Research Paper

Genetic diversity, population genetic structure and conservation strategies for Pleione formosana (Orchideace)

Wei-Chun Chao, Yea-Chen Liu, Ming-Tao Jiang, Sha-Sha Wu, Chun-Li Fang, Jia-Fang Ho, Chun-Lin Huang

Published on: 03 January 2021

Page: 20 - 30

DOI: 10.6165/tai.2021.66.20

  • BibTeX
    •
  • EndNote
    •
  • RIS
    •

    Abstract

    A population genomic approach was employed to investigate the diversity within species to create a more robust, lineage-specific conservation strategy for an endangered orchid. Pleione formosana is a species native to southeastern China and Taiwan, where it is distributed at an altitude range of 1,200–2,500 m the foggy mountain area and grows in mosses on half-shaded rocks or tree trunks. To identify whether the level of genetic diversity in the species, we used genotyping by sequencing (GBS) to analysis the sub-populations of the species. Fifty-eight individuals of P. formosana were sampled from a total of nine populations within continental island Taiwan and three populations in China as outgroup. Treatment of all samples involved five major steps: sample preparation, library assembly, sequencing, SNP calling and diversity analysis. GBS markers confirmed the China outgroup as distinct, and provided resolution of two clusters of population genetic structure in Taiwan. Outliers provide higher genetic differentiation, and some GBS tags associated with climatic factor were found. Genomic diversity identified among the three clusters suggests that conservation of this species will be best served by considering them as three evolutionary significant units (ESUs). This approach will maximize evolutionary potential among all species during increased isolation and environmental change. According to the genetic consequences, restoration strategies should be carried out in all populations to preserve genetic diversity and evolutionary potential for different environmental factors.

    Keyword: Genotyping by sequencing (GBS), next-generation sequencing, Orchidaceae, Pleione formosana, population genomics

    Literature Cited

    Bothwell, H., S. Bisbing, N.O. Therkildsen, L. Crawford, N. Alvarez, R. Holderegger and S. Manel. 2013. Identifying genetic signatures of selection in a non-model species, alpine gentian (Gentiana nivalis L.), using a landscape genetic approach. Conserv. Genet. 14(2): 467–481.
    DOI: 10.1007/s10592-012-0411-5View Article Google Scholar

    Chao, W.-C., C.-L. Huang, Y.-C. Liu. 2017. The genetic diversity analysis and population dynamic changes project of Pleione formosana in Taiwan Pleione Nature Reserve, Chiayi Forest District Management Office, Forestry Bureau, Concil of Agriculture, Executive Yuan, Taiwan.

    Chen, J.-L., Y.-Z. Zhou, S.-S. Wu, S.-R. Lan and D.-H. Peng. 2019. Pollination mechanism and breeding system of Pleione formosana. Journal of Forest and Environment 39: 460–466.

    Cribb, P., and I. Butterfield. 1999. The Genus Pleione, 2nd ed. Richmond: Royal Botanic Gardens, Kew.

    Dobson, A.J. and A.G. Barnett. 2008. An introduction to generalized linear models, 3rd ed. Chapman and Hall/CRC, London, UK.

    Doyle, J.J. and J.L. Doyle. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin 19: 11–15.

    Edmands, S. and C.C. Timmerman. 2003. Modeling factors affecting the severity of outbreeding depression. Conserv. Biol. 17(3): 883–892.
    DOI: 10.1046/j.1523-1739.2003.02026.xView Article Google Scholar

    Elshire, R.J., J.C. Glaubitz, Q. Sun, J.A. Poland, K. Kawamoto, E.S. Buckler and S.E. Mitchell. 2011. A robust, simple genotyping by sequencing (GBS) approach for high diversity species. PLoS One 6(5): e19379.
    DOI: 10.1371/journal.pone.0019379View Article Google Scholar

    Evanno, G., S. Regnaut and J. Goudet. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol. Ecol. 14(8): 2611–2620.
    DOI: 10.1111/j.1365-294X.2005.02553.xView Article Google Scholar

    Flanagan, S.P., B.R. Forester, E.K. Latch, S.N. Aitken and S. Hoban. 2018. Guidelines for planning genomic assessment and monitoring of locally adaptive variation to inform species conservation. Evol. Appl. 11(7): 1035–1052.
    DOI: 10.1111/eva.12569View Article Google Scholar

    Foll, M. and O. Gaggiotti. 2008. A genome-scan method to identify selected loci appropriate for both dominant and codominant markers: a Bayesian perspective. Genetics 180(2): 977–993.
    DOI: 10.1534/genetics.108.092221View Article Google Scholar

