The fragrant orchid <i>Vanilla chamissonis</i>: an appraisal of the genetic structure of wild populations from Osununú Natural Reserve (Misiones, Argentina)
DOI:
https://doi.org/10.15517/lank.v23i3.56432Palabras clave:
filogenética, genética poblacional, genotipado molecular, orquídeas silvestres, Osununú, provincia de MisionesResumen
Debido a diversos factores los cultivos comerciales de vainilla son altamente vulnerables a la erosión genética. Se ha demostrado que la especie Vanilla chamissonis produce compuestos bioeconómicos interesantes que podrían diversificar el mercado. En Argentina, la distribución de esta orquídea fragante se restringe a regiones específicas del noreste, como, por ejemplo, la Reserva Natural Osununú (San Ignacio, Misiones) donde crece de manera silvestre en sectores (núcleos). Este germoplasma, inexplorado, representa un endemismo localmente adaptado y, por lo tanto, es un recurso valioso que amerita preservarse. En este trabajo se llevó a cabo la caracterización genética de germoplasma de V. chamissonis. Además, se realizó la identificación molecular de los especímenes en un contexto filogenético empleando tanto marcadores nucleares como plastidiales. El genotipado expuso que, al menos, cuatro acervos genéticos contribuyen a la diversidad genética de estas plantas, y que ca. del 81% de la variación genética total se asigna dentro de las poblaciones. Los resultados actuales sugieren un predominio de la reproducción sexual, que el núcleo N1 emerge como una unidad candidata a conservarse, y la ocurrencia de una discontinuidad genética entre las poblaciones del noreste y del suroeste, que muestran constituciones genéticas diferentes. También se develó la ocurrencia de un tenue aislamiento por distancia. Nuestros resultados filogenéticos sugieren que es apropiado considerar al germoplasma estudiado como V. chamissonis. El conocimiento básico generado en este trabajo ayudará a guiar la iniciativa de manejo y conservación in situ, en curso en la reserva de Osununú.
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Andriamihaja, C. F., Ramarosandratana, A. V., Grisoni, M., Jeannoda, V. H. & Besse, P. (2021). Drivers of population divergence and species differentiation in a recent group of indigenous orchids (Vanilla spp.) in Madagascar. Ecology and Evolution, 11(6), 2681–2700. doi: 10.1002/ece3.7224
Besse, P., Da Silva, D. & Grisoni, M. (2021). Plant DNA barcoding principles and limits: A case study in the genus Vanilla. Methods in Molecular Biology, 2222, 131–148. doi: 10.1007/978-1-0716-0997-2_8
Biganzoli, F. & Múlgura de Romero, M. E. (2004). Inventario Florístico del Parque Provincial Teyú Cuaré y alrededores (Misiones, Argentina). Darwiniana, 42(1–4), 1–24.
Bonin, A., Bellemain, E., Bronken Eidesen, P., Pompanon, F., Brochmann, C. & Taberlet, P. (2004). How to track and assess genotyping errors in population genetics studies. Molecular Ecology, 13(11), 3261–3273. doi: 10.1111/j.1365-294X.2004.02346.x
Bory, S., Da Silva, D., Risterucci, A. M., Grisoni, M., Besse, P. & Duval, M. F. (2008a). Development of microsatellite markers in cultivated vanilla: Polymorphism and transferability to other Vanilla species. Scientia horticulturae, 115(4), 420–425. doi: 10.1016/j.scienta.2007.10.020
Bory, S., Catrice, O., Brown, S., Leitch, I. J., Gigant, R., Chiroleu, F., Grisoni, M., Duval, M. F. & Besse, P. (2008b). Natural polyploidy in Vanilla planifolia (Orchidaceae). Genome, 51(10), 816–826. doi: 10.1139/G08-068
Bouetard, A., Lefeuvre, P., Gigant, R., Bory, S., Pignal, M., Besse, P. & Grisoni, M. (2010). Evidence of transoceanic dispersion of the genus Vanilla based on plastid DNA phylogenetic analysis. Molecular Phylogenetics and Evolution, 55(2), 621–630. doi: doi.org/10.1016/j.ympev.2010.01.021
Bramel, P. & Frey, F. (2021). Global strategy for the conservation and use of Vanilla genetic resources. Bonn: Global Crop Diversity Trust.
