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


CONCLUSIONS
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.
Mascarell-Creus
Albert
A
Molecular Genetics Department, Centre for Research in Agricultural Genomics CRAG (CSIC-IRTA-UAB), Barcelona (08034), Spain. albert.mascarell@cid.csic.es
Cañizares
Joaquin
J
Vilarrasa-Blasi
Josep
J
Mora-García
Santiago
S
Blanca
José
J
Gonzalez-Ibeas
Daniel
D
Saladié
Montserrat
M
Roig
Cristina
C
Deleu
Wim
W
Picó-Silvent
Belén
B
López-Bigas
Nuria
N
Aranda
Miguel A
MA
Garcia-Mas
Jordi
J
Nuez
Fernando
F
Puigdomènech
Pere
P
Caño-Delgado
Ana I
AI
D028463:Cucumis melo / Q000235:genetics* / Q000502:physiology; D018744:DNA, Plant / Q000235:genetics; D020224:Expressed Sequence Tags; D005638:Fruit / Q000235:genetics / Q000502:physiology; D020869:Gene Expression Profiling; D015723:Gene Library; D017343:Genes, Plant; D018745:Genome, Plant; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D017422:Sequence Analysis, DNA
D018744:DNA, Plant