    Frankham, R. 2010. Where are we in conservation genetics and where do we need to go? Conserv. Genet. 11(2): 661–663.
    DOI: 10.1007/s10592-009-0010-2View Article Google Scholar

    Frankham, R., J.D. Ballou and D.A. Briscoe. 2004. A primer of conservation genetics. Cambridge University Press, Cambridge, UK.
    DOI: 10.1017/CBO9780511817359View Article

    Fraser, D.J. and L. Bernatchez. 2001. Adaptive evolutionary conservation: towards a unified concept for defining conservation units. Mol. Eco. 10(12: 2741–2752.
    DOI: 10.1046/j.1365-294X.2001.t01-1-01411.xView Article Google Scholar

    Galindo, J., P. Mor?n and E. Rol?n-Alvarez. 2009. Comparing geographical genetic differentiation between candidate and noncandidate loci for adaptation strengthens support for parallel ecological divergence in the marine snail Littorina saxatilis. Mol. Eco. 18(5): 919–930.
    DOI: 10.1111/j.1365-294X.2008.04076.xView Article Google Scholar

    Gebremedhin, B., G. Ficetola, S. Naderi, H. R. Rezaei, C. Maudet, D. Rioux, G. Luikart, ?. Flagstad, W. Thuiller and P. Taberlet. 2009. Frontiers in identifying conservation units: from neutral markers to adaptive genetic variation. Anim. Conserv. 12(2): 107–109.
    DOI: 10.1111/j.1469-1795.2009.00255.xView Article Google Scholar

    Glaubitz, J. C., T. M. Casstevens, F. Lu, J. Harriman, R. J. Elshire, Q. Sun and E. S. Buckler. 2014. TASSEL-GBS: a high capacity genotyping by sequencing analysis pipeline. PLoS One 9(2): e90346.
    DOI: 10.1371/journal.pone.0090346View Article Google Scholar

    Goudet, J. 2005. HIERFSTAT, a package for R to compute and test hierarchical F-tatistics. Mol. Eco. Notes 5(1): 184–186.
    DOI: 10.1111/j.1471-8286.2004.00828.xView Article Google Scholar

    Gravendeel, B., M. C.M. Eurlings, C. van den Berg and P.J. Cribb. 2004. Phylogeny of Pleione (Orchidaceae) and parentage analysis of its wild hybrids based on plastid and nuclear ribosomal ITS sequences and morphological data. Syst. Bot. 29(1): 50–63.
    DOI: 10.1600/036364404772973988View Article Google Scholar

    Guo, B., Z. Li and J. Meril?. 2016. Population genomic evidence for adaptive differentiation in the Baltic Sea herring. Mol. Eco. 25(12): 2833–2852.
    DOI: 10.1111/mec.13657View Article Google Scholar

    Hijmans, R.J., S.E. Cameron, J.L. Parra, P.G. Jones and A. Jarvis. 2005. Very high resolution interpolated climate surfaces for global land areas. Int. J. Climatol. 25(15): 1965–1978.
    DOI: 10.1002/joc.1276View Article Google Scholar

    Hsu, R. C.-C., W. L.M. Tamis, N. Raes, G.R. de Snoo, J.H.D. Wolf, G. Oostermeijer and S.-H. Lin. 2012. Simulating climate change impacts on forests and associated vascular epiphytes in a subtropical island of East Asia. Divers. Distrib. 18(4): 334–347.
    DOI: 10.1111/j.1472-4642.2011.00819.xView Article Google Scholar

    Huang, S.-F., S.-Y. Hwang, J.-C. Wang and T.-P. Lin. 2004. Phylogeography of Trochodendron aralioides (Trochodendraceae) in Taiwan and its adjacent areas. J. Biogeogr. 31(8): 1251–1259.
    DOI: 10.1111/j.1365-2699.2004.01082.xView Article Google Scholar

    Hufford, K.M. and S.J. Mazer. 2003. Plant ecotypes: genetic differentiation in the age of ecological restoration. Trends Ecol. Evol. 18(3): 147–155.
    DOI: 10.1016/S0169-5347(03)00002-8View Article Google Scholar

    Jiang, M.-T., W.-C. Chao, C.-L. Huang, S.-R. Lan, Z.-J. Liu and S.-S. Wu. 2019. The complete chloroplast genome of Pleione formosana (Orchidaceae). Mitochondrial DNA Part B 4(1): 1044–1046.
    DOI: 10.1080/23802359.2019.1584063View Article Google Scholar

    Jombart, T. and I. Ahmed. 2011. Adegenet 1.3-1: new tools for the analysis of genome-wide SNP data. Bioinformatics 27(21): 3070–3071.
    DOI: 10.1093/bioinformatics/btr521View Article Google Scholar

