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An oligo-based microarray offers novel transcriptomic approaches for the analysis of pathogen resistance and fruit quality traits in melon (Cucumis melo L.)
- Source :
- Digital.CSIC. Repositorio Institucional del CSIC, instname, BMC Genomics, Vol 10, Iss 1, p 467 (2009), Recercat. Dipósit de la Recerca de Catalunya, Dipòsit Digital de Documents de la UAB, Universitat Autònoma de Barcelona, Recercat: Dipósit de la Recerca de Catalunya, Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya), CONICET Digital (CONICET), Consejo Nacional de Investigaciones Científicas y Técnicas, instacron:CONICET, BMC Genomics
- Publication Year :
- 2009
- Publisher :
- BioMed Central, 2009.
-
Abstract
- 15 pages, 4 figures, 3 tables, 1 appendix, 3 additional files.<br />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.<br />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.<br />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.<br />This work was supported by grants from the Spanish Ministry of Education and Science (BIO2005/007 to A.C-D; GEN2003-20237-C06 and AGL2006-08069/ AGR to M.A.A.). W.D., C.R. and D. G-I. are recipients of CRAG and "Juan de la Cierva" postdoctoral contracts from the Spanish Ministry of Education and Science. S.M-G was funded by PIV2 program (AGAUR; Generalitat de Catalunya, Spain). A.M-C and J.V. are PhD students funded by I3P program (CSIC; Spain) in A.I. C-D laboratory. A.I. C-D is funded by a HFSPO/Career Development Award (CDA2004/007). A.I. C-D is a "Ramón y Cajal" researcher from the Spanish Ministry of Education and Science.
- Subjects :
- DNA, Plant
lcsh:QH426-470
Melon
lcsh:Biotechnology
Genomics
Computational biology
Genes, Plant
Genome
purl.org/becyt/ford/1 [https]
Ciencias Biológicas
Cucumis melo
lcsh:TP248.13-248.65
melon
Genetics
purl.org/becyt/ford/1.6 [https]
Gene Library
Oligonucleotide Array Sequence Analysis
Expressed Sequence Tags
Genetic diversity
Expressed sequence tag
biology
business.industry
Gene Expression Profiling
fruit quality
food and beverages
Sequence Analysis, DNA
Bioquímica y Biología Molecular
biology.organism_classification
Biotechnology
Gene expression profiling
lcsh:Genetics
Fruit
pathogen resistance
DNA microarray
business
microarray
Cucumis
Genome, Plant
CIENCIAS NATURALES Y EXACTAS
Research Article
Subjects
Details
- Database :
- OpenAIRE
- Journal :
- Digital.CSIC. Repositorio Institucional del CSIC, instname, BMC Genomics, Vol 10, Iss 1, p 467 (2009), Recercat. Dipósit de la Recerca de Catalunya, Dipòsit Digital de Documents de la UAB, Universitat Autònoma de Barcelona, Recercat: Dipósit de la Recerca de Catalunya, Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya), CONICET Digital (CONICET), Consejo Nacional de Investigaciones Científicas y Técnicas, instacron:CONICET, BMC Genomics
- Accession number :
- edsair.doi.dedup.....b4ccc1d010e368d354e2c53845271a6b