Genetic diversity and structure of Rhododendron meddianum, a plant species with extremely small populations

doi:10.1016/j.pld.2021.05.005

Plant Diversity ›› 2021, Vol. 43 ›› Issue (06): 472-479.DOI: 10.1016/j.pld.2021.05.005

• Articles • Previous Articles Next Articles

Genetic diversity and structure of Rhododendron meddianum, a plant species with extremely small populations

Xiu-Jiao Zhang^a,b,d, Xiong-Fang Liu^a, De-Tuan Liu^c, Yu-Rong Cao^a,b, Zheng-Hong Li^a, Yong-Peng Ma^c, Hong Ma^a

a Research Institute of Resources Insects, Chinese Academy of Forestry, Kunming, 650224, Yunnan, China;
b College of Forestry, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China;
c Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China;
d Yunnan Key Laboratory of Plant Reproductive Adaption and Evolutionary Ecology, School of Ecology and Environmental Science, Yunnan University, Kunming 650504, Yunnan, China

Received:2020-12-15 Revised:2021-05-25 Online:2022-01-11 Published:2021-12-25
Contact: Yong-Peng Ma, Hong Ma
Supported by:
This work was supported by the Fundamental Research Funds for the Central Non-profit Research Institution of the Chinese Academy of Forestry (Grant No. CAFYBB2019ZB007); the Biodiversity Survey and Assessment Project of the Ministry of Ecology and Environment, China (Grant No. 2019HJ2096001006); the Ten Thousand Talent Program of Yunnan Province (Grant No. YNWRQNBJ-2019-010; YNWR-QNBJ-2018-174); and the Young and Middle-aged Academic and Technical Leader Reserve Talent Project of Yunnan Province (Grant No. 2018HB066).

Genetic diversity and structure of Rhododendron meddianum, a plant species with extremely small populations

Xiu-Jiao Zhang^a,b,d, Xiong-Fang Liu^a, De-Tuan Liu^c, Yu-Rong Cao^a,b, Zheng-Hong Li^a, Yong-Peng Ma^c, Hong Ma^a

a Research Institute of Resources Insects, Chinese Academy of Forestry, Kunming, 650224, Yunnan, China;
b College of Forestry, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China;
c Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China;
d Yunnan Key Laboratory of Plant Reproductive Adaption and Evolutionary Ecology, School of Ecology and Environmental Science, Yunnan University, Kunming 650504, Yunnan, China

通讯作者: Yong-Peng Ma, Hong Ma
基金资助:
This work was supported by the Fundamental Research Funds for the Central Non-profit Research Institution of the Chinese Academy of Forestry (Grant No. CAFYBB2019ZB007); the Biodiversity Survey and Assessment Project of the Ministry of Ecology and Environment, China (Grant No. 2019HJ2096001006); the Ten Thousand Talent Program of Yunnan Province (Grant No. YNWRQNBJ-2019-010; YNWR-QNBJ-2018-174); and the Young and Middle-aged Academic and Technical Leader Reserve Talent Project of Yunnan Province (Grant No. 2018HB066).

Abstract

Abstract: Rhododendron meddianum is a critically endangered species with important ornamental value and is also a plant species with extremely small populations. In this study, we used double digest restriction-siteassociated DNA sequencing (ddRAD) technology to assess the genetic diversity, genetic structure and demographic history of the three extant populations of R. meddianum. Analysis of SNPs indicated that R. meddianum populations have a high genetic diversity (π=0.0772 ±0.0024, H_E=0.0742 ±0.002). Both F_ST values (0.1582-0.2388) and AMOVA showed a moderate genetic differentiation among the R. meddianum populations. Meanwhile, STRUCTURE, PCoA and NJ trees indicated that the R. meddianum samples were clustered into three distinct genetic groups. Using the stairway plot, we found that R. meddianum underwent a population bottleneck about 70,000 years ago. Furthermore, demographic models of R. meddianum and its relative, Rhododendron cyanocarpum, revealed that these species diverged about 3.05 (2.21-5.03) million years ago. This divergence may have been caused by environmental changes that occurred after the late Pliocene, e.g., the Asian winter monsoon intensified, leading to a drier climate. Based on these findings, we recommend that R. meddianum be conserved through in situ, ex situ approaches and that its seeds be collected for germplasm.

