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Deep-sequencing transcriptome analysis of field-grown Medicago sativa L. crown buds acclimated to freezing stress

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Abstract

Medicago sativa L. (alfalfa) ‘Zhaodong’ is an important forage legume that can safely survive in northern China where winter temperatures reach as low as −30 °C. Survival of alfalfa following freezing stress depends on the amount and revival ability of crown buds. In order to investigate the molecular mechanisms of frost tolerance in alfalfa, we used transcriptome sequencing technology and bioinformatics strategies to analyze crown buds of field-grown alfalfa during winter. We statistically identified a total of 5605 differentially expressed genes (DEGs) involved in freezing stress including 1900 upregulated and 3705 downregulated DEGs. We validated 36 candidate DEGs using qPCR to confirm the accuracy of the RNA-seq data. Unlike other recent studies, this study employed alfalfa plants grown in the natural environment. Our results indicate that not only the CBF orthologs but also membrane proteins, hormone signal transduction pathways, and ubiquitin-mediated proteolysis pathways indicate the presence of a special freezing adaptation mechanism in alfalfa. The antioxidant defense system may rapidly confer freezing tolerance to alfalfa. Importantly, biosynthesis of secondary metabolites and phenylalanine metabolism, which is of potential importance in coordinating freezing tolerance with growth and development, were downregulated in subzero temperatures. The adaptive mechanism for frost tolerance is a complex multigenic process that is not well understood. This systematic analysis provided an in-depth view of stress tolerance mechanisms in alfalfa.

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Abbreviations

Nt:

NCBI nonredundant nucleotide

Nr:

NCBI nonredundant protein

GO:

Gene Ontology

KEGG:

Kyoto Encyclopedia of Genes and Genomes

KOG:

EuKaryotic Orthologous Groups

DEGs:

Differentially expressed genes

CBF:

C-repeat binding factor

qPCR:

Quantitative real-time polymerase chain reaction

TF:

Transcription factor

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Acknowledgments

This work was supported by the MOST 863 project (2013AA102607-5), the Graduate Innovation Fund of Harbin Normal University (HSDBSCX2014-04), Key Scientific and Technological Project of Heilongjiang Province of China (GA15B105-1), and the Natural and Science Foundation of China (Nos. 31302019 and 31470571).

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Authors and Affiliations

  1. Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, 150025, Heilongjiang, China

    Lili Song, Lin Jiang, Yue Chen, Yongjun Shu, Yan Bai & Changhong Guo

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  1. Lili Song
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  2. Lin Jiang
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  3. Yue Chen
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  4. Yongjun Shu
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  5. Yan Bai
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  6. Changhong Guo
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Correspondence to Changhong Guo.

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Song, L., Jiang, L., Chen, Y. et al. Deep-sequencing transcriptome analysis of field-grown Medicago sativa L. crown buds acclimated to freezing stress. Funct Integr Genomics 16, 495–511 (2016). https://doi.org/10.1007/s10142-016-0500-5

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  • DOI: https://doi.org/10.1007/s10142-016-0500-5

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