Cameron, K. (2011). Vanilla orchids: natural history and cultivation. Portland-London: Timber Press.
Cascales, J., Bracco, M., Poggio, L. & Gottlieb, A. M. (2014). Genetic diversity of wild germplasm of “yerba mate” (Ilex paraguariensis St. Hil.) from Uruguay. Genetica, 142(6), 563–573. doi: 10.1007/s10709-014-9804-3
CITES. (2022). Convention on International Trade in Endangered Species of Wild Fauna and Flora. Retrieved from https://checklist.cites.org/ Accessed December 2022.
da Silva Oliveira, J. P., Garrett, R., Bello Koblitz, M. G. & Furtado Macedo, A. (2022). Vanilla flavor: Species from the Atlantic Forest as natural alternatives. Food Chemistry, 375, 131891. doi: 10.1016/j.foodchem.2021.131891
Edgar, R. C. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research, 32(5), 1792–1797. doi: 10.1093/nar/gkh340
Excoffier, L., Smouse, P. E. & Quattro J. M. (1992). Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics, 131(2), 479–491. doi: 10.1007/s00424-009-0730-7
Flanagan, N. S., Chavarriaga, P. & Mosquera-Espinosa, A. T. (2018). Conservation and sustainable use of Vanilla crop wild relatives in Colombia. In: D. Havkin-Frenkel & F. Belanger (Eds.), Handbook of Vanilla science and technology (pp. 85–110). Singapore: Wiley-Blackwell.
George, S., Sharma, J. & Yadon, V. L. (2009). Genetic diversity of the endangered and narrow endemic Piperia yadonii (Orchidaceae) assessed with ISSR polymorphisms. American Journal of Botany, 96(11), 2022–2030. doi: 10.3732/ajb.0800368
Gigant, R.L., Brugel, A., De Bruyn, A., Risterucci, A.‐M., Guiot, V., Viscardi, G., Humeau, L., Grisoni, M. & Besse, P. (2012). Nineteen polymorphic microsatellite markers from two African Vanilla species: across‐species transferability and diversity in a wild population of V. humblotii from Mayotte. Conservation Genetics Resources, 4(1),121–125. doi: 10.1007/s12686‐011‐9489‐1
Gigant, R. L., Rakotomanga, N., Goulié, C., Da Silva, D., Barre, N., Citadelle, G., Silvestre, D., Grisoni, M. & Besse, P. (2016). Microsatellite markers confirm self-pollination and autogamy in wild populations of Vanilla mexicana Mill. (syn. V. inodora) (Orchidaceae) in the Island of Guadeloupe. In: I. Y. Abdurakhmonov (Ed.), Microsatellite markers (pp. 73–93). London: InTechOpen.
Guindon, S., Dufayard, J. F., Lefort, V., Anisimova, M., Hordijk, W. & Gascuel, O. (2010). New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0. Systematic Biology, 59(3), 307–321. doi: 10.1093/sysbio/syq010
Hall, T.A. (1999). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series, 41, 95-98.
