Research Paper
Population genetic diversity and genetic structure of Amorphophallus yunnanensis in Southwestern China and its conservation implication
Si Yin, Honglong Chu, Yanan Zhang, Feidong Lu, Lizhou Tang, Yong Gao
Published on: 24 March 2021
Page: 126 - 134
DOI: 10.6165/tai.2021.66.126
Abstract
Amorphophallus yunnanensis is a perennial herb distributed throughout southwestern China. The degradation and reduction of habitats due to human activities caused declines in A. yunnanensis. We developed simple sequence repeat (SSR) markers with restriction site-associated DNA sequencing (RAD-seq) to estimate the genetic diversity and evaluate population differentiation of A. yunnanensis in southwestern China. We found that the genetic diversity of A. yunnanensis was relatively low compared to the widely distributed Amorphophallus konjac. Population structure analyses revealed three genetic groups that corresponded to geographic distributions. One of these genetic groups (group A) that consisted of two populations in the relatively southern part exhibited the highest genetic diversity and more rare alleles, suggesting a hotspot of diversification in A. yunnanensis. These results indicated that the three genetic groups should be treated as distinct evolutionarily significant units and a higher conservation priority should be placed on group A.
Keyword: Amorphophallus yunnanensis, Genetics diversity, Genetic monitoring, Population structure, RAD-seq, SSR
Literature Cited
Baird, N.A., P.D. Etter, T.S. Atwood, M.C. Currey, A.L. Shiver, Z.A. Lewis, E.U. Selker, W.A. Cresko, E.A. Johnson. 2008. Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers. Plos One 3(10): e3376.
DOI: 10.1371/journal.pone.0003376View Article
Google Scholar
Chae, W.B., S.J. Hong, J.M. Gifford, A.L. Rayburn, E.J. Sacks and J.A. Juvik. 2014. Plant morphology, genome size, and SSR markers differentiate five distinct taxonomic groups among accessions in the genus Miscanthus. GCB Bioenergy 6(6): 646?660.
DOI: 10.1111/gcbb.12101View Article
Google Scholar
Chua, M., T.C. Baldwin, T.J. Hocking and K. Chan. 2010. Traditional uses and potential health benefits of Amorphophallus konjac K. Koch ex N.E.Br. J. Ethnopharmacol. 128(2): 268?278.
DOI: 10.1016/j.jep.2010.01.021View Article
Google Scholar
Curry, C.J., P.A. White and J.N. Derr. 2019. Genetic analysis of African lions (Panthera leo) in Zambia support movement across anthropogenic and geographical barriers. Plos One 14(5): e0217179.
DOI: 10.1371/journal.pone.0217179View Article
Google Scholar
Dizon, A.E., C. Lockyer, W.F. Perrin and D.J. Sisson. 1992. Rethinking the stock concept: a phylogeographic approach. Conserv. Biol. 6(1): 24?36.
DOI: 10.1046/j.1523-1739.1992.610024.xView Article
Google Scholar
Earl, D.A. and B.M. Vonholdt. 2012. STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conser. Genet. Res. 4(2): 359?361.
DOI: 10.1007/s12686-011-9548-7View Article
Google Scholar
Eku?, M.R.M., O. Gailing and R. Finkeldey. 2009. Transferability of simple sequence repeat (SSR) markers developed in Litchi chinensis to Blighia sapida (Sapindaceae). Plant Mol. Biol. Rep. 27(4): 570?574.
DOI: 10.1007/s11105-009-0115-2View 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
Excoffier, L. and H.E.L. Lischer. 2010. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol. Ecol. Resour. 10(3): 564?567.
DOI: 10.1111/j.1755-0998.2010.02847.xView Article
Google Scholar
Faith, D.P. 1994. Genetic diversity and taxonomic priorities for conservation. Biol. Conserv. 68(1): 69?74.
Francisco?Ortega, J., A. Santos?Guerra, S.C. Kim and D.J. Crawford. 2000. Plant genetic diversity in the Canary Islands: a conservation perspective. Am. J. Bot. 87(7): 909?919.
DOI: 10.2307/2656988View Article
Google Scholar
Fraser, D.J. and L. Bernatchez. 2010. Adaptive evolutionary conservation: towards a unified concept for defining conservation units. Mol. Ecol. 10(12): 2741?2752.
DOI: 10.1046/j.1365-294X.2001.t01-1-01411.xView Article
Google Scholar
Gao, Y., S. Yin, H. Yang, L. Wu and Y. Yan. 2017. Genetic diversity and phylogenetic relationships of seven Amorphophallus species in southwestern China revealed by chloroplast DNA sequences. Mitochondrial DNA A 29(5): 679?686.
DOI: 10.1080/24701394.2017.1350855View Article
Google Scholar
Gao, Y., S. Yin, C. Liu, H. Wang, H. Chu and L. Tang. 2018a. A rapid approach for SSR development in Amorphophallus paeoniifolius using RAD-seq. Taiwania 63(3): 281?285.
