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Transcriptome Profile Analysis of Maize Seedlings in Response to High-salinity, Drought and Cold Stresses by Deep Sequencing

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Abstract

To identify the crosstalk between gene expression and metabolism in response to cold, drought and salt stresses, digital gene expression (DGE) analysis was performed on maize (Zea mays L.) seedlings subjected to these stresses. A total of 103,953 (70.79 %), 111,130 (68.62 %), 94,435 (69.33 %) and 94,577 (68.92 %) tags were matched to reference genes. The most differentially regulated tags, with a log2 ratio ≥1 or ≤−1 (P < 0.01 and FDR ≤0.001), were further analysed. Many genes and biological pathways were affected by multiple abiotic stresses. In particular, expression changes for the gibberellin (GA) metabolic genes could improve understanding of the molecular basis of the response of the GA pathway to stress conditions. In addition, a large dataset of tag-mapped transcripts was obtained that provide a strong basis for future research on the response to abiotic stress in maize. And a new list of candidate targets for functional studies on genes involved in cold, drought and salt stresses has been generated. In this study, we revealed complex changes at the transcriptional level in maize seedlings under different abiotic stresses. Such studies could lead to a better understanding of the genetic basis of the maize response to different environmental stimuli and would be essential for improving the abiotic stress tolerance of maize.

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Acknowledgments

This study was supported by the National Natural Science Foundation of China (No. 31100192 and No. 31100242) and the Science Development Planning of Jilin Province (No. 20110752).

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Authors and Affiliations

  1. College of Plant Science, Jilin University, Changchun, 130062, China

    Xiaohui Shan & Yaping Yuan

  2. Agro-Biotechnology Research Institute, Jilin Academy of Agricultural Sciences, Changchun, 130033, China

    Yidan Li, Yu Jiang, Zhilei Jiang & Wenyuan Hao

Authors
  1. Xiaohui Shan
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  2. Yidan Li
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  3. Yu Jiang
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  4. Zhilei Jiang
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  5. Wenyuan Hao
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  6. Yaping Yuan
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Corresponding author

Correspondence to Yidan Li.

Electronic supplementary material

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Figure S1

Statistics of distinct clean tag alignment (JPEG 59 kb)

High Resolution Image (TIFF 1885 kb)

Figure S2

Statistics of number of Differentially Expressed Genes (DEGs) under different stress treatments (JPEG 10 kb)

High Resolution Image (TIFF 52 kb)

Figure S3

Clustering Analysis of Differentially Expressed Genes (DEGs) under different stress treatments (JPEG 1448 kb)

High Resolution Image (TIFF 650 kb)

Figure S4

DEGs enriched in maize GA metabolism pathway under different stress treatments. Red and green boxes represent the up- and down-regulated genes respectively. 4.2.3.19, 1.14.13.79, 1.14.11.12, 1.14.11.15 and 1.14.11.13 represent KS (ent-kaurene synthase), KAO (ent-kaurenoic acid oxidase), GA20ox (GA 20-oxidase), GA3ox (GA 3-oxidase), and GA2ox (GA 2-oxidase) respectively. (JPEG 40 kb)

High Resolution Image (TIFF 425 kb)

Supplementary Table 1

(XLS 120 kb)

Supplementary Table 2

Different gene expression under cold treatment from the other two stress treatments. (DOCX 14.9 kb)

Supplementary Table 3

Enriched pathways involved in different stress reactions. (DOCX 14.7 kb)

Supplementary Table 4

GA metabolic gene expression alteration under cold, drought, and salt stress. (DOCX 13.8 kb)

Supplementary Table 5

Differentially expressed genes in transcription factor families and stress related gene families in response to different stress treatments. (DOCX 22.3 kb)

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Shan, X., Li, Y., Jiang, Y. et al. Transcriptome Profile Analysis of Maize Seedlings in Response to High-salinity, Drought and Cold Stresses by Deep Sequencing. Plant Mol Biol Rep 31, 1485–1491 (2013). https://doi.org/10.1007/s11105-013-0622-z

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  • DOI: https://doi.org/10.1007/s11105-013-0622-z

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