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Genome-Wide Identification of Drought Response Genes in Soybean Seedlings and Development of Biomarkers for Early Diagnoses

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Abstract

Drought is a yield-limiting factor for soybean (Glycine max L. Merrill) production in North America. Understanding molecular mechanisms underlying early responses of the soybean plant to drought may help develop new techniques to manage the abiotic stress. The objectives of this research were to identify expressed genes responsive to drought stress at the seedling stage and to develop biomarkers for early diagnostic of genotypic difference in the stress tolerance. Using a GeneChip Soybean Genome Array and an improved algorithm, we identified 697 differentially expressed genes (DEGs), with 420 upregulated and 277 downregulated by a 6-h dehydration treatment. A majority of these DEGs encode transcription factors, protein kinases, hormone biosynthetic/signaling enzymes, or other regulatory proteins. MAPMAN and KEGG enrichment showed that the DEGs were mainly involved in the metabolic and hormone signaling pathways and identified the GmHDZ72/PYL/PP2C module as negative feedback of abscisic acid signaling pathway induced by dehydration stress. Ten DEGs were selected from various pathways and validated in a sample of 20 soybean cultivars varying in the level of drought tolerance. Five of the 10 validated DEGs, Glyma03g30040, Glyma11g05960, Glyma11g11430, Glyma12g22880, and Glyma16g02390, showed expression profiles strongly correlated with the plant height reduction after a 14-d drought treatment. These genes are the best candidate biomarkers to monitor plant early responses to drought stress before a symptom appears and to screen for drought-tolerant genotypes. This research provided a new set of transcriptomic data to develop gene regulatory networks underlying sensing drought signal and possible acclimatization in the early stage and enriched the genomics toolbox with a set of biomarkers for early diagnosis of drought damage and molecular breeding of drought tolerance in soybean.

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Funding

This research was supported by South Dakota Excellence Center for Drought Research and South Dakota Soybean Research and Promotion Council. The use of instruments available at South Dakota State University’s Functional Genomics Core Facility and BioSNTR supported in part by the National Science Foundation/EPSCoR grant no. 0091948 and Cooperative Agreement no. IIA-1355423, and by the State of South Dakota, are gratefully acknowledged.

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Authors and Affiliations

  1. Department of Biology and Microbiology, South Dakota State University, Brookings, SD, 57007, USA

    Lei Hua, Ghana Shyam Challa, Senthil Subramanian, Xingyou Gu & Wanlong Li

  2. Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, 57007, USA

    Senthil Subramanian, Xingyou Gu & Wanlong Li

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  1. Lei Hua
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  2. Ghana Shyam Challa
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  4. Xingyou Gu
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  5. Wanlong Li
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Correspondence to Wanlong Li.

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Hua, L., Challa, G.S., Subramanian, S. et al. Genome-Wide Identification of Drought Response Genes in Soybean Seedlings and Development of Biomarkers for Early Diagnoses. Plant Mol Biol Rep 36, 350–362 (2018). https://doi.org/10.1007/s11105-018-1085-z

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