Transcriptional analysis in four wild and cultivated rice genotypes identifies aluminum-induced genes

J. J. Gallo-Franco; I. Zuluaga-Yusti; A. M. Restrepo-García; C. C. Sosa; S. Zapata-Balanta; J. P. Gutiérrez-Marín; T. Ghneim-Herrera; M. Quimbaya

doi:10.1016/j.stress.2023.100247

Transcriptional analysis in four wild and cultivated rice genotypes identifies aluminum-induced genes

Título traducido de la contribución: El análisis transcripcional en cuatro genotipos de arroz silvestre y cultivado identifica genes inducidos por aluminio

J. J. Gallo-Franco, I. Zuluaga-Yusti, A. M. Restrepo-García, C. C. Sosa, S. Zapata-Balanta, J. P. Gutiérrez-Marín, T. Ghneim-Herrera, M. Quimbaya

Pontificia Universidad Javeriana

Producción: Contribución a una revista › Artículo › revisión exhaustiva

1 Cita (Scopus)

Resumen

El análisis de expresión génica diferencial es un enfoque ampliamente utilizado para identificar genes relevantes y mecanismos funcionales que influyen en la tolerancia de las plantas al estrés abiótico. En este estudio, evaluamos las respuestas transcripcionales de genotipos contrastantes de arroz a la exposición prolongada al aluminio (Al), en especies de arroz cultivadas (Oryza sativa) y silvestres (Oryza glumaepatula), a través de experimentos de RNA-Seq. Después de comparar las respuestas transcripcionales en condiciones de control y de tratamiento con Al, se identificaron genes expresados diferencialmente (DEG) para cada genotipo. Además, los niveles de transcripción de seis DEG se validaron mediante PCR cuantitativa en tiempo real. Los análisis funcionales de los DEG identificados proporcionaron información sobre la acción coordinada de los mecanismos de exclusión y de desintoxicación asociados con las respuestas al Al en el arroz. Además, informamos un grupo de 28 genes que se expresaron diferencialmente en todas las especies y genotipos analizados, señalando un conjunto central de mecanismos que se desencadenan por la exposición al Al. Asimismo, se identificaron 14 DEG únicamente en genotipos tolerantes al Al, lo que representa un potencial elemento clave para comprender la respuesta adaptativa exitosa a condiciones tóxicas que adoptan estos genotipos. Dado que muchos de estos genes identificados no se han reportado ni caracterizado previamente, podrían considerarse nuevos reguladores vinculados con la tolerancia al Al y candidatos prometedores para la generación de variedades de arroz agronómicamente mejoradas.

Título traducido de la contribución	El análisis transcripcional en cuatro genotipos de arroz silvestre y cultivado identifica genes inducidos por aluminio
Idioma original	Inglés
Número de artículo	100247
Páginas (desde-hasta)	1-12
Número de páginas	12
Publicación	Plant Stress
Volumen	10
DOI	https://doi.org/10.1016/j.stress.2023.100247
Estado	Publicada - dic. 2023

Palabras clave

Estrés abiótico
Mecanismos de desintoxicación de Al
Oryza glumaepatula
Oryza sativa
Experimentos de ARN-Seq

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10.1016/j.stress.2023.100247Licencia: CC BY-NC-ND

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title = "Transcriptional analysis in four wild and cultivated rice genotypes identifies aluminum-induced genes",

abstract = "Differential gene expression analysis is a widely used approach to identify relevant genes and functional mechanisms that influence plant tolerance to abiotic stresses. In this study, we evaluated the transcriptional responses of contrasting rice genotypes to prolonged aluminum (Al) exposure, in cultivated (Oryza sativa) and wild (Oryza glumaepatula) rice species, through RNA-Seq experiments. After comparing transcriptional responses under control and Al treatment conditions, differentially expressed genes (DEGs) were identified for each genotype. Additionally, the transcription levels of six DEGs were validated by quantitative real-time PCR. Functional analyses of the identified DEGs provided insights into the coordinated action of both exclusion and detoxification mechanisms associated with Al responses in rice. Furthermore, we report a group of 28 genes that were differentially expressed in all analyzed species and genotypes, pinpointing a core set of mechanisms that are triggered by Al exposure. Likewise, 14 DEGs were identified only in Al-tolerant genotypes, representing potential key elements for the understanding of the successful adaptive response to toxic conditions adopted by tolerant genotypes. Given that many of these identified genes have not been previously reported or characterized, they could be considered novel regulators linked with Al tolerance responses, and promising candidates for the generation of agronomically improved rice varieties.",

