An oligo-based microarray offers novel transcriptomic approaches for the analysis of pathogen resistance and fruit quality traits in melon (Cucumis melo L.)

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.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.Cucurbits, comprising up to 750 different species distributed in 90 genera, are among the most important horticultural crops worldwide [1]. Species of this family have been independently and repeatedly domesticated by different cultures in both the Old and New World, either for food or as materials for a range of products. As a result, they display an enormous, and mostly untapped, genetic diversity.Melon (Cucumis melo) belongs to this family and is one of the most important fleshy fruits for fresh consumption in temperate, subtropical and tropical regions [1]. It has been classified into two subspecies, C. melo ssp. agrestis and C. melo ssp. melo, with India and Africa as their centers of origin, respectively [2,3]. Melon is a diploid species, with a basic number of chromosomes x = 12 (2x = 2n = 24) and an estimated genome size of 450 to 500 M [4], similar in size to the rice genome (419 Mb) [5,6] and about four times the size of the Arabidopsis genome (125 Mb) [7].Based on its relatively small genome, wide morphological, physiological and biochemical diversity and the ability to produce hybrids between unrelated cultivars, C. melo has a grea