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Genetic diversity and population structure analysis of Franklinia alatamaha, a tree species existing only in cultivation

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Abstract

Franklinia alatamaha is a small tree in the tea family (Theaceae) that has been valued for its ornamental qualities since 1765, when it was first recorded by John and William Bartram on the Georgia Coastal Plain. The only known population of F. alatamaha became extinct in the wild by the early 1800s. However, F. alatamaha has been cultivated as an ornamental for nearly 250 years. The plants existing today are derived from seeds collected from the Georgia population by the Bartrams. To examine the genetic variation of the cultivated F. alatamaha population, leaves from live and herbarium accessions were obtained from 42 sites worldwide. Genotyping-by-sequencing (GBS) was used to determine the genetic diversity and structure of 76 F. alatamaha accessions, including a 178-year-old herbarium specimen. STRUCTURE analysis with 9604 high-quality single-nucleotide polymorphisms (SNPs) identified two subpopulations within the cultivated accessions. This result was supported by UPGMA (unweighted pair group method with arithmetic mean) and principal component analyses. F statistics indicated that there was a moderate level of genetic diversity among the cultivated accessions (FST = 0.09), with more genetic diversity among accessions within a subpopulation than between the two subpopulations. The inbreeding coefficient of the cultivated accessions was low (FIS = − 0.4902), indicating that the sampled trees represent what was once a highly outcrossing population. Polymorphism was also detected by GBS analysis of 19 F. alatamaha plants grown from gamma-irradiated seeds. The genetic differentiation identified in this study may be useful for further development of new horticultural traits of F. alatamaha.

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References

  • Ahloowalia BS, Maluszynski M, Nichterlein K (2004) Global impact of mutation-derived varieties. Euphytica 135:187–204

    Article  Google Scholar 

  • Al-Safadi B, Arabi MIE (2003) In vitro induction, isolation and selection of potato mutants resistant to late blight. J Genet Breed 57:359–364

    Google Scholar 

  • Beck JB, Semple JC (2015) Next-generation sampling: pairing genomics with herbarium specimens provides species-level signal in Solidago (Asteraceae). Appl Plant Sci 3(6):1500014

    Article  Google Scholar 

  • Catchen J, Hohenloe PA, Bassham S, Amores A, Cresko WA (2013) Stacks: an analysis tool set for population genomics. Mol Ecol 22:3124–3140

    Article  Google Scholar 

  • Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, McVean G, Durbin R (2011) The variant call format and VCFtools. Bioinformatics 27(15):2156–2158

    Article  CAS  Google Scholar 

  • de Meeûs T, Goudet J (2007) A step-by-step tutorial to use HierFstat to analyze populations hierarchically structured at multiple levels. Infect Genet Evol 7(6):731–735

    Article  Google Scholar 

  • Del Tredici P (2005) Against all odds: growing F. alatamaha in Boston. Arnoldia 63(4):2–7

    Google Scholar 

  • Earl DA, vonHoldt BM (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour 4(2):359–361

    Article  Google Scholar 

  • Falush D, Stephens M, Pritchard JK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164(4):1567–1587

    Article  CAS  Google Scholar 

  • Frankham R, Ballou JD, Briscoe DA (2002) Introduction to conservation genetics. Cambridge University Press, New York

    Book  Google Scholar 

  • Gladfelter HJ (2019) Enhancing the ornamental potential of rare Theaceae species through genetic diversity and tissue culture research. University of Georgia, ProQuest Dissertations Publishing,

  • Gladfelter HJ, Johnston J, Wilde HD, Merkle SA (2020) Adventitious shoot-based propagation of Franklinia alatamaha for commercial horticulture. In Vitro Cell. Dev. Biol.- Plant. https://doi.org/10.1007/s11627-020-10087-8Z

  • Hamrick JL, Godt MJW (1989) Allozyme diversity in plant species. In: Brown AHD, Clegg MT, AL ALK, Weir BS (eds) Plant population genetics. Breeding and Genetic Resources. Sinauer Associated Inc., Sunderland, pp 43–63

    Google Scholar 

  • Harper F, Leeds AN (1937) A supplementary chapter on Franklinia alatamaha. Bartonia 19:1–13

    Google Scholar 

  • Hembree WG, Ranney TG, Jackson BE, Weathington M (2019) Cytogenetics, ploidy, and genome sizes of Camellia and related genera. HortScience 54:1124–1142

  • Ikeda T, Mishima K, Takata K, Tomaru N (2019) The origin and genetic variability of vegetatively propagated clones identified from old planted trees and plantations of Thujopsis dolabrata var. hondae in Ishikawa Prefecture, Japan. Tree Genet Genomes 15:80

    Article  Google Scholar 

  • Jombart T (2008) adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics 24(11):1403–1405

