Development, Characterization and Experimental Validation of a Cultivated Sunflower (Helianthus annuus L.) Gene Expression Oligonucleotide Microarray

Fil: Soria, Marcelo Abel. Universidad de Buenos Aires. Facultad de Agronomía. Buenos Aires, Argentina.

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Detalles Bibliográficos
Autores principales:	Fernández, Paula, Soria, Marcelo Abel, Blesa, David, Di Rienzo, Julio Alejandro, Moschen, Sebastián, Rivarola, Máximo, Clavijo, Bernardo José, González, Sergio, Peluffo, Lucila, Príncipi, Darío, Dosio, Guillermo Aníbal Adrián, Aguirrezábal, Luis Adolfo Nazareno, García García, Francisco, Conesa, Ana, Hopp, Horacio Esteban, Dopazo, Joaquín, Heinz, Ruth Amelia, Paniego, Norma
Formato:	article Artículo publishedVersion
Lenguaje:	Inglés
Publicado:	2012
Materias:	COMPUTER PROGRAM CONTIG MAPPING CONTROLLED STUDY CROP IMPROVEMENT DNA MICROARRAY EXPRESSED SEQUENCE TAG GENE EXPRESSION GENETIC TRANSCRIPTION GENOME ANALYSIS HELIANTHUS ANNUUS MOLECULAR PROBE NONHUMAN PLANT BREEDING PLANT GENETICS REAL TIME POLYMERASE CHAIN REACTION SENESCENCE SEQUENCE ANALYSIS SPECIES CULTIVATION VALIDATION STUDY WATER DEFICIT WATER STRESS EXPRESSED SEQUENCE TAGS GENE EXPRESSION REGULATION, PLANT HELIANTHUS OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS
Acceso en línea:	http://ri.agro.uba.ar/greenstone3/library/collection/arti/document/2012Fernandez
Aporte de:	FAUBA Digital - Facultad de Agronomía (UBA) de Universidad de Buenos Aires