keywords = "Abiotic stress, Al-detoxification mechanisms, Oryza glumaepatula, Oryza sativa, RNA-Seq experiments, Estr{\'e}s abi{\'o}tico, Mecanismos de desintoxicaci{\'o}n de Al, Oryza glumaepatula, Oryza sativa, Experimentos de ARN-Seq",

author = "Gallo-Franco, \{J. J.\} and I. Zuluaga-Yusti and Restrepo-Garc{\'i}a, \{A. M.\} and Sosa, \{C. C.\} and S. Zapata-Balanta and Guti{\'e}rrez-Mar{\'i}n, \{J. P.\} and T. Ghneim-Herrera and M. Quimbaya",

note = "Publisher Copyright: {\textcopyright} 2023 The Author(s)",

year = "2023",

month = dec,

doi = "10.1016/j.stress.2023.100247",

language = "English",

volume = "10",

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TY - JOUR

T1 - Transcriptional analysis in four wild and cultivated rice genotypes identifies aluminum-induced genes

AU - Gallo-Franco, J. J.

AU - Zuluaga-Yusti, I.

AU - Restrepo-García, A. M.

AU - Sosa, C. C.

AU - Zapata-Balanta, S.

AU - Gutiérrez-Marín, J. P.

AU - Ghneim-Herrera, T.

AU - Quimbaya, M.

PY - 2023/12

Y1 - 2023/12

N2 - Differential gene expression analysis is a widely used approach to identify relevant genes and functional mechanisms that influence plant tolerance to abiotic stresses. In this study, we evaluated the transcriptional responses of contrasting rice genotypes to prolonged aluminum (Al) exposure, in cultivated (Oryza sativa) and wild (Oryza glumaepatula) rice species, through RNA-Seq experiments. After comparing transcriptional responses under control and Al treatment conditions, differentially expressed genes (DEGs) were identified for each genotype. Additionally, the transcription levels of six DEGs were validated by quantitative real-time PCR. Functional analyses of the identified DEGs provided insights into the coordinated action of both exclusion and detoxification mechanisms associated with Al responses in rice. Furthermore, we report a group of 28 genes that were differentially expressed in all analyzed species and genotypes, pinpointing a core set of mechanisms that are triggered by Al exposure. Likewise, 14 DEGs were identified only in Al-tolerant genotypes, representing potential key elements for the understanding of the successful adaptive response to toxic conditions adopted by tolerant genotypes. Given that many of these identified genes have not been previously reported or characterized, they could be considered novel regulators linked with Al tolerance responses, and promising candidates for the generation of agronomically improved rice varieties.

AB - Differential gene expression analysis is a widely used approach to identify relevant genes and functional mechanisms that influence plant tolerance to abiotic stresses. In this study, we evaluated the transcriptional responses of contrasting rice genotypes to prolonged aluminum (Al) exposure, in cultivated (Oryza sativa) and wild (Oryza glumaepatula) rice species, through RNA-Seq experiments. After comparing transcriptional responses under control and Al treatment conditions, differentially expressed genes (DEGs) were identified for each genotype. Additionally, the transcription levels of six DEGs were validated by quantitative real-time PCR. Functional analyses of the identified DEGs provided insights into the coordinated action of both exclusion and detoxification mechanisms associated with Al responses in rice. Furthermore, we report a group of 28 genes that were differentially expressed in all analyzed species and genotypes, pinpointing a core set of mechanisms that are triggered by Al exposure. Likewise, 14 DEGs were identified only in Al-tolerant genotypes, representing potential key elements for the understanding of the successful adaptive response to toxic conditions adopted by tolerant genotypes. Given that many of these identified genes have not been previously reported or characterized, they could be considered novel regulators linked with Al tolerance responses, and promising candidates for the generation of agronomically improved rice varieties.

KW - Abiotic stress

KW - Al-detoxification mechanisms

KW - Oryza glumaepatula

KW - Oryza sativa

KW - RNA-Seq experiments

KW - Estrés abiótico

KW - Mecanismos de desintoxicación de Al

KW - Oryza glumaepatula

KW - Oryza sativa

KW - Experimentos de ARN-Seq

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DO - 10.1016/j.stress.2023.100247

M3 - Article

AN - SCOPUS:85173463494

SN - 2667-064X

VL - 10

SP - 1

EP - 12

JO - Plant Stress

JF - Plant Stress

M1 - 100247

ER -

Transcriptional analysis in four wild and cultivated rice genotypes identifies aluminum-induced genes

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