Key words: Rhododendron meddianum, ddRAD, Genetic diversity, Population demography, Conservation implications

摘要： Rhododendron meddianum is a critically endangered species with important ornamental value and is also a plant species with extremely small populations. In this study, we used double digest restriction-siteassociated DNA sequencing (ddRAD) technology to assess the genetic diversity, genetic structure and demographic history of the three extant populations of R. meddianum. Analysis of SNPs indicated that R. meddianum populations have a high genetic diversity (π=0.0772 ±0.0024, H_E=0.0742 ±0.002). Both F_ST values (0.1582-0.2388) and AMOVA showed a moderate genetic differentiation among the R. meddianum populations. Meanwhile, STRUCTURE, PCoA and NJ trees indicated that the R. meddianum samples were clustered into three distinct genetic groups. Using the stairway plot, we found that R. meddianum underwent a population bottleneck about 70,000 years ago. Furthermore, demographic models of R. meddianum and its relative, Rhododendron cyanocarpum, revealed that these species diverged about 3.05 (2.21-5.03) million years ago. This divergence may have been caused by environmental changes that occurred after the late Pliocene, e.g., the Asian winter monsoon intensified, leading to a drier climate. Based on these findings, we recommend that R. meddianum be conserved through in situ, ex situ approaches and that its seeds be collected for germplasm.

关键词: Rhododendron meddianum, ddRAD, Genetic diversity, Population demography, Conservation implications

Xiu-Jiao Zhang, Xiong-Fang Liu, De-Tuan Liu, Yu-Rong Cao, Zheng-Hong Li, Yong-Peng Ma, Hong Ma. Genetic diversity and structure of Rhododendron meddianum, a plant species with extremely small populations[J]. Plant Diversity, 2021, 43(06): 472-479.