    Joost, S., A. Bonin, M.W. Bruford, L. Despr?s, C. Conord, G. Erhardt and P. Taberlet. 2007. A spatial analysis method (SAM) to detect candidate loci for selection: towards a landscape genomics approach to adaptation. Mol. Eco. 16(18): 3955–3969.
    DOI: 10.1111/j.1365-294X.2007.03442.xView Article Google Scholar

    Jost, L. 2008. GST and its relatives do not measure differentiation. Mol. Eco. 17(18):4015–4026.
    DOI: 10.1111/j.1365-294X.2008.03887.xView Article Google Scholar

    Kamvar, Z.N., J.F. Tabima and N.J. Gr?nwald. 2014. Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction. PeerJ 2: e281.
    DOI: 10.7717/peerj.281View Article Google Scholar

    Lu, F., A.E. Lipka, J. Glaubitz, R. Elshire, J.H. Cherney, M.D. Casler, E.S. Buckler and D.E. Costich. 2013. Switchgrass genomic diversity, ploidy, and evolution: novel insights from a network-based SNP discovery protocol. PLoS Genetics 9(1): e1003215.
    DOI: 10.1371/journal.pgen.1003215View Article Google Scholar

    Luu, K., E. Bazin and M.G.B. Blum. 2017. Pcadapt: an R package to perform genome scans for selection based on principal component analysis. Mol. Ecol. Resour. 17(1):67–77.
    DOI: 10.1111/1755-0998.12592View Article Google Scholar

    Moritz, C. 1994. Defining ‘evolutionarily significant units’ for conservation. Trends Ecol. Evol. 9(10): 373–375.
    DOI: 10.1016/0169-5347(94)90057-4View Article Google Scholar

    Nei, M. 1987. Molecular evolutionary genetics. Columbia university press, New York, USA.
    DOI: 10.7312/nei-92038View Article

    Peterson, B.K., J.N. Weber, E.H. Kay, H.S. Fisher and H.E. Hoekstra. 2012. Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS One 7(5): e37135.
    DOI: 10.1371/journal.pone.0037135View Article Google Scholar

    Phillips, R.D., K.W. Dixon and R. Peakall. 2012. Low population genetic differentiation in the Orchidaceae: implications for the diversification of the family. Mol. Eco. 21(21): 5208–5220.
    DOI: 10.1111/mec.12036View Article Google Scholar

    Pritchard, J.K., M. Stephens and P. Donnelly. 2000. Inference of population structure using multilocus genotype data. Genetics 155: 945–959.

    R Development Core Team. 2015. R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. Available at http:// www.R-project.org.

    Reed, D.H. and R. Frankham. 2003. Correlation between fitness and genetic diversity. Conserv. Biol. 17(1): 230–237.
    DOI: 10.1046/j.1523-1739.2003.01236.xView Article Google Scholar

    Rellstab, C., F. Gugerli, A.J. Eckert, A.M. Hancock and R. Holderegger. 2015. A practical guide to environmental association analysis in landscape genomics. Mol. Eco. 24(17): 4348–4370.
    DOI: 10.1111/mec.13322View Article Google Scholar

    Shi, Y., L. Yang, Z. Yang and Y. Ji. 2018. The complete chloroplast genome of Pleione bulbocodioides (Orchidaceae). Conserv. Genet. Resour. 10(1): 21–25.
    DOI: 10.1007/s12686-017-0753-xView Article Google Scholar

    Storey, J.D., A.J. Bass, A. Dabney and D. Robinson. 2019. Qvalue: Q-value estimation for false discovery rate control. R package version 2.16.0, https://github.com/jdstorey/qvalue.

    Stronen, A.V., B. J?drzejewska, C. Pertoldi, D. Demontis, E. Randi, M. Niedzia?kowska, T. Borowik, V.E. Sidorovich, J. Kusak and I. Kojola. 2015. Genome-wide analyses suggest parallel selection for universal traits may eclipse local environmental selection in a highly mobile carnivore. Ecol. Evol. 5(19): 4410–4425.
    DOI: 10.1002/ece3.1695View Article Google Scholar

    Su, H.-J. 1984. Studies on the climate and vegetation types of the natural forest in Taiwan (II). Altitudinal vegetation zones in relation to temperature gradient. Quarterly Journal of Chinese Forestry 17: 57–73.

    Su, H.-J. 1988. Research Study of Vegetation Ecosystems in Alishan Taiwan Pleione Nature Reserve. Forestry Bureau, Council of Agriculture, Executive Yuan. Taipei. (press in Chinese)

    Wright, S. 1951. The genetical structure of populations. Ann. Hum. Biol. 15(1): 323–354.
    DOI: 10.1111/j.1469-1809.1949.tb02451.xView Article Google Scholar