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Transcriptome profiling of Vitis amurensis, an extremely cold-tolerant Chinese wild Vitis species, reveals candidate genes and events that potentially connected to cold stress

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Abstract

Vitis amurensis Rupr. is an exceptional wild-growing Vitis (grape) species that can safely survive a wide range of cold conditions, but the underlying cold-adaptive mechanism associated with gene regulation is poorly investigated. We have analyzed the physiochemical and transcriptomic changes caused by cold stress in a cold-tolerant accession, ‘Heilongjiang seedling’, of Chinese wild V. amurensis. We statistically determined that a total of 6,850 cold-regulated transcripts were involved in cold regulation, including 3,676 up-regulated and 3,174 down-regulated transcripts. A global survey of messenger RNA revealed that skipped exon is the most prevalent form of alternative spicing event. Importantly, we found that the total splicing events increased with the prolonged cold stress. We also identified thirty-eight major TF families that were involved in cold regulation, some of which were previously unknown. Moreover, a large number of candidate pathways for the metabolism or biosynthesis of secondary metabolites were found to be regulated by cold, which is of potential importance in coordinating cold tolerance with growth and development. Several heat shock proteins and heat shock factors were also detected to be intensively cold-regulated. Furthermore, we validated the expression profiles of 16 candidates using qRT-PCR to further confirm the accuracy of the RNA-seq data. Our results provide a genome-wide view of the dynamic changes in the transcriptome of V. amurensis, in which it is evident that various structural and regulatory genes are crucial for cold tolerance/adaptation. Moreover, our robust dataset advances our knowledge of the genes involved in the complex regulatory networks of cold stress and leads to a better understanding of cold tolerance mechanisms in this extremely cold-tolerant Vitis species.

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Acknowledgments

This work was supported by the Ningxia Natural Science Foundation (Grant No. NZ1108) and National Natural Science Foundation of China (Grant No. 31101512).

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Authors and Affiliations

  1. School of Agronomy, Ningxia University, Yinchuan, 750021, Ningxia, People’s Republic of China

    Weirong Xu, Ningbo Zhang & Zhenping Wang

  2. Ningxia Engineering and Technology Research Center of Grape and Wine, Ningxia University, Yinchuan, 750021, Ningxia, People’s Republic of China

    Weirong Xu, Ningbo Zhang & Zhenping Wang

  3. Engineering Research Center of Grape and Wine, Ministry of Education, Ningxia University, Yinchuan, 750021, Ningxia, People’s Republic of China

    Weirong Xu, Ningbo Zhang & Zhenping Wang

  4. Ningxia Research Center of Grape and Wine, Yinchuan, Ningxia, People’s Republic of China

    Weirong Xu, Ningbo Zhang & Zhenping Wang

  5. College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, People’s Republic of China

    Ruimin Li, Fuli Ma & Yuntong Jiao

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  1. Weirong Xu
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  2. Ruimin Li
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Correspondence to Zhenping Wang.

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Weirong Xu and Ruimin Li have contributed equally to this work.

Electronic supplementary material

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11103_2014_245_MOESM1_ESM.xls

Supplementary Table S1 Primers used for qRT-PCR experiments. All the forward and reverse primer sequences were included. Supplementary material 1 (XLS 20 kb)

11103_2014_245_MOESM2_ESM.xls

Supplementary Table S2 Statistics of the generated V. amurensis reads and comparison to the ‘Pinot Noir’ reference genome (12X) Supplementary material 2 (XLS 17 kb)

11103_2014_245_MOESM3_ESM.xls

Supplementary Table S3 Statistical analysis of GO annotations for up-regulated and down-regulated DEGs. Supplementary material 3 (XLS 14 kb)

11103_2014_245_MOESM4_ESM.xls

Supplementary Table S4 K-means clusters (K1-K6) of DEGs from the time course of cold stress based on Mapman functional categories. Supplementary material 4 (XLS 22 kb)

Supplementary Table S5 KEGG pathway analysis of cold-responsive DEGs. Supplementary material 5 (XLS 2436 kb)

11103_2014_245_MOESM6_ESM.xls

Supplementary Table S6 Summary of differential alternative splicing events identified in V. amurensis. Supplementary material 6 (XLS 273 kb)

11103_2014_245_MOESM7_ESM.xls

Supplementary Table S7 GO terms of cold responsive DEGs related to ‘Response to abiotic and biotic stimulus’ and ‘Response to stress’. Supplementary material 7 (XLS 15 kb)

11103_2014_245_MOESM8_ESM.xls

Supplementary Table S8 Cold-responsive transcripts exclusively related to ‘cold’ response. Supplementary material 8 (XLS 207 kb)

11103_2014_245_MOESM9_ESM.xls

Supplementary Table S9 Cold-responsive transcription factors during the process of low temperature treatment. Supplementary material 9 (XLS 39 kb)

11103_2014_245_MOESM10_ESM.xls

Supplementary Table S10 Correlation between RNA-seq and qRT-PCR data on the 16 candidates. Supplementary material 10 (XLS 78 kb)

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Xu, W., Li, R., Zhang, N. et al. Transcriptome profiling of Vitis amurensis, an extremely cold-tolerant Chinese wild Vitis species, reveals candidate genes and events that potentially connected to cold stress. Plant Mol Biol 86, 527–541 (2014). https://doi.org/10.1007/s11103-014-0245-2

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