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Natural population re-sequencing detects the genetic basis of local adaptation to low temperature in a woody plant

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Abstract

Key message

Total of 14 SNPs associated with overwintering-related traits and 75 selective regions were detected. Important candidate genes were identified and a possible network of cold-stress responses in woody plants was proposed.

Abstract

Local adaptation to low temperature is essential for woody plants to against changeable climate and safely survive the winter. To uncover the specific molecular mechanism of low temperature adaptation in woody plants, we sequenced 134 core individuals selected from 494 paper mulberry (Broussonetia papyrifera), which naturally distributed in different climate zones and latitudes. The population structure analysis, PCA analysis and neighbor-joining tree analysis indicated that the individuals were classified into three clusters, which showed forceful geographic distribution patterns because of the adaptation to local climate. Using two overwintering phenotypic data collected at high latitudes of 40°N and one bioclimatic variable, genome–phenotype and genome–environment associations, and genome-wide scans were performed. We detected 75 selective regions which possibly undergone temperature selection and identified 14 trait-associated SNPs that corresponded to 16 candidate genes (including LRR-RLK, PP2A, BCS1, etc.). Meanwhile, low temperature adaptation was also supported by other three trait-associated SNPs which exhibiting significant differences in overwintering traits between alleles within three geographic groups. To sum up, a possible network of cold signal perception and responses in woody plants were proposed, including important genes that have been confirmed in previous studies while others could be key potential candidates of woody plants. Overall, our results highlighted the specific and complex molecular mechanism of low temperature adaptation and overwintering of woody plants.

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Data availability

The RAD-seq sequences underlying this study have been deposited in NCBI database under BioProject code: PRJNA635706. The re-sequencing sequences underlying this study have been deposited in NCBI database under BioProject code: PRJNA635453. The phenotypic data and other relevant data supporting the findings of this work are contained within this paper and its Supplementary Files.

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Acknowledgements

We thank Hui Chen, Zhi Pi, Feng Tang, Xiaokang Zhang, Jie Hu, Jinshan Wang, Songwei Li and Pu Shu for their help of sample collection and cultivation in this study. This work was supported by the National Natural Science Foundation of China (31870247, 32070358, 31770360) and the Beijing Natural Science Foundation (6202026).

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  1. Yanmin Hu and Xianjun Peng contributed equally to the article.

Authors and Affiliations

  1. Key Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China

    Yanmin Hu, Xianjun Peng, Fenfen Wang, Peilin Chen, Meiling Zhao & Shihua Shen

  2. University of Chinese Academy of Sciences, Beijing, 100049, China

    Yanmin Hu, Fenfen Wang, Peilin Chen & Meiling Zhao

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  1. Yanmin Hu
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Contributions

Y.H. and X.P. performed the research, collected genetic and phenotypic data, analyzed the data, and drafted the manuscript. F.W., M.Z. and P.C. contributed to the acquisition of the climate and common garden data. S.S. conceived and designed the experiments. S.S. and X.P. provided funding. All authors approved the final manuscript.

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Correspondence to Shihua Shen.

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Hu, Y., Peng, X., Wang, F. et al. Natural population re-sequencing detects the genetic basis of local adaptation to low temperature in a woody plant. Plant Mol Biol 105, 585–599 (2021). https://doi.org/10.1007/s11103-020-01111-x

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