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Development of EST-SSR markers and their application in an analysis of the genetic diversity of the endangered species Magnolia sinostellata

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Abstract

Magnolia sinostellata is an endemic species of Magnoliaceae that is narrowly distributed in the south of Zhejiang Province, China. To explore the genetic diversity and population structure of this endangered species, this study developed sequence tag-simple sequence repeat (EST-SSR) markers based on transcriptome data of M. sinostellata. In total, 25472 SSRs were identified among 110644 unique assembled sequences with a total of 90.83 Mb and an average frequency of 23.02%. The mononucleotide (33.53%) and dinucleotide (42.08%) motifs appeared to be the most abundant. In total, 150 potential loci were randomly selected to validate the quality of the developed SSR markers; an effective PCR rate of 32.00% and a polymorphism rate of 15.33% were obtained for these loci. After performing sequencing and cloning for validation, 23 pairs of SSR primers were retained and used to characterize the genetic diversity and population structure of M. sinostellata. Overall, 204 alleles were amplified. The results of Shannon’s information index (I), heterozygosity (Ho), heterozygosity (He) and Nei’s expected heterozygosity (H) indicated rich genetic diversity in M. sinostellata. However, the high inbreeding coefficient and differential coefficient suggest that serious genetic drift occurred within populations, and genetic differentiation is apparent among the populations. Consequently, although M. sinostellata has high genetic diversity among populations, it is still in a serious and dangerous condition. Habitat destruction caused by human activities is the main threat to this species, and enhancing the species abundance by adopting some conservation measures should be favourable for saving the species.

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Acknowledgements

We thank Prof. Yanru Zeng from Zhejiang A & F University for her modification of the text. We thank Caoyutang in Jingning County, Wenzhou Forestry Bureau and Mr. Junfeng Wang from Lishui Academic of Forestry for their help with the sample plot survey. We also thank Pengjie Chang, Sainan and Ninghang Wang for preparing the samples.

Funding

This work was supported by the National Natural Science Foundation of China [31400599]; the 13th Five-Year-Plan for Floriculture Special Breeding of Zhejiang Province, China [2016C02056-12]; and the Public Welfare Forestry Industry Project of State Forestry Administration, China [201504322].

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Authors and Affiliations

  1. School of Landscape and Architecture, Zhejiang A&F University, 666# Wusu Road, Lin’an, 311300, Zhejiang, China

    Xingli Wang, Qin Yu, Zhigao Liu, Mingru Zhang & Yamei Shen

  2. Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, 666# Wusu Road, Lin’an, 311300, Zhejiang, China

    Wenchong Chen & Jia Luo

  3. Shenzhen Fairy Lake Botanical Garden, 160# Xianhu Road, Shenzhen, 518004, Guangdong, China

    Zhangxiu Yao & Shouzhou Zhang

  4. Xi’an Botanical Garden of Shaanxi Academy of Science, 17# Cuihua South Road, Xi’an, 710061, Shaanxi, China

    Yaling Wang

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  1. Xingli Wang
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  3. Jia Luo
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Contributions

XW and YS were the equal chief scientists in this study, designed the experiments, conducted statistical analysis, and wrote the manuscript; WC, JL, ZY and QY, the major participants in this study, were responsible for data collection; YW, SZ, ZL and MZ, the major participants in this study, were responsible for manuscript revision and language improvement.

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Correspondence to Yamei Shen.

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This article does not contain any studies involving human participants or animals performed by any of the authors.

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Informed consent was obtained from all individual participants included in the study.

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Communicated by S. Hohmann.

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Wang, X., Chen, W., Luo, J. et al. Development of EST-SSR markers and their application in an analysis of the genetic diversity of the endangered species Magnolia sinostellata. Mol Genet Genomics 294, 135–147 (2019). https://doi.org/10.1007/s00438-018-1493-7

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