References

Amor, M.D., Johnson, J.C., James, E.A., 2020. Identification of clonemates and genetic lineages using next-generation sequencing (ddRADseq) guides conservation of a rare species, Bossiaea vombata (Fabaceae). Perspect. Plant Ecol. Evol. Systemat. 45, 125544.
Catchen, J., Hohenlohe, P.A., Bassham, S., et al., 2013. Stacks: an analysis tool set for population genomics. Mol. Ecol. 22, 3124-3140.
Catchen, J.M., Amores, A., Hohenlohe, P., et al., 2011. Stacks: building and genotyping Loci de novo from short-read sequences. G3-Genes Genome. Genet. 1, 171-182.
Cronk, Q., 1995. Images of nature. Nature 376, 652-653.
Cross, J.R., 1975. Biological flora of the British isles. Rhododendron ponticum L. J. Ecol. 63, 345-364.
Danecek, P., Auton, A., Abecasis, G., et al., 2011. The variant call format and VCFtools. Bioinformatics 27, 2156-2158.
Deschamps, S., Llaca, V., May, G.D., 2012. Genotyping-by-sequencing in plants. Biology 1, 460-483.
Doyle, J., Doyle, J., 1987. A rapid DNA isolation procedure from small quantities of fresh leaf tissues. Phytochem. Bull. 19, 11-15.
Evanno, G., Regnaut, S., Goudet, J., 2005. Detecting the number of clusters of individuals using the software structure: a simulation study. Mol. Ecol. 14, 2611-2620.
Everaert, H., De Wever, J., Tang, T.K.H., et al., 2020. Genetic classification of Vietnamese cacao cultivars assessed by SNP and SSR markers. Tree Genet. Genomes 16, 43.
Excoffier, L., Dupanloup, I., Huerta-Sánchez, E., et al., 2013. Robust demographic inference from genomic and SNP data. PLoS Genet. 9, e1003905.
Excoffier, L., Laval, G., Schneider, S., 2007. Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evol. Bioinf. Online 1, 47-50.
Falush, D., Stephens, M., Pritchard, J.K., 2003. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164, 1567-1587.
Fang, M.Y., Fang, R.C., He, M.Y., et al., 2005. Rhododendron Linnaeus. In: Wu, Z.Y., Raven, P., Hong, D.Y. (Eds.), Flora of China, vol. 14. Science Press, Bejing. China and Missouri Botanical Garden Press, St. Louis Missouri USA, pp. 260-455.
Feng, X.Y., Wang, Y.H., Gong, X., 2014. Genetic diversity, genetic structure and demographic history of Cycas simplicipinna (Cycadaceae) assessed by DNA sequences and SSR markers. BMC Plant Biol. 14, 187.
Foll, M., Gaggiotti, O., 2008. A genome-scan method to identify selected loci appropriate for both dominant and codominant markers: a bayesian perspective. Genetics 180, 977-993.
Gibbs, D., Chamberlain, D., Argent, G., 2011. The red list of rhododendrons. Botanic Gardens Conservation International, Richmond, UK, p. 57.
Godt, M.J.W., Walker, J., Hamrick, J.L., 1997. Genetic diversity in the endangered lily Harperocallis flava and a close relative, Tofieldia racemosa. Conserv. Biol. 11, 361-366.
Goetsch, L., Eckert, A.J., Hall, B.D., 2005. The molecular systematics of Rhododendron(Ericaceae): a phylogeny based upon RPB2 gene sequences. Syst. Bot. 30, 616-626.
Groom, M.J., Chyi, Y.S., Carroll, C.R., 2006. Principles of Conservation Biology. Sinauer, Sunderland, MA.
Hamrick, J.L., Godt, M.J.W., 1990. Plant Population Genetics, Breeding and Genetic Resources. Sinauer, Sunderland, MA.
Huang, C.L., Chen, J.H., Chang, C.T., et al., 2016. Disentangling the effects of isolationby-distance and isolation-by-environment on genetic differentiation among Rhododendron lineages in the subgenus Tsutsusi. Tree Genet. Genomes 12, 1-22.
