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Transcriptome profiling of mild-salt responses in Lycium ruthenicum early seedlings to reveal salinity-adaptive strategies

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Abstract

The traditional Chinese desert shrub Lycium ruthenicum is widely distributed in arid environments such as north-west China, exhibiting ideal salt tolerance to cope with soil desertification, salinity, and alkalinity. However, the salt-tolerance mechanism of L. ruthenicum, especially of its young seedlings at early vegetative stages, remains largely unknown. In the present study, we collected whole-seedling samples from Lycium ruthenicum at a-pair-leaf stage with and without a mild salt (75 mM sodium chloride) treatment, and then performed transcriptome profiling to compare their gene expression patterns. The de novo assembly achieved 94,651 unigenes with 55,156 annotated. Among them, 199 differentially expressed genes (DEGs) were identified between salt-treated seedlings and control, with 41 up-regulated and 158 down-regulated. These DEGs were highly enriched into gene ontology (GO) classifications ‘metabolic process’ and ‘catalytic activity’, into Clusters of Orthologous Groups (COG) function classifications ‘translation, ribosomal structure and biogenesis’ and ‘energy production and conversion’, and into Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways ‘ribosome’ and ‘oxidative phosphorylation’. Specifically, genes involved in energy metabolism (oxidative phosphorylation) and related energy-consuming metabolisms, including ribosome-associated biogenesis and biosynthesis of organic nitrogen-derived compatible solutes (i.e., arginine and proline), were generally down-regulated. Specific genes involved in abscisic acid (ABA) biosynthesis and signaling pathway were simultaneously up-regulated. Changes in the transcript levels of salt-responsive DEGs selected from the transcriptomic profiling were further validated by real-time quantitative polymerase chain reaction (RT-qPCR) analysis. Based on these results, salinity-adaptive strategies for the L. ruthenicum early seedlings are discussed.

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Abbreviations

AASCL:

Amino acid solute carrier like

ABA:

Abscisic acid

BP:

Biological process

CC:

Cellular component

COG:

Clusters of Orthologous Groups

DEG:

Differentially expressed gene

EDTA:

Ethylenediaminetetraacetic acid

EF:

Elongation factor

ELISA:

Enzyme-linked immunosorbent assay

FPKM:

Fragments per kb per million fragments

GA:

Gibberellic acid

GAPDH:

Glyceraldehyde 3-phosphate dehydrogenase

GDH:

Glutamate dehydrogenase

GO:

Gene ontology

GS:

Glutamine synthetase

JA:

Jasmonate

KEGG:

Kyoto Encyclopedia of Genes and Genomes

KOG:

EuKaryotic Orthologous Groups

MAPKKK:

Mitogen-activated protein kinase kinase kinase

MAPKs:

Mitogen-activated protein kinases

MF:

Molecular function

NADH-UQ:

NADH-ubiquinone oxidoreductase

NCED:

9-Cis-epoxycarotenoid dioxygenase

NDPK:

Nucleoside-diphosphate kinase

NR:

Non-redundant

ODC:

Ornithine decarboxylase

Pfm:

Protein family

PP2C:

Protein phosphatase 2C

RT-qPCR:

Real-time quantitative PCR

ROS:

Reactive oxygen species

RPL:

Ribosome protein large unit (60S)

RPS:

Ribosome protein small unit (40S

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Acknowledgements

This work was supported by Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology Project (Grant no. XJDX1414-2015-01) and the National Natural Science Foundations of China (Grant nos. 31371669 and 31101595). We sincerely thank Dr. Xuemin Wang (Department of Biology, University of Missouri, United States; Donald Danforth Plant Science Center, United States) for his helpful suggestions in the research and English language editing.

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  1. Hongbin Wang and Jilin Guo have contributed equally to this work.

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  1. Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, College of Life Science, Xinjiang Normal University, Urumqi, 830054, China

    Hongbin Wang, Jilin Guo, Zhongping Tian, Jin Li & Yong Zheng

  2. Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China

    Lingfu Deng, Yong Zheng & Yongze Yuan

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  1. Hongbin Wang
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Wang, H., Guo, J., Tian, Z. et al. Transcriptome profiling of mild-salt responses in Lycium ruthenicum early seedlings to reveal salinity-adaptive strategies. Acta Physiol Plant 42, 63 (2020). https://doi.org/10.1007/s11738-020-03048-6

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