Abstract
Upland cotton (Gossypium hirsutum) is a salt-tolerant crop that can endure high salt concentrations without apparent damage. However, the plant’s response to salinity stress is a complex biological process. An analysis of the dynamic changes in transcript profiles will provide a global picture of the cotton response to salinity stress. Here, we monitored the transcriptome changes in two cotton genotypes, the salt-tolerant H15, and sensitive ZM12, at 0, 0.25, 1, 3, 6, 12, 24, and 48 h in roots exposed to 200-mM NaCl. In total, 13,894 and 5057 differentially expressed genes were identified as being involved in salt-stress tolerance in H15 and ZM12, respectively. Of these, 3825 genes were common to both genotypes. A differential expression analysis revealed that the number of differentially expressed genes increased significantly during the first 24 h after the salt-stress treatment and then significantly decreased at 48 h in both genotypes. A transcription factor (TF) analysis revealed three different patterns based on the expression of 45 TFs’ families, with the majority of differentially expressed TFs increasing rapidly after the salt-stress treatment in both genotypes. A weighted gene co-expression network analysis showed that two gene modules were related to salinity, and genes in these modules were mainly involved in plant–pathogen interactions, the plant MAPK signaling pathway, and diterpenoid biosynthesis. Our results increase the understanding of cotton metabolic pathways involved in responses to salt stress.
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Abbreviations
- BCAT:
-
Branched-chain aminotransferase
- CAT:
-
Catalase
- CPKs/CDPKs:
-
Calcium-dependent protein kinases
- DEG:
-
Differentially expressed gene
- FPKM:
-
Fragments per kilobase per million
- GO:
-
Gene ontology
- GPX:
-
Glutathione peroxidase
- GR:
-
Glutathione reductase
- HAK:
-
High-affinity K+ transporter
- HMGR:
-
Hydroxy methylglutaryl CoA reductase
- HRGPs:
-
Hydroxyproline-rich glycoproteins
- KEGG:
-
Kyoto encyclopedia of genes and genomes
- MAPK:
-
Mitogen-activated protein kinase
- MYB:
-
Myb domain protein
- PANK:
-
Pantothenate kinase genes
- POD:
-
Peroxidase
- REC:
-
Relative electrical conductivity
- ROS:
-
Reactive oxygen species
- RWC:
-
Relative water content
- TF:
-
Transcription factor
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Acknowledgements
This work was sponsored by Financial Foundation of Hebei Academy of Agriculture and Forestry Sciences (F17C2017039345), Innovation project of Hebei Academy of Agriculture and Forestry Sciences (2019-1-3-2), and Hebei Science and Technology Plan Project (16226303D). We would like to thank Lesley Benyon, PhD, from Liwen Bianji, Edanz Group China (https://www.liwenbianji.cn/ac), for editing the English text of a draft of this manuscript.
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Supplementary file1 Supplementary Figure S1 The effect of exposure to 200 mM NaCl on the H15 and ZM12 varieties of upland cotton. (TIF 5543 kb)
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Supplementary file2 Supplementary Figure S2 Comparison of the expression of 12 randomly selected genes by using RNA-seq and qRT-PCR. The gene expression values by qRT-PCR were transformed to log2 scale. (TIF 4407 kb)
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Supplementary file3 Supplementary Figure S3 Venn diagram analysis of the numbers of DE genes in two cotton genotypes under different time points. (TIF 5271 kb)
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Supplementary file4 Supplementary Figure S4 Heat map analysis of the expression levels of ROS genes based on log2 fold change. (TIF 7006 kb)
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Supplementary file7 Supplementary Table S3 Differentially expressed genes after salt stress in the roots of H15. (XLS 7662 kb)
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Supplementary file8 Supplementary Table S4 Differentially expressed genes after salt stress in the roots of ZM12. (XLS 2819 kb)
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Supplementary file9 Supplementary Table S5 Detailed information of quantitative RT-PCR results and DESeq2 results. (XLS 26 kb)
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Supplementary file12 Supplementary Table S8. H15-specific differentially expressed genes encoding CyP450 enzymes. (XLS 42 kb)
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Supplementary file14 Supplementary Table S10. H15-specific differentially expressed genes for coenzyme A metabolic process. (XLS 24 kb)
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Wang, Y., Liu, J., Zhao, G. et al. Dynamic transcriptome and co-expression network analysis of the cotton (Gossypium hirsutum) root response to salinity stress at the seedling stage. Acta Physiol Plant 42, 143 (2020). https://doi.org/10.1007/s11738-020-03117-w
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DOI: https://doi.org/10.1007/s11738-020-03117-w