Huang, Z.H., Song, Y.P., Huang, S.Q., 2017. Evidence for passerine bird pollination in Rhododendron species. AoB Plants 9, x62.
Jiang, X.L., Gardner, E.M., Meng, H.H., et al., 2019. Land bridges in the Pleistocene contributed to flora assembly on the continental islands of South China: insights from the evolutionary history of Quercus championii. Mol. Phylogenet. Evol. 132, 36-45.
Kaeuffer, R., Réale, D., Coltman, D.W., et al., 2007. Detecting population structure using STRUCTURE software: effect of background linkage disequilibrium. Heredity 99, 374-380.
Kumar, S., Stecher, G., Li, M., et al., 2018. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 35, 1547-1549.
Lee, K.M., Ranta, P., Saarikivi, J., et al., 2020. Using genomic information for management planning of an endangered perennial, Viola uliginosa. Ecol. Evol. 10, 2638-2649.
Li, M.W., Chen, S.F., Shi, S., et al., 2015. High genetic diversity and weak population structure of Rhododendron jinggangshanicum, a threatened endemic species in Mount Jinggangshan of China. Biochem. Systemat. Ecol. 58, 178-186.
Li, T.Q., Liu, X.F., Li, Z.H., et al., 2018. Study on reproductive biology of Rhododendron longipedicellatum: a newly discovered and special threatened plant surviving in limestone habitat in Southeast Yunnan, China. Front. Plant Sci. 9, 33.
Lischer, H.E.L., Excoffier, L., 2012. PGDSpider: an automated data conversion tool for connecting population genetics and genomics programs. Bioinformatics 28, 298-299.
Liu, D.T., Zhang, L., Wang, J.H., et al., 2020a. Conservation genomics of a threatened Rhododendron: contrasting patterns of population structure revealed from neutral and selected SNPs. Front. Genet. 11, 757.
Liu, X.F., Ma, Y.P., Wan, Y.M., et al., 2020b. Genetic diversity of Phyllanthus emblica from two different climate type areas. Front. Plant Sci. 11, 580812.
Liu, X.M., Fu, Y.X., 2015. Exploring population size changes using SNP frequency spectra. Nat. Genet. 47, 555-559.
Ma, Y.P., Wu, Z.K., Dong, K., et al., 2015. Pollination biology of Rhododendron cyanocarpum (Ericaceae): an alpine species endemic to NW Yunnan, China. J. Systemat. Evol. 53, 63-71.
Meffe, G.K., Carroll, C.R., 1997. Principles of Conservation Biology. Sinauer, Sunderland, MA.
Milne, R.I., 2004. Phylogeny and biogeography of Rhododendron subsection Pontica, a group with a Tertiary relict distribution. Mol. Phylogenet. Evol. 33, 389-401.
Morimoto, J., Shibata, S., Hasegawa, S., 2003. Habitat requirement of Rhododendron reticulatum and Rhododendron macrosepalum in germination and seedling stages-filed experiment for restoration of native Rhododendron by seedling. J. Jpn. Soc. Reveg. Technol. 29, 15-140.
Ng, S., Corlett, R.T., 2000. Comparative reproductive biology of the six species of Rhododendron (Ericaceae) in Hong Kong, South China. Can. J. Bot. 78, 221-229.
Nybom, H., 2004. Comparison of different nuclear DNA markers for estimating intraspecific genetic diversity in plants. Mol. Ecol. 13, 1143-1155.
Peterson, B.K., Weber, J.N., Kay, E.H., et al., 2012. Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and nonmodel species. PLoS One 7, e37135.
Pritchard, J.K., Stephens, M., Donnelly, P., 2000. Inference of population structure using multilocus genotype data. Genetics 155, 945-959.
Purcell, S., Neale, B., Todd-Brown, K., et al., 2007. Plink: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559-575.
Qin, H.N., Yang, Y., Dong, S.Y., 2017. Threatened species list of China's higher plants. Biodivers. Sci. 25, 696-744.