id	snrd:2012Fernandez
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spelling	snrd:2012Fernandez2021-10-15T16:56:07Z Fernández, Paula Soria, Marcelo Abel Blesa, David Di Rienzo, Julio Alejandro Moschen, Sebastián Rivarola, Máximo Clavijo, Bernardo José González, Sergio Peluffo, Lucila Príncipi, Darío Dosio, Guillermo Aníbal Adrián Aguirrezábal, Luis Adolfo Nazareno García García, Francisco Conesa, Ana Hopp, Horacio Esteban Dopazo, Joaquín Heinz, Ruth Amelia Paniego, Norma 2012 Fil: Soria, Marcelo Abel. Universidad de Buenos Aires. Facultad de Agronomía. Buenos Aires, Argentina. Oligonucleotide-based microarrays with accurate gene coverage represent a key strategy for transcriptional studies in orphan species such as sunflower, H. annuus L., which lacks full genome sequences. The goal of this study was the development and functional annotation of a comprehensive sunflower unigene collection and the design and validation of a custom sunflower oligonucleotide-based microarray. A large scale EST (greater than 130,000 ESTs) curation, assembly and sequence annotation was performed using Blast2GO (www.blast2go.de). The EST assembly comprises 41,013 putative transcripts (12,924 contigs and 28,089 singletons). The resulting Sunflower Unigen Resource (SUR version 1.0) was used to design an oligonucleotide-based Agilent microarray for cultivated sunflower. This microarray includes a total of 42,326 features: 1,417 Agilent controls, 74 control probes for sunflower replicated 10 times (740 controls) and 40,169 different non-control probes. Microarray performance was validated using a model experiment examining the induction of senescence by water deficit. Pre-processing and differential expression analysis of Agilent microarrays was performed using the Bioconductor limma package. The analyses based on p-values calculated by eBayes (p less than 0.01) allowed the detection of 558 differentially expressed genes between water stress and control conditions; from these, ten genes were further validated by qPCR. Over-represented ontologies were identified using FatiScan in the Babelomics suite. This work generated a curated and trustable sunflower unigene collection, and a custom, validated sunflower oligonucleotide-based microarray using Agilent technology. Both the curated unigene collection and the validated oligonucleotide microarray provide key resources for sunflower genome analysis, transcriptional studies, and molecular breeding for crop improvement. application/pdf doi:10.1371/journal.pone.0045899 issn:1932-6203 http://ri.agro.uba.ar/greenstone3/library/collection/arti/document/2012Fernandez eng info:eu-repo/semantics/openAccess openAccess http://ri.agro.uba.ar/greenstone3/library/page/biblioteca#section4 Plos One Vol.7, no.10 e45899 http://www.plos.org/ COMPUTER PROGRAM CONTIG MAPPING CONTROLLED STUDY CROP IMPROVEMENT DNA MICROARRAY EXPRESSED SEQUENCE TAG GENE EXPRESSION GENETIC TRANSCRIPTION GENOME ANALYSIS HELIANTHUS ANNUUS MOLECULAR PROBE NONHUMAN PLANT BREEDING PLANT GENETICS REAL TIME POLYMERASE CHAIN REACTION SENESCENCE SEQUENCE ANALYSIS SPECIES CULTIVATION VALIDATION STUDY WATER DEFICIT WATER STRESS EXPRESSED SEQUENCE TAGS GENE EXPRESSION REGULATION, PLANT HELIANTHUS OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS Development, Characterization and Experimental Validation of a Cultivated Sunflower (Helianthus annuus L.) Gene Expression Oligonucleotide Microarray article info:eu-repo/semantics/article info:ar-repo/semantics/artículo publishedVersion info:eu-repo/semantics/publishedVersion
institution	Universidad de Buenos Aires
institution_str	I-28
repository_str	R-140
collection	FAUBA Digital - Facultad de Agronomía (UBA)
language	Inglés
orig_language_str_mv	eng
topic	COMPUTER PROGRAM CONTIG MAPPING CONTROLLED STUDY CROP IMPROVEMENT DNA MICROARRAY EXPRESSED SEQUENCE TAG GENE EXPRESSION GENETIC TRANSCRIPTION GENOME ANALYSIS HELIANTHUS ANNUUS MOLECULAR PROBE NONHUMAN PLANT BREEDING PLANT GENETICS REAL TIME POLYMERASE CHAIN REACTION SENESCENCE SEQUENCE ANALYSIS SPECIES CULTIVATION VALIDATION STUDY WATER DEFICIT WATER STRESS EXPRESSED SEQUENCE TAGS GENE EXPRESSION REGULATION, PLANT HELIANTHUS OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS
spellingShingle	COMPUTER PROGRAM CONTIG MAPPING CONTROLLED STUDY CROP IMPROVEMENT DNA MICROARRAY EXPRESSED SEQUENCE TAG GENE EXPRESSION GENETIC TRANSCRIPTION GENOME ANALYSIS HELIANTHUS ANNUUS MOLECULAR PROBE NONHUMAN PLANT BREEDING PLANT GENETICS REAL TIME POLYMERASE CHAIN REACTION SENESCENCE SEQUENCE ANALYSIS SPECIES CULTIVATION VALIDATION STUDY WATER DEFICIT WATER STRESS EXPRESSED SEQUENCE TAGS GENE EXPRESSION REGULATION, PLANT HELIANTHUS OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS Fernández, Paula Soria, Marcelo Abel Blesa, David Di Rienzo, Julio Alejandro Moschen, Sebastián Rivarola, Máximo Clavijo, Bernardo José González, Sergio Peluffo, Lucila Príncipi, Darío Dosio, Guillermo Aníbal Adrián Aguirrezábal, Luis Adolfo Nazareno García García, Francisco Conesa, Ana Hopp, Horacio Esteban Dopazo, Joaquín Heinz, Ruth Amelia Paniego, Norma Development, Characterization and Experimental Validation of a Cultivated Sunflower (Helianthus annuus L.) Gene Expression Oligonucleotide Microarray
topic_facet	COMPUTER PROGRAM CONTIG MAPPING CONTROLLED STUDY CROP IMPROVEMENT DNA MICROARRAY EXPRESSED SEQUENCE TAG GENE EXPRESSION GENETIC TRANSCRIPTION GENOME ANALYSIS HELIANTHUS ANNUUS MOLECULAR PROBE NONHUMAN PLANT BREEDING PLANT GENETICS REAL TIME POLYMERASE CHAIN REACTION SENESCENCE SEQUENCE ANALYSIS SPECIES CULTIVATION VALIDATION STUDY WATER DEFICIT WATER STRESS EXPRESSED SEQUENCE TAGS GENE EXPRESSION REGULATION, PLANT HELIANTHUS OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS
description	Fil: Soria, Marcelo Abel. Universidad de Buenos Aires. Facultad de Agronomía. Buenos Aires, Argentina.
format	article Artículo Artículo publishedVersion publishedVersion
author	Fernández, Paula Soria, Marcelo Abel Blesa, David Di Rienzo, Julio Alejandro Moschen, Sebastián Rivarola, Máximo Clavijo, Bernardo José González, Sergio Peluffo, Lucila Príncipi, Darío Dosio, Guillermo Aníbal Adrián Aguirrezábal, Luis Adolfo Nazareno García García, Francisco Conesa, Ana Hopp, Horacio Esteban Dopazo, Joaquín Heinz, Ruth Amelia Paniego, Norma
author_facet	Fernández, Paula Soria, Marcelo Abel Blesa, David Di Rienzo, Julio Alejandro Moschen, Sebastián Rivarola, Máximo Clavijo, Bernardo José González, Sergio Peluffo, Lucila Príncipi, Darío Dosio, Guillermo Aníbal Adrián Aguirrezábal, Luis Adolfo Nazareno García García, Francisco Conesa, Ana Hopp, Horacio Esteban Dopazo, Joaquín Heinz, Ruth Amelia Paniego, Norma
author_sort	Fernández, Paula
title	Development, Characterization and Experimental Validation of a Cultivated Sunflower (Helianthus annuus L.) Gene Expression Oligonucleotide Microarray
title_short	Development, Characterization and Experimental Validation of a Cultivated Sunflower (Helianthus annuus L.) Gene Expression Oligonucleotide Microarray
title_full	Development, Characterization and Experimental Validation of a Cultivated Sunflower (Helianthus annuus L.) Gene Expression Oligonucleotide Microarray
title_fullStr	Development, Characterization and Experimental Validation of a Cultivated Sunflower (Helianthus annuus L.) Gene Expression Oligonucleotide Microarray
title_full_unstemmed	Development, Characterization and Experimental Validation of a Cultivated Sunflower (Helianthus annuus L.) Gene Expression Oligonucleotide Microarray
title_sort	development, characterization and experimental validation of a cultivated sunflower (helianthus annuus l.) gene expression oligonucleotide microarray
publishDate	2012
url	http://ri.agro.uba.ar/greenstone3/library/collection/arti/document/2012Fernandez
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Development, Characterization and Experimental Validation of a Cultivated Sunflower (Helianthus annuus L.) Gene Expression Oligonucleotide Microarray

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