Differential transcriptome profiling of chilling stress response between shoots and rhizomes of Oryza longistaminata using RNA sequencing.

Ting Zhang,Yinxiao Wang,Xiuqin Zhao,Fengyi Hu,Shilai Zhang,Liyu Huang,Wensheng Wang,Jing Zhang,Zhikang Li,Binying Fu,Daichang Yang

doi:10.1371/journal.pone.0188625

Abstract

Rice (Oryza sativa) is very sensitive to chilling stress at seedling and reproductive stages, whereas wild rice, O. longistaminata, tolerates non-freezing cold temperatures and has overwintering ability. Elucidating the molecular mechanisms of chilling tolerance (CT) in O. longistaminata should thus provide a basis for rice CT improvement through molecular breeding. In this study, high-throughput RNA sequencing was performed to profile global transcriptome alterations and crucial genes involved in response to long-term low temperature in O. longistaminata shoots and rhizomes subjected to 7 days of chilling stress. A total of 605 and 403 genes were respectively identified as up- and down-regulated in O. longistaminata under 7 days of chilling stress, with 354 and 371 differentially expressed genes (DEGs) found exclusively in shoots and rhizomes, respectively. GO enrichment and KEGG pathway analyses revealed that multiple transcriptional regulatory pathways were enriched in commonly induced genes in both tissues; in contrast, only the photosynthesis pathway was prevalent in genes uniquely induced in shoots, whereas several key metabolic pathways and the programmed cell death process were enriched in genes induced only in rhizomes. Further analysis of these tissue-specific DEGs showed that the CBF/DREB1 regulon and other transcription factors (TFs), including AP2/EREBPs, MYBs, and WRKYs, were synergistically involved in transcriptional regulation of chilling stress response in shoots. Different sets of TFs, such as OsERF922, OsNAC9, OsWRKY25, and WRKY74, and eight genes encoding antioxidant enzymes were exclusively activated in rhizomes under long-term low-temperature treatment. Furthermore, several cis-regulatory elements, including the ICE1-binding site, the GATA element for phytochrome regulation, and the W-box for WRKY binding, were highly abundant in both tissues, confirming the involvement of multiple regulatory genes and complex networks in the transcriptional regulation of CT in O. longistaminata. Finally, most chilling-induced genes with alternative splicing exclusive to shoots were associated with photosynthesis and regulation of gene expression, while those enriched in rhizomes were primarily related to stress signal transduction; this indicates that tissue-specific transcriptional and post-transcriptional regulation mechanisms synergistically contribute to O. longistaminata long-term CT. Our findings provide an overview of the complex regulatory networks of CT in O. longistaminata.

Highlights

Rice (Oryza sativa), one of the most important cereal crops, provides food for more than half of the world’s population
Transcriptome profiling of Oryza longistaminata under chilling stress controls, exhibited significantly higher soluble sugar contents after 1-day and 3-day chilling stress, while free proline contents were markedly higher after 12 and 24 h of chilling stress and remained at these levels through the duration of the 7-day treatment. These results demonstrate that O. longistaminata plants accumulate soluble sugars and free proline in both types of tissues for protection against low temperature stress, with shoots responding more rapidly than rhizomes
Proline accumulation is closely related to abiotic stress tolerance [35], and increased proline content has been observed to be accompanied by a rise in the concentration of soluble sugars [36]

Summary

Introduction

Rice (Oryza sativa), one of the most important cereal crops, provides food for more than half of the world’s population. In terms of stress tolerance, genetic variability in cultivated rice germplasm is very limited; broadening the useful gene pool for rice is urgently needed [1]. Wild rice relatives are very important genetic resources for the improvement of rice resistance to biotic and abiotic stresses. Among the 20 known wild rice species, O. longistaminata has been identified as a potential gene donor for a number of valuable agronomic traits, such as disease resistance [2], high biomass production [3], and chilling tolerance (CT) [4]. Elucidating the genetic and molecular mechanisms of these traits could facilitate the use of these genes for rice improvement. Unlike cultivated annual rice varieties, O. longistaminata is able to overwinter in southern China, where the average winter temperature is approximately 5 to 10 ̊C [5].

Methods

Results

Conclusion