Hoang, D. T., Chernomor, O., Von Haeseler, A., Minh, B. Q. & Vinh, L. S. (2018). UFBoot2: Improving the ultrafast bootstrap approximation. Molecular Biology and Evolution, 35(2), 518–522. doi: 10.1093/molbev/msx281
Hou, B., Tian, M., Luo, J., Ji, Y., Xue, Q. & Ding, X. (2012). Genetic diversity assessment and ex situ conservation strategy of the endangered Dendrobium officinale (Orchidaceae) using new trinucleotide microsatellite markers. Plant Systematics and Evolution, 298(8), 1483–1491. doi: 10.1007/s00606-012-0651-3
Huang, R., Chu, Q. H., Lu, G. H. & Wang, Y. Q. (2019). Comparative studies on population genetic structure of two closely related selfing and outcrossing Zingiber species in Hainan Island. Scientific Reports, 9(1), 17997. doi: 10.1038/s41598-019-54526-y
Hu, Y., Resende, M. F. R., Bombarely, A., Brym, M., Bassil, E. & Chambers, A. H. (2019). Genomics-based diversity analysis of Vanilla species using a Vanilla planifolia draft genome and Genotyping-By-Sequencing. Scientific Reports, 9, 3416. https://doi.org/10.1038/s41598-019-40144-1
IUCN. (2022). The IUCN Red List of Threatened Species [online]. Available from https://www.iucnredlist.org/en [Accessed 14 Dec 2022].
Johnson, A. E. (2001). Las orquídeas del Parque Nacional Iguazú. Buenos Aires: L. O. L. A.
Jombart, T., Devillard, S. & Balloux, F. (2010). Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC Genetics, 11(1), 94. doi: 10.1186/1471-2156-11-94
Jombart, T. & Collins, C. (2015). A tutorial for Discriminant Analysis of Principal Components (DAPC) using adegenet 2.0.0. [online]. Available from http://adegenet.r-forge.r-project.org/files/tutorial-dapc.pdf [Accessed 10 Aug 2022].
Jørgensen, P.M., Nee, M.H. & Beck., S.G. (eds.) (2013). Catálogo de las plantas vasculares de Bolivia. Monographs in Systematic Botany from the Missouri Botanical Garden, 127, 1-1741. Missouri Botanical Garden.
Kalyaanamoorthy, S., Minh, B. Q., Wong, T. K. F., Von Haeseler, A. & Jermiin, L. S. (2017). ModelFinder: Fast model selection for accurate phylogenetic estimates. Nature Methods, 14(6), 587–589. doi: 10.1038/nmeth.4285
Kamvar, Z.N., Brooks, J.C. & Grünwald, N.J. (2015). Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality. Frontiers in Genetics 6: 208. doi:10.3389/fgene.2015.00208, https://doi.org/10.3389/fgene.2015.00208.
Kamvar, Z.N., Tabima, J.F.& Grünwald, N.J. (2014) Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction. PeerJ 2:e281.
Karremans, A. P., Chinchilla, I. F., Rojas-Alvarado, G., Cedeño-Fonseca, M., Damián, A. & Léotard, G. (2020). A reappraisal of neotropical Vanilla. With a note on taxonomic inflation and the importance of alpha taxonomy in biological studies. Lankesteriana, 20(3), 395–497. doi: 10.15517/lank.v20i3.45203
Karremans, A. P., Bogarín, D., Otárola, M. F., Sharma, J., Watteyn, C., Warner, J., Rodríguez Herrera, B., Chinchilla, I. F., Carman, E., Rojas Valerio, E., Pillco Huarcaya, R., & Whitworth, A. (2023). First evidence for multimodal animal seed dispersal in orchids. Current Biology, 33(2), 364-371.e3. doi:10.1016/j.cub.2022.11.041.
Keller, H. A., Keller, K. M. & Rojas, L. J. (2019). Estudio florístico de la Reserva Natural Osununú (San Ignacio Misiones). Ambientes, riqueza, especies con alto valor de conservación y plantas invasoras. Misiones: FCF-UnaM.
Kumar, S., Stecher, G. & Tamura, K. (2016). MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Molecular Biology and Evolution, 33(7), 1870–1874. doi: 10.1093/MOLBEV/MSW054
Legendre, P. & Legendre, L. (1998). Numerical ecology. Amsterdam: Elsevier.
