Research article
An oligo-based microarray offers novel transcriptomic approaches for the analysis of pathogen resistance and fruit quality traits in melon (Cucumis melo L.)
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* Corresponding author: Ana I Caño-Delgado ana.cano@cid.csic.es
1 Molecular Genetics Department, Centre for Research in Agricultural Genomics CRAG (CSIC-IRTA-UAB), Barcelona (08034), Spain
2 IRTA, Plant Genetics Department Centre for Research in Agricultural Genomics CRAG (CSIC-IRTA-UAB), Cabrils (08348), Spain
3 Departamento de Biología del Estrés y Patología Vegetal, Centro de Edafología y Biología Aplicada del Segura (CEBAS)-CSIC, Apdo. correos 164, 30100 Espinardo (Murcia), Spain
4 Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV-UPV), CPI, Ed.8E, Camino de Vera s/n, 46022 Valencia, Spain
5 Research Unit on Biomedical Informatics (GRIB), Experimental and Health Science Department (Universitat Pompeu Fabra) Barcelona (08080), Spain
BMC Genomics 2009, 10:467 doi:10.1186/1471-2164-10-467
Published: 12 October 2009Abstract
Background
Melon (Cucumis melo) is a horticultural specie of significant nutritional value, which belongs to the Cucurbitaceae family, whose economic importance is second only to the Solanaceae. Its small genome of approx. 450 Mb coupled to the high genetic diversity has prompted the development of genetic tools in the last decade. However, the unprecedented existence of a transcriptomic approaches in melon, highlight the importance of designing new tools for high-throughput analysis of gene expression.
Results
We report the construction of an oligo-based microarray using a total of 17,510 unigenes derived from 33,418 high-quality melon ESTs. This chip is particularly enriched with genes that are expressed in fruit and during interaction with pathogens. Hybridizations for three independent experiments allowed the characterization of global gene expression profiles during fruit ripening, as well as in response to viral and fungal infections in plant cotyledons and roots, respectively. Microarray construction, statistical analyses and validation together with functional-enrichment analysis are presented in this study.
Conclusion
The platform validation and enrichment analyses shown in our study indicate that this oligo-based microarray is amenable for future genetic and functional genomic studies of a wide range of experimental conditions in melon.