Transcriptome profiling of short-term response to chilling stress in tolerant and sensitive Oryza sativa ssp. Japonica seedlings
Low temperature is a major factor limiting rice growth and yield, and seedling is one of the developmental stages at which sensitivity to chilling stress is higher. Tolerance to chilling is a complex quantitative trait, so one of the most effective approaches to identify genes and pathways involved is to compare the stress-induced expression changes between tolerant and sensitive genotypes. Phenotypic responses to chilling of 13 Japonica cultivars were evaluated, and Thaibonnet and Volano were selected as sensitive and tolerant genotypes, respectively. To thoroughly profile the short-term response of the two cultivars to chilling, RNA-Seq was performed on Thaibonnet and Volano seedlings after 0 (not stressed), 2, and 10 h at 10 °C. Differential expression analysis revealed that the ICE-DREB1/CBF pathway plays a primary role in chilling tolerance, mainly due to some important transcription factors involved (some of which had never been reported before). Moreover, the expression trends of some genes that were radically different between Thaibonnet and Volano (i.e., calcium-dependent protein kinases OsCDPK21 and OsCDPK23, cytochrome P450 monooxygenase CYP76M8, etc.) suggest their involvement in low temperature tolerance too. Density of differentially expressed genes along rice genome was determined and linked to the position of known QTLs: remarkable co-locations were reported, delivering an overview of genomic regions determinant for low temperature response at seedling stage. Our study contributes to a better understanding of the molecular mechanisms underlying rice response to chilling and provides a solid background for development of low temperature-tolerant germplasm.
KeywordsOryza sativa Chilling tolerance Short-term response RNA-Seq Differentially expressed genes
Thanks are due to Marco Moretto and Paolo Sonego (Fondazione Edmund Mach, San Michele all’Adige ITALY) for their precious help with RNA-Seq data treatment.
MP, DR, VTH, and CP performed rice plants phenotiping, RNA extractions and RT-qPCR. MB and JAM performed the RNA-Seq analysis. MB wrote the manuscript. EF, NP, and PP conceived the experiment, participated in the interpretation and discussion of results, and contributed to the writing of the paper.
This work was supported by Progetto AGER, grant n° 2010-2369—Integrated Genetic And Genomic Approaches For New Italian Rice Breeding Strategies (RISINNOVA).
Compliance with ethical standards
Conflict of interest
The authors declare that they have no conflict of interest.
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