanoid, ascorbate, folate and one carbon metabolism, sterol, vitamin E, vitamin K and carotenoids, terpenoid and MYB transcription factors. In addition, a set of 178 unigenes was selected that showed homology to members of the Arabidopsis transmembrane protein database "Agamemnon".

The remaining 214 genes, required for a collection of 1000 genes, consisted of genes that were known to be induced or repressed during tomato fruit ripening, together with control genes required for background subtraction and normalisation. Unique 70-mer oligonucleotides have been designed for all of the 1000 selected genes. These oligonucleotides have been spotted onto 100 microarray slides. Conditions for spotting and hybridisation of these oligonucleotide arrays were optimised and hybridisation results could be confirmed using other detection methods such as realt-time RT-PCR, indicating that this microarray platform led to reliable results.

Microarray slides have been used to monitor gene expression changes in tomato fruits, in order to obtain insight in (i) the process of tomato fruit ripening and (ii)the effect of transgene expression on quality-related metabolic pathways

The results of these studies have been presented at several scientific conferences and have resulted in additional collaborations with partners in and outside PROFOOD.

The oligonucleotides were synthesised in excess and may be used to design additional batches of microarrays which can be used in future collaborations for gene expression profiling studies of quality-related genes in tomato.

Contact

Arnaud BOVY, (Senior scientist)
Tel.: +31-317476864
E-mail
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