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Whole genome re-sequencing reveals the genetic diversity and evolutionary patterns of Eucommia ulmoides

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Abstract

Eucommia ulmoides (E. ulmoides) is a deciduous perennial tree belonging to the order Garryales, and is known as “living fossil” plant, along with ginkgo (Ginkgo biloba), metaspaca (Metasequoia glyptostroboides) and dove tree (Davidia involucrata Baill). However, the genetic diversity and population structure of E. ulmoides are still  ambiguous nowdays. In this study, we re-sequenced the genomes of 12 E. ulmoides accessions from different major climatic geography regions in China to elucidate the genetic diversity, population structure and evolutionary pattern. By integration of phylogenetic analysis, principal component analysis and population structure analysis based on a number of high-quality SNPs, a total of 12 E. ulmoides accessions were clustered into four different groups. This result is consistent with their geographical location except for group samples from Shanghai and Hunan province. E. ulmoides accessions from Hunan province exhibited a closer genetic relationship with E. ulmoides accessions from Shanghai in China compared with other regions, which is also supported by the result of population structure analyses. Genetic diversity analysis further revealed that E. ulmoides samples in Shanghai and Hunan province were with higher genetic diversity than those in other regions in this study. In addition, we treated the E. ulmoides materials from Shanghai and Hunan province as group A, and the other materials from other places as group B, and then analyzed the evolutionary pattern of E. ulmoides. The result showed the significant differentiation (Fst = 0.1545) between group A and group B. Some candidate highly divergent genome regions were identified in group A by selective sweep analyses, and the function analysis of candidate genes in these regions showed that biological regulation processes could be correlated with the Eu-rubber biosynthesis. Notably, nine genes were identified from selective sweep regions. They were involved in the Eu-rubber biosynthesis and expressed in rubber containing tissues. The genetic diversity research and evolution model of E. ulmoides were preliminarily explored in this study, which laid the foundation for the protection of germplasm resources and the development and utilization of multipurpose germplasm resources in the future.

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source population. (C) Principal component (PC) analysis, PC 1 against PC 2 and PC 3

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Acknowledgements

The authors sincerely thank the Research Institute of Non-timber Forestry, Chinese Academy of Forestry and Key Laboratory of Non-timber Forest Germplasm Enhancement & Utilization of State Forestry and Grassland Administration for the material, laboratory and data analysis guidance.

Funding

This work was financially supported by the Demonstration of Key Technologies and Industrial Applications of Eucommia Rubber (2019JZZY020223).

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Author notes

  1. Jun Qing and Yi-De Meng contributed equally.

Authors and Affiliations

  1. Research Institute of Non-Timber Forestry, Chinese Academy of Forestry (CAF), Zhengzhou, 450003, China

    Jun Qing, Yi-De Meng, Feng He, Qing-Xin Du, Jian Zhong, Hong-Yan Du, Pan-Feng Liu, Lan-Ying Du & Lu Wang

  2. Key Laboratory of Non-Timber Forest Germplasm Enhancement and Utilization of State Forestry and Grassland Administration, Zhengzhou, 450003, China

    Jun Qing, Yi-De Meng, Feng He, Qing-Xin Du, Jian Zhong, Hong-Yan Du, Pan-Feng Liu, Lan-Ying Du & Lu Wang

  3. Non-Timber Forest R&D Center, Chinese Academy of Forestry, Zhengzhou, 450003, China

    Jun Qing, Yi-De Meng, Feng He, Qing-Xin Du, Jian Zhong, Hong-Yan Du, Pan-Feng Liu, Lan-Ying Du & Lu Wang

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  1. Jun Qing
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Qing, J., Meng, YD., He, F. et al. Whole genome re-sequencing reveals the genetic diversity and evolutionary patterns of Eucommia ulmoides. Mol Genet Genomics 297, 485–494 (2022). https://doi.org/10.1007/s00438-022-01864-8

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