Qin, H.T., 2017. Population Genomics of Natural Hybrid Species of Taxus in Hengduan Mountains Region. University of Chinese Academy of Sciences.
R Core Team, 2016. R: a Language and Environment for Statistical Computing. Available from:. R foundation for statistical computing, Vienna, Austria https://www.R-project.org/.
Roy, S.C., Moitra, K., De Sarker, D., 2016. Assessment of genetic diversity among four orchids based on ddRAD sequencing data for conservation purposes. Physiol. Mol. Biol. Plants 23, 169-183.
Setoguchi, H., Mitsui, Y., Ikeda, H., et al., 2011. Genetic structure of the critically endangered plant Tricyrtis ishiiana (Convallariaceae) in relict populations of Japan. Conserv. Genet. 12, 491-501.
Spicer, R.A., Farnsworth, A., Su, T., 2020. Cenozoic topography, monsoons and biodiversity conservation within the Tibetan region: An evolving story. Plant Divers. 42, 229-254.
Stone, B.W., Ward, A., Farenwald, M., et al., 2019. Genetic diversity and population structure in Cary's Beardtongue Penstemon caryi (Plantaginaceae), a rare plant endemic to the eastern Rocky Mountains of Wyoming and Montana. Conserv. Genet. 20, 1149-1161.
Su, T., Jacques, F., Spicer, R.A., et al., 2013a. Post-Pliocene establishment of the present monsoonal climate in SW China: evidence from the late Pliocene Longmen megaflora. Clim. Past 9, 1911-1920.
Su, T., Liu, Y.S., Jacques, F., et al., 2013b. The intensification of the East Asian winter monsoon contributed to the disappearance of Cedrus (Pinaceae) in southwestern China. Quat. Res. (Tokyo) 80, 316-325.
Tajima, F., 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123, 585-595.
Wagutu, G.K., Fan, X., Njeri, H.K., et al., 2020. Development and characterization of EST-SSR markers for the endangered tree Magnolia patungensis (Magnoliaceae). Ann. Bot. Fenn. 57, 97-107.
Wang, B., 2006. The Asian Monsoon. Springer Praxis Books, Springer, Berlin, Heidelberg.
Wright, S., 1922. Coefficients of inbreeding and relationship. Am. Nat. 56, 330-338.
Wu, F.Q., Shen, S.K., Zhang, X., et al., 2017. Inferences of genetic structure and demographic history of Rhododendron protistum var. giganteum-The world's largest Rhododendron using microsatellite markers. Flora 233, 1-6.
Wu, F.Q., Shen, S.K., Zhang, X.J., et al., 2015. Genetic diversity and population structure of an extremely endangered species: the world's largest Rhododendron. AoB Plants 7, plu082.
Xiao, J.H., Ding, X., Li, L., et al., 2020. Miocene diversification of a golden-thread nanmu tree species (Phoebe zhennan, Lauraceae) around the Sichuan Basin shaped by the East Asian monsoon. Ecol. Evol. 10, 10543-10557.
Yamashita, H., Katai, H., Kawaguchi, L., et al., 2019. Analyses of single nucleotide polymorphisms identified by ddRAD-seq reveal genetic structure of tea germplasm and Japanese landraces for tea breeding. PLoS One 14, e220981.
Yilmaz, A., 2016. Analysis of genetic variation among some Turkish oaks using random amplified polymorphic DNA (RAPD) method. Afr. J. Biotechnol. 231, 17-18.
Yoichi, W., Tamaki, I., Sakaguchi, S., et al., 2016. Population demographic history of a temperate shrub, Rhododendron weyrichii (Ericaceae), on continental islands of Japan and South Korea. Ecol. Evol. 6, 8800-8810.
Zhang, X., Liu, Y.H., Wang, Y.H., et al., 2020. Genetic diversity and population structure of Rhododendron rex subsp. rex inferred from microsatellite markers and chloroplast DNA sequences. Plants 9, 338.

