Use of RNA-seq data to identify and validate RT-qPCR reference genes for studying the tomato-<i>Pseudomonas pathosystem</i>

The agronomical relevant tomato-Pseudomonas syringae pv. tomato pathosystem is widely used to explore and understand the underlying mechanisms of the plant immune response. Transcript abundance estimation, mainly through reverse transcription-quantitative PCR (RT-qPCR), is a common approach employed...

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Autores principales: Pombo, Marina Alejandra, Zheng, Yi, Fei, Zhangjun, Gregory, Martin B., Rosli, Hernán
Formato: Articulo
Lenguaje:Inglés
Publicado: 2017
Materias:
Biología
Botánica
tomato
plant immune response
genes
Acceso en línea:http://sedici.unlp.edu.ar/handle/10915/87540
Aporte de:
SEDICI (UNLP) de Universidad Nacional de La Plata
id I19-R120-10915-87540
record_format dspace
institution Universidad Nacional de La Plata
institution_str I-19
repository_str R-120
collection SEDICI (UNLP)
language Inglés
topic Biología
Botánica
tomato
plant immune response
genes
spellingShingle Biología
Botánica
tomato
plant immune response
genes
Pombo, Marina Alejandra
Zheng, Yi
Fei, Zhangjun
Gregory, Martin B.
Rosli, Hernán
Use of RNA-seq data to identify and validate RT-qPCR reference genes for studying the tomato-<i>Pseudomonas pathosystem</i>
topic_facet Biología
Botánica
tomato
plant immune response
genes
description The agronomical relevant tomato-Pseudomonas syringae pv. tomato pathosystem is widely used to explore and understand the underlying mechanisms of the plant immune response. Transcript abundance estimation, mainly through reverse transcription-quantitative PCR (RT-qPCR), is a common approach employed to investigate the possible role of a candidate gene in certain biological process under study. The accuracy of this technique relies heavily on the selection of adequate reference genes. Initially, genes derived from other techniques (such as Northern blots) were used as reference genes in RT-qPCR experiments, but recent studies in different systems suggest that many of these genes are not stably expressed. The development of high throughput transcriptomic techniques, such as RNA-seq, provides an opportunity for the identification of transcriptionally stable genes that can be adopted as novel and robust reference genes. Here we take advantage of a large set of RNA-seq data originating from tomato leaves infiltrated with different immunity inducers and bacterial strains. We assessed and validated 9 genes that are much more stable than two traditional reference genes. Specifically, ARD2 and VIN3 were the most stably expressed genes and consequently we propose they be adopted for RT-qPCR experiments involving this pathosystem.
format Articulo
Articulo
author Pombo, Marina Alejandra
Zheng, Yi
Fei, Zhangjun
Gregory, Martin B.
Rosli, Hernán
author_facet Pombo, Marina Alejandra
Zheng, Yi
Fei, Zhangjun
Gregory, Martin B.
Rosli, Hernán
author_sort Pombo, Marina Alejandra
title Use of RNA-seq data to identify and validate RT-qPCR reference genes for studying the tomato-<i>Pseudomonas pathosystem</i>
title_short Use of RNA-seq data to identify and validate RT-qPCR reference genes for studying the tomato-<i>Pseudomonas pathosystem</i>
title_full Use of RNA-seq data to identify and validate RT-qPCR reference genes for studying the tomato-<i>Pseudomonas pathosystem</i>
title_fullStr Use of RNA-seq data to identify and validate RT-qPCR reference genes for studying the tomato-<i>Pseudomonas pathosystem</i>
title_full_unstemmed Use of RNA-seq data to identify and validate RT-qPCR reference genes for studying the tomato-<i>Pseudomonas pathosystem</i>
title_sort use of rna-seq data to identify and validate rt-qpcr reference genes for studying the tomato-<i>pseudomonas pathosystem</i>
publishDate 2017
url http://sedici.unlp.edu.ar/handle/10915/87540
work_keys_str_mv AT pombomarinaalejandra useofrnaseqdatatoidentifyandvalidatertqpcrreferencegenesforstudyingthetomatoipseudomonaspathosystemi
AT zhengyi useofrnaseqdatatoidentifyandvalidatertqpcrreferencegenesforstudyingthetomatoipseudomonaspathosystemi
AT feizhangjun useofrnaseqdatatoidentifyandvalidatertqpcrreferencegenesforstudyingthetomatoipseudomonaspathosystemi
AT gregorymartinb useofrnaseqdatatoidentifyandvalidatertqpcrreferencegenesforstudyingthetomatoipseudomonaspathosystemi
AT roslihernan useofrnaseqdatatoidentifyandvalidatertqpcrreferencegenesforstudyingthetomatoipseudomonaspathosystemi
bdutipo_str Repositorios
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