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

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Título

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

Autor(es)

Pombo, Marina Alejandra; Zheng, Yi; Fei, Zhangjun; Martin, Gregory; Rosli, Hernan Guillermo

Afiliación(es) del/de los autor(es)

Pombo, Marina Alejandra. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Fisiología Vegetal. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. Instituto de Fisiología Vegetal; Argentina
Zheng, Yi. Cornell University; Estados Unidos
Fei, Zhangjun. Cornell University; Estados Unidos
Martin, Gregory. Cornell University; Estados Unidos
Rosli, Hernan Guillermo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Fisiología Vegetal. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. Instituto de Fisiología Vegetal; Argentina

Resumen

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 di erent 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 identi cation 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 in ltrated with di erent immunity inducers and bacterial strains. We assessed and validated 9 genes that are much more stable than two traditional reference genes. Speci cally, ARD2 and VIN3 were the most stably expressed genes and consequently we propose they be adopted for RT- qPCR experiments involving this pathosystem.

Año de publicación

2025

Idioma

inglés

Formato (Tipo MIME)

application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
application/vnd.ms-excel

Clasificación temática de acuerdo a la FORD

Ciencias biológicas

Condiciones de uso

Disponible en acceso abierto bajo licencia Creative Commons https://creativecommons.org/licenses/by-nc-sa/2.5/ar/

Repositorio digital

CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas

Identificador de proyecto

Ministerio de Ciencia. Tecnología e Innovación Productiva. Agencia Nacional de Promoción Científica y Tecnológica/PICT2014-1589

Identificador de proyecto

Consejo Nacional de Investigaciones Científicas y Técnicas/PICT2014-1589