Transcriptome Analysis of Salt Stress Responsiveness in the Seedlings of Dongxiang Wild Rice (Oryza rufipogon Griff.)

Abstract

Dongxiang wild rice (Oryza rufipogon Griff.) is the progenitor of cultivated rice (Oryza sativa L.), and is well known for its superior level of tolerance against cold, drought and diseases. To date, however, little is known about the salt-tolerant character of Dongxiang wild rice. To elucidate the molecular genetic mechanisms of salt-stress tolerance in Dongxiang wild rice, the Illumina HiSeq 2000 platform was used to analyze the transcriptome profiles of the leaves and roots at the seedling stage under salt stress compared with those under normal conditions. The analysis results for the sequencing data showed that 6,867 transcripts were differentially expressed in the leaves (2,216 up-regulated and 4,651 down-regulated) and 4,988 transcripts in the roots (3,105 up-regulated and 1,883 down-regulated). Among these differentially expressed genes, the detection of many transcription factor genes demonstrated that multiple regulatory pathways were involved in salt stress tolerance. In addition, the differentially expressed genes were compared with the previous RNA-Seq analysis of salt-stress responses in cultivated rice Nipponbare, indicating the possible specific molecular mechanisms of salt-stress responses for Dongxiang wild rice. A large number of the salt-inducible genes identified in this study were co-localized onto fine-mapped salt-tolerance-related quantitative trait loci, providing candidates for gene cloning and elucidation of molecular mechanisms responsible for salt-stress tolerance in rice.

Fig 1. The seedlings of DXWR showed stronger salt resistance than the seedlings of XB.

Fig 2. The number of up- and down-regulated transcripts in the LS and RS compared with the LCK and RCK.

LS, leaves with salt treatment; RS, roots with salt treatment; LCK, leaves without salt treatment; RCK, roots without salt treatment.

Fig 3. Gene ontology (GO) classification of the unigenes from the LS-vs-LCK (A) and RS-vs-RCK (B).

Fig 4. KEGG pathway assignments in the LS vs. LCK (A) and RS vs. RCK (B).

The represented categories (Q-value≤ 0.05) and the number of transcripts predicted to belong to each category are shown.

Fig 5. The number of up- and down-regulated genes in the LS (LS vs. LCK), RS (RS vs. RCK), shoots, and roots.

(A), up-regulated genes in the LS, shoots, and roots; (B), up-regulated genes in the RS, shoots, and roots; (C), down-regulated genes in the LS, shoots, and roots; (D), down-regulated genes in the RS, shoots, and roots.