[1]	Mustaqeem Ahmad, Ya-Huang Luo (罗亚皇), Sonia Rathee, Robert A. Spicer, Jian Zhang (张健), Moses C. Wambulwa, Guang-Fu Zhu (朱光福), Marc W. Cadotte, Zeng-Yuan Wu (吴增源), Shujaul Mulk Khan, Debabrata Maity, De-Zhu Li (李德铢), Jie Liu (刘杰). Multifaceted plant diversity patterns across the Himalaya: Status and outlook [J]. Plant Diversity, 2025, 47(04): 529-543.
[2]	Jianchao Liang, Zhifeng Ding, Ganwen Lie, Zhixin Zhou, Zhixiang Zhang, Huijian Hu. Climate-driven environmental filtering determines hump-shaped elevational pattern of seed plant beta diversity in the central Himalayas [J]. Plant Diversity, 2025, 47(02): 264-272.
[3]	Hong Qian, Oriol Grau. Geographic patterns and ecological causes of phylogenetic structure in mosses along an elevational gradient in the central Himalaya [J]. Plant Diversity, 2025, 47(01): 98-105.
[4]	Zhiliang Yao, Xia Pan, Xin Yang, Xiaona Shao, Bin Wang, Yun Deng, Zhiming Zhang, Qiaoming Li, Luxiang Lin. Canopy structural heterogeneity drives α and β species-genetic diversity correlations in a Chinese subtropical forest [J]. Plant Diversity, 2025, 47(01): 106-114.
[5]	Linjiang Ye, Robabeh Shahi Shavvon, Hailing Qi, Hongyu Wu, Pengzhen Fan, Mohammad Nasir Shalizi, Safiullah Khurram, Mamadzhanov Davletbek, Yerlan Turuspekov, Jie Liu. Population genetic insights into the conservation of common walnut (Juglans regia) in Central Asia [J]. Plant Diversity, 2024, 46(05): 600-610.
[6]	Yixian Li, Xuyao Zhao, Manli Xia, Xinzeng Wei, Hongwei Hou. Temperature is a cryptic factor shaping the geographical pattern of genetic variation in Ceratophyllum demersum across a subtropical freshwater lake [J]. Plant Diversity, 2024, 46(05): 630-639.
[7]	Miao-Miao Li, Muditha K. Meegahakumbura, Moses C. Wambulwa, Kevin S. Burgess, Michael Möller, Zong-Fang Shen, De-Zhu Li, Lian-Ming Gao. Genetic analyses of ancient tea trees provide insights into the breeding history and dissemination of Chinese Assam tea (Camellia sinensis var. assamica) [J]. Plant Diversity, 2024, 46(02): 229-237.
[8]	Hong Qian, Jian Zhang, Meichen Jiang. Global patterns of taxonomic and phylogenetic diversity of flowering plants:Biodiversity hotspots and coldspots [J]. Plant Diversity, 2023, 45(03): 265-271.
[9]	Jing-Xia Liu, Zu-Chang Xu, Yu-Xiao Zhang, Meng-Yuan Zhou, De-Zhu Li. The identity of Dinochloa species and enumeration of Melocalamus (Poaceae: Bambusoideae) in China [J]. Plant Diversity, 2023, 45(02): 133-146.
[10]	Han-Yang Lin, Miao Sun, Ya-Jun Hao, Daijiang Li, Matthew A. Gitzendanner, Cheng-Xin Fu, Douglas E. Soltis, Pamela S. Soltis, Yun-Peng Zhao. Phylogenetic diversity of eastern Asia-eastern North America disjunct plants is mainly associated with divergence time [J]. Plant Diversity, 2023, 45(01): 27-35.
[11]	Moses C. Wambulwa, Peng-Zhen Fan, Richard Milne, Zeng-Yuan Wu, Ya-Huang Luo, Yue-Hua Wang, Hong Wang, Lian-Ming Gao, Zuo-Ying Xiahou, Ye-Chuan Jin, Lin-Jiang Ye, Zu-Chang Xu, Zhi-Chun Yang, De-Zhu Li, Jie Liu. Genetic analysis of walnut cultivars from southwest China: Implications for germplasm improvement [J]. Plant Diversity, 2022, 44(06): 530-541.
[12]	Xiaxia Li, Lijun Qiao, Birong Chen, Yujie Zheng, Chengchen Zhi, Siyu Zhang, Yupeng Pan, Zhihui Cheng. SSR markers development and their application in genetic diversity evaluation of garlic (Allium sativum) germplasm [J]. Plant Diversity, 2022, 44(05): 481-491.
[13]	Ya-Zhou Zhang, Li-Shen Qian, Xu-Fang Chen, Lu Sun, Hang Sun, Jian-Guo Chen. Diversity patterns of cushion plants on the Qinghai-Tibet Plateau: A basic study for future conservation efforts on alpine ecosystems [J]. Plant Diversity, 2022, 44(03): 231-242.
[14]	Qiao-Ming Li, Chao-Nan Cai, Wu-Mei Xu, Min Cao, Li-Qing Sha, Lu-Xiang Lin, Tian-Hua He. Adaptive genetic diversity of dominant species contributes to species co-existence and community assembly [J]. Plant Diversity, 2022, 44(03): 271-278.
[15]	Changkyun Kim, Dong-Kap Kim, Hang Sun, Joo-Hwan Kim. Phylogenetic relationship, biogeography, and conservation genetics of endangered Fraxinus chiisanensis (Oleaceae), endemic to South Korea [J]. Plant Diversity, 2022, 44(02): 170-180.

Genetic diversity and structure of Rhododendron meddianum, a plant species with extremely small populations

Genetic diversity and structure of Rhododendron meddianum, a plant species with extremely small populations

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

References

Related Articles 15

Recommended Articles

Metrics

Comments