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Genetic diversity of Rhododendron delavayi var. delavayi (C. B. Clarke) Ridley inferred from nuclear and chloroplast DNA: implications for the conservation of fragmented populations

Plant Systematics and Evolution volume 300, pages 1853–1866 (2014)Cite this article

Abstract

Rhododendron delavayi Franch. is an ecologically and horticulturally important tree species distributed in a global biodiversity hotspot in southwest China, an area with high level of human-induced habitat degradation and fragmentation. In an attempt to explore the level of genetic diversity and population differentiation in the remnant populations of R. delavayi var. delavayi (C. B. Clarke) Ridley, we assessed patterns of chloroplast (trnS-trnG and trnL-trnF) and nuclear (RPB2-i) DNA variation in 327 individuals representing 17 natural populations from southwest China. Analyses revealed two phylogeographic groups, with similar circumscription between the two markers. We found moderate levels of genetic differentiation (cpDNA: N ST = 0.125; G ST = 0.114 and nuclear DNA: N ST = 0.261; G ST = 0.152). Both genomes demonstrate significant correlation between genetic and geographic distances (cpDNA: r 2 = 0.248, p = 0.001 and nuclear DNA: r 2 = 0.250, p = 0.001). The genetic diversity was positively associated with an increase in longitude. Populations from the eastern region of the Yungui plateau, representing potential refugial area for R. delavayi var. delavayi, registered higher haplotype diversity and allelic richness. The mismatch distribution analysis rejected rapid population expansion. The overall population expansion time for R. delavayi var. delavayi was estimated to be 0.208–0.624 mya. The complex landscape of southwest China and the human-induced fragmentation of the natural habitat have led to significant pairwise population differentiation and moderate genetic diversity (cpDNA: 0.626 and nuclear DNA: 0.506) and haplotypic richness (cpDNA: 4.01 and nuclear DNA: 2.589) in R. delavayi var. delavayi. Based on these findings, we recommend strategies for the conservation and sustainable management of R. delavayi var. delavayi.

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Acknowledgments

We are thankful to the local people who helped us in finding Rhododendron populations. We are grateful to Hang Sun, Lianming Gao and Hongguang Zha for their guidance and support. We thank Zhonglang Wang, Yuanxue Lu, Nan Jiang, Rongquan Ren, Shuang Wang, Xiaojian Hu, Xinya Huang, for their help in plant collection. First author is also grateful to Anamika Sharma, Peter E Mortimer, Yongpeng Ma, Xiaolin Sui, Yunfeng Xie, Yan Chen, M.K. Meegahakumbura, Md. Iqbal Hosen, Sailesh Ranjitkar, and Rajdeep Bomjan for their help in improving this paper. We would like to thank two anonymous reviewers for their constructive comments. This study was supported by (1) Main direction program of knowledge innovation of Chinese Academy of Sciences, grant no. KSCX2- YW-Z1019. (2) Financial support for the first author was granted from the Key laboratory of biodiversity and biogeography, Kunming institute of botany, Chinese academy of sciences.

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Authors and Affiliations

  1. Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, 650201, China

    Anup Sharma, Airong Li, Jianchu Xu & Kaiyun Guan

  2. Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650204, China

    Anup Sharma, Airong Li, Jianchu Xu & Kaiyun Guan

  3. Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Xinjiang, 830011, China

    Kaiyun Guan

  4. Key Laboratory of Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650204, China

    Anup Sharma, Ram Chandra Poudel & Jianchu Xu

  5. Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 830011, China

    Ram Chandra Poudel

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  1. Anup Sharma
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Correspondence to Kaiyun Guan.

Electronic supplementary material

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606_2014_1012_MOESM1_ESM.doc

Chloroplast haplotype diversity for 27 woody plant species including Rhododendron delavayi var. delavayi. Tree species found in southwest China are shown in blue bars. (DOC 76 kb)

Supplementary material 2 (DOC 46 kb)

606_2014_1012_MOESM3_ESM.doc

The contribution to the total haplotype diversity (CT) and haplotypic richness of the 17 populations of Rhododendron delavayi var. delavayi using nuclear marker. The grey and white bars represent the contribution of diversity (CS and CSR) and differentiation (CD and CDR), respectively. (DOC 46 kb)

606_2014_1012_MOESM4_ESM.doc

The contribution to the total haplotype diversity (CT) and haplotypic richness of the 17 populations of Rhododendron delavayi var. delavayi using chloroplast markers. The grey and white bars represent the contribution of diversity (CS and CSR) and differentiation (CD and CDR), respectively. (DOC 46 kb)

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Sharma, A., Poudel, R.C., Li, A. et al. Genetic diversity of Rhododendron delavayi var. delavayi (C. B. Clarke) Ridley inferred from nuclear and chloroplast DNA: implications for the conservation of fragmented populations. Plant Syst Evol 300, 1853–1866 (2014). https://doi.org/10.1007/s00606-014-1012-1

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Keywords

  • Rhododendron delavayi var. delavayi
  • Genetic diversity
  • Habitat fragmentation
  • Yungui plateau
  • Chloroplast and nuclear DNA
  • Conservation

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