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Transcriptome analysis of sweet Sorghum inbred lines differing in salt tolerance provides novel insights into salt exclusion by roots

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Abstract

Backgrounds and aims

Sweet sorghum is an annual C4 crop with a high salt tolerance. However, little is known about the molecular mechanisms of salt exclusion in roots of sweet sorghum. In this study, the physiological parameters and transcript profiles of two inbred lines of sweet sorghum roots (salt-tolerant M-81E and salt-sensitive Roma) were analyzed in the presence of 0 or 150 mM NaCl in order to elucidate the molecular mechanisms of salt exclusion.

Results

We found that the Na+ concentrations in both shoots and roots of M-81E were lower than that of Roma. Moreover, we identified 2085 and 3172 differentially expressed genes between control plants and those subjected to salt stress in M-81E and Roma strains, respectively. The differentially expressed genes involved in pathways related to salt exclusion such as formation of root casparian bands and suberin lamellae, membrane-bound ion translocating proteins. Many of these genes underwent greater change in M-81E compared to Roma. These results revealed that the better ability of salt exclusion in M-81E may be caused by the combination of physical barrier effect of root apoplastic barriers and the transportation of Na+ out of the xylem by HKT1;5. Moreover, some genes encoding transcription factors were also differentially expressed, which may be involved in the regulation of genes related to salt exclusion.

Conclusions

This RNA-seq dataset provide comprehensive insights into the transcriptomic landscape to reveal molecular mechanisms of salt exclusion in roots of sweet sorghum.

Keywords

Genes Roots Salt exclusion Sweet sorghum Transcriptomic profile 

Abbreviations

CB

casparian bands

SL

suberin lamellae

FW

fresh weight

CCR

cinnamoyl CoA reductase

CAD

cinnamyl alcohol dehydrogenase

4CL

4-coumarate-CoA ligase

KCS

β-ketoacyl-CoA synthase

CBL

calcineurin B-like protein

CIPK

CBL-interacting protein kinase

APX

ascorbate peroxidase

GST

glutathione-S-transferases

HSP

Heat shock proteins

RNA-seq

RNA-sequencing

DEGs

differentially expressed genes

RPKM

Reads per KB per million

FDR

false discovery rate

GO

Gene Ontology

COG

Clusters of Orthologous Groups

KEGG

Kyoto Encyclopedia of Genes and Genomes

qRT -PCR

quantitative real-time PCR

TF

transcription factors

PIP

plasma membrane intrinsic proteins

TIPs

tonoplast intrinsic proteins

C3H

p-coumarate 3-hydroxylase

Notes

Acknowledgements

We are grateful for financial support from Natural Science Research Foundation of Shandong Province (ZR2016JL028, ZR2014CZ002), Major Program of Shandong Provincial Natural Science Foundation (2017C03), the NSFC (National Natural Science Research Foundation of China, project No. 31770288), Independent innovation and achievement transformation of special major key technical plans of Shandong Province (2015ZDJS03002).

Authors’ contributions

ZY wrote this manuscript; ZY, HZ and XW performed experiments; ZY and JS collected data and carried out all analyses; NS and BW conceptualized the idea and revised the manuscript.

Compliance with ethical standards

Competing interests

The authors declare that they have no competing interests.

Supplementary material

11104_2018_3736_Fig7_ESM.png (109 kb)
Fig. S1

Na+/K+ ratio in shoots and roots of M-81E and Roma under different salt treatments (0 and 150 mM) for 48 h. Bars with the different letters are significantly different at p = 0.05. Bars with same letters are not significantly different. (PNG 109 kb)

11104_2018_3736_MOESM1_ESM.tif (356 kb)
High Resolution (TIF 356 kb)
11104_2018_3736_Fig8_ESM.png (288 kb)
Fig. S2

Clusters of orthologous groups (COG) classification. (PNG 288 kb)

11104_2018_3736_MOESM2_ESM.tif (663 kb)
High Resolution (TIF 663 kb)
11104_2018_3736_Fig9_ESM.png (1.3 mb)
Fig. S3

KEGG map of the phenylpropanoid biosynthesis pathway (A: M-81E, B: Roma). It’s an analysis of DEGs, comparing salt-treated samples to untreated control. Boxes with a red frame indicate the corresponding DEGs are up-regulated in the salt-treated samples, boxes with a green frame indicate the corresponding DEGs are down-regulated in the salt-treated samples, boxes with blue frame indicate some of the corresponding DEGs are down-regulated and others are up-regulated, and those without any colored frame indicate the expression level of corresponding genes are not changed, as determined by RNA-seq. (PNG 1380 kb)

11104_2018_3736_MOESM3_ESM.tif (1.4 mb)
High Resolution (TIF 1459 kb)
11104_2018_3736_MOESM4_ESM.xlsx (15 kb)
Table S1 The p value between different data of content of Na+, K+ of shoots and roots of M-81E and Roma under 150 mM salt treatments for different hours (0, 12, 24, 36 and 48). M0, M12, M24, M36 and M48 represent the corresponding data after 0, 12, 24, 36 and 48 h treatment of 150 mM NaCl in M-81E. R0, R12, R24, R36 and R48 represent the corresponding data after 0, 12, 24, 36 and 48 h treatment of 150 mM NaCl in Roma. (XLSX 14 kb)
11104_2018_3736_MOESM5_ESM.docx (22 kb)
Table S2 Primer pairs for real-time quantitative PCR (DOCX 21 kb)
11104_2018_3736_MOESM6_ESM.docx (17 kb)
Table S3 Clean reads used for further analysis (DOCX 16 kb)
11104_2018_3736_MOESM7_ESM.docx (25 kb)
Table S4 DEGs related to the ROS scavenging system (DOCX 25 kb)
11104_2018_3736_MOESM8_ESM.docx (24 kb)
Table S5 Up-regulated genes related to transcription factor (DOCX 24 kb)
11104_2018_3736_MOESM9_ESM.docx (18 kb)
Table S6 DEGs related to aquaporin (DOCX 17 kb)
11104_2018_3736_MOESM10_ESM.docx (18 kb)
Table S7 DEGs related to heat shock proteins (DOCX 18 kb)

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Authors and Affiliations

  1. 1.Shandong Provincial Key Laboratory of Plant Stress, College of life SciencesShandong Normal UniversityJinanPeople’s Republic of China
  2. 2.Shandong Provincial Key Laboratory of Microbial Engineering, School of Biologic EngineeringQilu University of Technology (Shandong Academy of Sciences)JinanChina

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