    Article  CAS  Google Scholar 

  • Kim WJ, Ryu J, Im J, Kim SH, Kang SY, Lee JH, Jo SH, Ha BK (2018) Molecular characterization of proton beam-induced mutations in soybean using genotyping-by-sequencing. Mol Gen Genomics 293:1169–1180

    Article  CAS  Google Scholar 

  • Koslow G, Peterson JL (1980) Phytophthora root and crown rot of Franklinia trees. J Arboricult 6:89–92

    Google Scholar 

  • Li MM, Li JH, Del Tredici P, Corajod J, Fu CX (2013) Phylogenetics and biogeography of Theaceae based on sequences of plastid genes. J Syst Evol 51(4):396–404

    Article  Google Scholar 

  • Liao T, Yuan DY, Zou F, Gao C, Yang Y, Zhang L, Tan XF (2014) Self-sterility in Camellia oleifera may be due to the prezygotic late-acting self-incompatibility. PLos ONE e99639

  • Nei M, Roychoudhury AK (1974) Sampling variances of heterozygosity and genetic distance. Genetics 76(2):379–390

    Article  CAS  Google Scholar 

  • Niu S, Song Q, Koiwa H, Qiao D, Zhao D, Chen Z, Liu X, Wen X (2019) Genetic diversity, linkage disequilibrium, and population structure analysis of the tea plant (Camellia sinensis) from an origin center, Guizhou plateau, using genome-wide SNPs developed by genotyping-by-sequencing. BMC Plant Biol 19(1):328

    Article  Google Scholar 

  • Pathirana R (1992) Gamma ray-induced field tolerance to Phytophthora blight in sesame. Plant Breed 108(4):314–319

    Article  Google Scholar 

  • Peterson GW, Dong Y, Horbach C, Fu YB (2014) Genotype-by-sequencing for plant genetic diversity analysis: a lab guide for SNP genotyping. Diversity 6(4):665–680

    Article  Google Scholar 

  • Ramasamy RK, Ramasamy S, Bindroo BB, Naik VG (2014) STRUCTURE PLOT: a program for drawing elegant STRUCTURE bar plots in user friendly interface. SpringerPlus 3:431

    Article  Google Scholar 

  • Ranney TG, Fantz PR (2006) xGordlinia grandiflora (Theaceae): an intergeneric hybrid between Franklinia alatamaha and Gordonia lasianthus. HortScience 41(6):1386–1388

    Article  Google Scholar 

  • Ranney TG, Eaker TA, Fantz PR, Parks CR (2003) xSchimlinia floribunda (Theaceae): a new intergeneric hybrid between Franklinia alatamaha and Schima argentea. HortScience 38(6):1198–1200

    Article  Google Scholar 

  • Sena K, Dreaden TJ, Crocker E, Barton C (2018) Detection of Phtyophthora cinnamomi in forest soils by PCR on DNA extracted from leaf disc baits. Plant Health Progress 19:193–200

  • Sidhu G, Mohan A, Zheng P, Dhaliwal AK, Main D, Gill KS (2015) Sequencing-based high throughput mutation detection in bread wheat. BMC Genomics 16:962

    Article  Google Scholar 

  • Yang H, Zhang R, Song P, Zhou, Z (2017) The floral biology, breeding system and pollination efficiency of Schima superba Gardn et Champ. (Theaceae). Forests 19994907

  • Zedane L, Hong-Wa C, Murienne J, Jeziorski C, Baldwin BG, Besnard G (2016) Museomics illuminate the history of an extinct, paleoendemic plant lineage (Hesperelaea, Oleaceae) known from an 1875 collection from Guadalupe Island, Mexico. Biol J Linn Soc 117(1):44–57

    Article  Google Scholar 

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Acknowledgments

This research was made possible with the help from Joel Fry and Dr. Dorinda Dallmeyer and support from a Jeane Reeves Research Grant (Georgia Native Plant Society) and a Fothergill Award (Bartram Trail Conference). We would like to thank four anonymous reviewers for their suggestions that improved this paper.

Data archiving statement

The nucleotide sequence data from this study have been deposited in the NCBI Sequence Read Archive (accession SRP249739).

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Authors and Affiliations

  1. Department of Horticulture, University of Georgia, Athens, GA, 30602, USA

    Heather J. Gladfelter, Lav K. Yadav & H. Dayton Wilde

  2. Warnell School of Forestry & Natural Resources, University of Georgia, Athens, GA, 30602, USA

    Heather J. Gladfelter & Scott A. Merkle

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  1. Heather J. Gladfelter
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  2. Lav K. Yadav
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  3. Scott A. Merkle
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  4. H. Dayton Wilde
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Correspondence to H. Dayton Wilde.

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Communicated by Z. Kaya

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Gladfelter, H.J., Yadav, L.K., Merkle, S.A. et al. Genetic diversity and population structure analysis of Franklinia alatamaha, a tree species existing only in cultivation. Tree Genetics & Genomes 16, 60 (2020). https://doi.org/10.1007/s11295-020-01455-x

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