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.