DOI: 10.6165/tai.2018.63.281View Article
Google Scholar
Gao, Y., G. Yuan, C. Niu and L. Tang. 2018b. Genetic diversity and population structure of the devel's tongue arum (Amorphophallus konjac) in southwestern China. Pak. J. Bot. 50(3): 999?1004.
Goslee, S.C. and D.L. Urban. 2007. The ecodist package for dissimilarity-based analysis of ecological data. J. Stat. Softw. 22(7): 1?19.
DOI: 10.18637/jss.v022.i07View Article
Google Scholar
Goudet, J. 1995. FSTAT Vers. 2.9.3.: a computer program to calculate F-satistics. J. Hered. 86(6): 485–486.
DOI: 10.1093/oxfordjournals.jhered.a111627View Article
Google Scholar
Gupta, P.K., S. Rustgi, S. Sharma, R. Singh, N. Kumar and H.S. Balyan. 2003. Transferable EST-SSR markers for the study of polymorphism and genetic diversity in bread wheat. Mol. Genet. Genomics. 270(4): 315?323.
DOI: 10.1007/s00438-003-0921-4View Article
Google Scholar
Hedrick, P.W. 1983. Genetics of populations. Science Books International, Boston.
Jiang, X., Y. Chen, X. Chen, S. Yan, M. Xia, J. Shen and J. Zhang. 2019. Geographical distribution and characteristics of Konjac resources in Xishuangbanna, Yunnan Province. Agricultural Science. 1(4): 1?4.
Jombart, T. 2008. adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics. 24(11): 1403?1405.
DOI: 10.1093/bioinformatics/btn129View Article
Google Scholar
Kurniawan, A., I.P.A.H. Wibawa and B. Adjie. 2011. Species diversity of Amorphophallus (Araceae) in Bali and Lombok with attention to genetic study in A. paeoniifolius (Dennst.) Nicolson. Biodiversitas 12(1): 7?11.
DOI: 10.13057/biodiv/d120102View Article
Google Scholar
Li, C., J.L. Chen, Y.Y. Li and D.K. Tian. 2018. Genetic diversity of Begonia versicolor (Begoniaceae), a narrow endemic species in southeast Yunnan of China. Taiwania 63(1): 49?53.
DOI: 10.6165/tai.2018.63.49View Article
Google Scholar
Li, H., G. Zhu, P.C. Boyce, M. Jin, W.L.A. Hetterscheid, J. Bogner and N. Jacobsen. 2010. Araceae, In: Flora of China, vol. 23: 23–33. Missouri Botanical Garden Press, St. Louis.
Liu, P. 2003. Konjac, China Agriculture Press, Beijing.
Long, C., H. Li, Z. Ouyang, X. Yang, Q. Li and B. Trangmar. 2003. Strategies for agrobiodiversity conservation and promotion: A case from Yunnan, China. Biodivers. Conserv. 12(6): 1145?1156.
DOI: 10.1023/A:1023085922265View Article
Mullen, S.P. 2007. Conservation and the genetics of populations. Copeia. 2007(3): 774?775.
Nei, M., F. Tajima and Y. Tateno. 1983. Accuracy of estimated phylogenetic trees from molecular data. J. Mol. Evol. 19(2): 153?170.
DOI: 10.1007/BF02300753View Article
Google Scholar
Orsini, L., J. Vanoverbeke, I. Swillen, J. Mergeay and L. De Meester. 2013. Drivers of population genetic differentiation in the wild: isolation by dispersal limitation, isolation by adaptation and isolation by colonization. Mol. Ecol. 22(24): 5983?5999.
DOI: 10.1111/mec.12561View Article
Google Scholar
Pan, C., A.W. Gichira and J.M. Chen. 2015. Genetic variation in wild populations of the tuber crop Amorphophallus konjac (Araceae) in central China as revealed by AFLP markers. Genet. Mol. Res. 14(4): 18753?18763.
DOI: 10.4238/2015.December.28.24View Article
Google Scholar
Peakall, R. and P.E. Smouse. 2012. GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research - an update. Bioinformatics 28(19): 2537?2539.
DOI: 10.1093/bioinformatics/bts460View Article
Google Scholar
Pritchard, J.K., M. Stephens and P. Donnelly. 2000. Inference of population structure using multilocus genotype data. Genetics 155(2): 945?959.
Prunier, R. and K. Holsinger. 2010. Was it an explosion? Using population genetics to explore the dynamics of a recent radiation within Protea (Proteaceae L.). Mol. Ecol. 19(18): 3968?3980.
DOI: 10.1111/j.1365-294X.2010.04779.xView Article
Google Scholar
Rao, V.R. and T. Hodgkin. 2002. Genetic diversity and conservation and utilization of plant genetic resources. Plant Cell Tiss. Org. 68(1): 1?19.
