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Transcriptome-based gene expression profiling identifies differentially expressed genes critical for salt stress response in radish (Raphanus sativus L.)

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Abstract

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Transcriptome-based gene expression analysis identifies many critical salt-responsive genes in radish and facilitates further dissecting the molecular mechanism underlying salt stress response.

Abstract

Salt stress severely impacts plant growth and development. Radish, a moderately salt-sensitive vegetable crop, has been studied for decades towards the physiological and biochemical performances under salt stress. However, no systematic study on isolation and identification of genes involved in salt stress response has been performed in radish, and the molecular mechanism governing this process is still indistinct. Here, the RNA-Seq technique was applied to analyze the transcriptomic changes on radish roots treated with salt (200 mM NaCl) for 48 h in comparison with those cultured in normal condition. Totally 8709 differentially expressed genes (DEGs) including 3931 up- and 4778 down-regulated genes were identified. Functional annotation analysis indicated that many genes could be involved in several aspects of salt stress response including stress sensing and signal transduction, osmoregulation, ion homeostasis and ROS scavenging. The association analysis of salt-responsive genes and miRNAs exhibited that 36 miRNA–mRNA pairs had negative correlationship in expression trends. Reverse-transcription quantitative PCR (RT-qPCR) analysis revealed that the expression profiles of DEGs were in line with results from the RNA-Seq analysis. Furthermore, the putative model of DEGs and miRNA-mediated gene regulation was proposed to elucidate how radish sensed and responded to salt stress. This study represents the first comprehensive transcriptome-based gene expression profiling under salt stress in radish. The outcomes of this study could facilitate further dissecting the molecular mechanism underlying salt stress response and provide a valuable platform for further genetic improvement of salt tolerance in radish breeding programs.

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Abbreviations

DEG:

Differentially expressed gene

RT-qPCR:

Reverse-transcription quantitative PCR

KEGG:

Kyoto encyclopedia of genes and genomes

GO:

Gene ontology

RPKM:

Reads per kilobase per million reads

FDR:

False discovery rate

TF:

Transcription factor

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Acknowledgments

This work was in part supported by grants from the National Natural Science Foundation of China (31501759, 31171956, 31372064), Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement (2014017), Key Technology R&D Program of Jiangsu Province, China (BE2013429) and Jiangsu Agricultural Science and Technology Innovation Fund (CN) [JASTIF,CX (12)2006, CX (13)2007].

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Authors and Affiliations

  1. National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People’s Republic of China

    Xiaochuan Sun, Liang Xu, Yan Wang, Xiaobo Luo, Karanja Benard Kinuthia, Shanshan Nie, Haiyang Feng, Chao Li & Liwang Liu

  2. Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, 210014, People’s Republic of China

    Xiaochuan Sun, Liang Xu, Yan Wang, Shanshan Nie & Liwang Liu

  3. Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA

    Xianwen Zhu

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  1. Xiaochuan Sun
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  2. Liang Xu
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  3. Yan Wang
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  4. Xiaobo Luo
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Table S1 Primers used in RT-qPCR analysis (XLSX 10 kb)

Table S2 KEGG pathways of DEGs (XLSX 18 kb)

Table S3 The enriched GO terms of DEGs under salt stress (XLSX 16 kb)

Table S4 The DEGs involved in stress sensing and signaling transduction under salt stress in radish (XLSX 18 kb)

Table S5 The DEGs involved in osmotic adjustment under salt stress in radish (XLSX 13 kb)

Table S6 The DEGs involved in ROS scavenging under salt stress in radish (XLSX 15 kb)

Table S7 The DEGs encoding TFs under salt stress in radish (XLSX 21 kb)

Table S8 The DEGs involved in transport activities in salt stress response in radish (XLSX 17 kb)

Table S9 The DEGs encoding other significant proteins in salt stress response in radish (XLSX 25 kb)

299_2015_1887_MOESM10_ESM.xlsx

Table S10 The detailed information of association analysis between salt-responsive genes and miRNAs in radish (XLSX 22 kb)

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Sun, X., Xu, L., Wang, Y. et al. Transcriptome-based gene expression profiling identifies differentially expressed genes critical for salt stress response in radish (Raphanus sativus L.). Plant Cell Rep 35, 329–346 (2016). https://doi.org/10.1007/s00299-015-1887-5

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