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Transcriptomic analysis and discovery of genes in the response of Arachis hypogaea to drought stress

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Abstract

The peanut (Arachis hypogaea) is an important crop species that is threatened by drought stress. The genome sequences of peanut, which was officially released in 2016, may help explain the molecular mechanisms that underlie drought tolerance in this species. We report here a gene expression profiling of A. hypogaea to gain a global view of its drought resistance. Using whole-transcriptome sequencing, we analysed differential gene expression in response to drought stress in the drought-resistant peanut cultivar J11. Pooled samples obtained at 6, 12, 18, 24, and 48 h were compared with control samples at 0 h. In total, 51,554 genes were found, including 49,289 known genes and 2265 unknown genes. We identified 224 differentially expressed transcription factors, 296,335 SNPs and 28,391 InDELs. In addition, we detected significant differences in the gene expression profiles of the treatment and control groups. After comparing the two groups, 4648 genes were identified. An in-depth analysis of the data revealed that a large number of genes were associated with drought stress, including transcription factors and genes involved in photosynthesis–antenna proteins, carbon metabolism and the citrate cycle. The results of this study provide insights into the diverse mechanisms that underlie the successful establishment of drought resistance in the peanut, thereby facilitating the identification of important genes in the peanut related to drought management. Transcriptome analysis based on RNA-Seq is a powerful approach for gene discovery and molecular marker development for this species.

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Acknowledgements

We wish to thank Dr. Qing Kong for the excellent advice on this paper. This work was supported by the International Science and Technology Cooperation Program of China (2015DFA31190); Young Scholars Fundation of Shandong Academy of Agricultural Sciences (2016-YQN16); National Science and Technology Support Program (2014BAD11B00); Fine Breeds Project of Shandong Province (2014–2016). Shandong Provincial Natural Science Foundation, China (ZR2016CP03).

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  1. Xiaobo Zhao and Chunjuan Li have contributed equally to this work.

Authors and Affiliations

  1. Laboratory of Genetics and Breeding, Shandong Peanut Research Institute, Qingdao, 266100, Shandong Province, People’s Republic of China

    Xiaobo Zhao, Chunjuan Li, Tingting Zhang, Caixia Yan & Shihua Shan

  2. Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong Province, People’s Republic of China

    Shubo Wan

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  1. Xiaobo Zhao
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11033_2018_4145_MOESM1_ESM.tif

LEA gene expression of different organs in peanut with Real-time qPCR. The Y-axis represents Relative Expression Level. The X-axis represents different organs. R: root; S: stem; L: leaf. The expression levels of selected genes were normalized against those of Actin 11, which was used as an internal control. (Figure was created by MSOffice) (TIF 283 KB)

11033_2018_4145_MOESM2_ESM.tif

LEA gene expression at different time response to drought-stres. a: LEA 2; b: LEA3; c: LEA4. The Y-axis represents Relative Expression Level. The X-axis represents different time (h). The expression levels of selected genes were normalized against those of Actin 11, which was used as an internal control. (Figure was created by MSOffice) (TIF 598 KB)

11033_2018_4145_MOESM3_ESM.tif

Phylogeny inferred with NJ analysis using LEA sequences. Bootstrap values were obtained from 1000 replications. a: LEA 2; b: LEA3; c: LEA4. Numbers near each clade refer to the NJ bootstrap value, and are displayed when the bootstrap value is greater than 60. (Figure was created by Mega5.0) (TIF 1353 KB)

A species-based classification for unigenes. (Figure was created by MSOffice) (TIF 1305 KB)

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Zhao, X., Li, C., Wan, S. et al. Transcriptomic analysis and discovery of genes in the response of Arachis hypogaea to drought stress. Mol Biol Rep 45, 119–131 (2018). https://doi.org/10.1007/s11033-018-4145-4

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