Ren, P. and M. Pan. 2013. Population genetic structure of five Amorphophallus species from the south of Yunnan province by inter-simple sequences(ISSR) markers. J. Wuhan Univ. Nat. Sci. 28(2): 85–86.
Rozen, S. and H. Skaletsky. 2000. Primer 3 on the WWW for general users and for biologist programmers, In: Methods in Molecular Biology, vol. 132:365?386. Humana Press, USA.
Santosa, E., C.L. Lian, Y. Pisooksantivatana and N. Sugiyama. 2007. Isolation and characterization of polymorphic microsatellite markers in Amorphophallus paeoniifolius (Dennst.) Nicolson, Araceae. Mol. Ecol. Notes. 7(5): 814?817.
DOI: 10.1111/j.1471-8286.2007.01713.xView Article
Google Scholar
Setsuko, S., K. Sugai, I. Tamaki, K. Takayama, H. Kato and H. Yoshimaru. 2020. Genetic diversity, structure, and demography of Pandanus boninensis (Pandanaceae) with sea drifted seeds, endemic to the Ogasawara Islands of Japan: Comparison between young and old islands. Mol. Ecol. 29(6): 1050?1068.
DOI: 10.1111/mec.15383View Article
Google Scholar
Sinnott, R.W. 1984. Virtues of the Haversine. Sky and Telescope. 68(2): 159.
Smouse, P.E. and J.C. Long. 1992. Matrix correlation analysis in anthropology and genetics. Am. J. Phys. Anthropol. 35(S15): 187?213.
DOI: 10.1002/ajpa.1330350608View Article
Google Scholar
Srzednicki, G. and C. Borompichaichartkul. 2020. Konjac glucomannan-production, processing, and functional applications, CRC Press, Boca Raton.
Takezaki, N., M. Nei and K. Tamura. 2010. Software for constructing population trees from allele frequency data and computing other population statistics with windows interface. Mol. Biol. Evol. 27(4): 747?752.
DOI: 10.1093/molbev/msp312View Article
Google Scholar
Tang, R., B. Huang, W. Sun and G. Chen. 2020. Pollination biology of Amorphophallus albus (Araceae), an endemic plant in the dry-hot valley of Jinsha River. Plant Science Journal. 38(4): 458?466.
Thiel, T., W. Michalek, R.K. Varshney and A. Graner. 2003. Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor. Appl. Genet. 106(3): 411?422.
DOI: 10.1007/s00122-002-1031-0View Article
Google Scholar
Tian, Z., F. Zhang, H. Liu, Q. Gao and S. Chen. 2016. Development of SSR markers for a Tibetan medicinal plant, Lancea tibetica (Phrymaceae), based on RAD sequencing. Appl. Plant. Sci. 4(11): 1600076.
DOI: 10.3732/apps.1600076View Article
Google Scholar
Tomlinson, P.B., S.J. Mayo, J. Bogner and P.C. Boyce. 1998. The genera of Araceae. Kew Bull. 53(2): 505.
DOI: 10.2307/4114530View Article
Google Scholar
Van Oosterhout, C., W. F. Hutchinson, D.P.M. Wills, P. Shipley. 2004. MICRO?CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Mol. Ecol. Notes 4(3): 535?538.
DOI: 10.1111/j.1471-8286.2004.00684.xView Article
Google Scholar
Wigginton, J.E., D.J. Cutler and G.R. Abecasis. 2005. A note on exact tests of Hardy-Weinberg equilibrium. Am. J. Hum. Genet. 76(5): 887?893.
DOI: 10.1086/429864View Article
Google Scholar
Wu, X., X. Xu, D. Ma, R. Chen and Y. Cao. 2019. Virulence structure and its genetic diversity analyses of Blumeria graminis f. sp. tritici isolates in China. BMC Evol. Biol. 19(1): 183.
DOI: 10.1186/s12862-019-1511-3View Article
Google Scholar
Yin, S., Y. Yan, L. You, Q. Chen, Y. Zhou, K. Chen, R. Li, Z. Yang, L. Man and Y. Gao. 2019. Newly developed genomic SSRs reveal genetic diversity in wild and cultivated Amorphophallus albus germplasms. Plant Mol. Biol. Rep. 37(4): 365?375.
DOI: 10.1007/s11105-019-01162-5View Article
Google Scholar
Yuan, J.H., F.Y. Cheng and S.L. Zhou. 2012. Genetic structure of the tree peony (Paeonia rockii) and the Qinling Mountains as a geographic barrier driving the fragmentation of a large population. Plos One 7(4): e34955.
DOI: 10.1371/journal.pone.0034955View Article
Google Scholar
Zalapa, J.E., H. Cuevas, H. Zhu, S. Steffan, D. Senalik, E. Zeldin, B. McCown, R. Harbut and P. Simon. 2012. Using next-generation sequencing approaches to isolate simple sequence repeat (SSR) loci in the plant sciences. Am. J. Bot. 99(2): 193?208.
DOI: 10.3732/ajb.1100394View Article
Google Scholar