Lopes, A. B., Silva, M. M. & Ferreira Melo Júnior, J. C. (2019). Estratégias funcionais de Vanilla chamissonis (Orchidaceae) em ambiente arbustivo e florestal de restinga. Revista Brasileira de Geografia Física, 12(2), 355–364. doi: 10.26848/rbgf.v12.2.p355-364
Ma, J.-M. & Yin, S.-H. (2009). Genetic diversity of Dendrobium fimbriatum (Orchidaceae), an endangered species, detected by inter-simple sequence repeat (ISSR). Acta Botanica Yunnanica, 31(1), 35–41. doi: 10.3724/sp.j.1143.2009.08076
Miller, M. P. (2005). Alleles In Space (AIS): Computer software for the joint analysis of interindividual spatial and genetic information. The Journal of Heredity, 96(6), 722–724. doi: doi.org/10.1093/jhered/esi119
Minh, B. Q., Schmidt, H. A., Chernomor, O., Schrempf, D., Woodhams, M. D., Von Haeseler, A. & Lanfear, R. (2020). IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era. Molecular Biology and Evolution, 37(5), 1530–1534. doi: 10.1093/molbev/msaa015
Mújica, E., Raventós, J. & González, E. (2009). Análisis de la selección de sustrato por parte de Dendrophylax lindenii (Orchidaceae) en Cabo San Antonio, Península de Guanahacabibes, Pinar del Río, Cuba. Lankesteriana, 9(3), 533–540. doi: 10.15517/lank.v0i0.12116
Munno, M. A., Espíndola, M. & Flores, R. (2011). Estudio de poblaciones de Vanilla chamissonis (Klotzsch) var. chamissonis en la Reserva Natural Osununú. In: M. E. Rodríguez (Ed.), Boletín de la Sociedad Argentina de Botánica. Proceedings of the XXXIII Jornadas Argentinas de Botánica (pp. 239–240). Córdoba: Sociedad Argentina de Botánica.
Nguyen, L. T., Schmidt, H. A., Von Haeseler, A. & Minh, B. Q. (2015). IQ-TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Molecular Biology and Evolution, 32(1), 268–274. doi: 10.1093/molbev/msu300
Paiva, D. I., Cascales, J., Rosetti, M. E. N., Scherer, R. A., Gauchat, M. E. & Gottlieb, A. M. (2020). Unraveling the genetic complexity of a cultivated breeding population of “yerba mate” (Ilex paraguariensis St. Hil.). Anais da Academia Brasileira de Ciencias, 92, e20190113. doi: 10.1590/0001-3765202020190113
Pansarin, E. R. (2021). Unravelling the Enigma of Seed Dispersal in Vanilla. Plant Biology, 23, 974–80. doi:10.1111/plb.13331
Pansarin, E. R. (2022). Vanilla flowers: Much more than food-deception. Botanical Journal of the Linnean Society, 198(1), 57–73. doi: 10.1093/botlinnean/boab046
Pansarin, E. R. & Suetsugu, K. (2022). Mammal-mediated seed dispersal in Vanilla: Its rewards and clues to the evolution of fleshy fruits in orchids. Ecology, 103. Doi: 10.1002/ecy.3701
Pansarin, E. R., Salatino, A. & Salatino M. L. F. (2008). Phylogeny of South American Pogonieae (Orchidaceae, Vanilloideae) based on sequences of nuclear ribosomal (ITS) and chloroplast (psaB, rbcL, rps16, and trnL-F) DNA, with emphasis on Cleistes and discussion of biogeographic implications. Organisms, Diversity & Evolution, 8, 171–181. doi:10.1016/j.ode.2007.09.003
Peakall, R. & Smouse, P. E. (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/bts460
Pérez-Escobar, O. A., Dodsworth, S., Bogarín, D., Bellot, S., Balbuena, J. A., Schley, R. J., Kikuchi, I. A., Morris, S. K., Epitawalage, N., Cowan, R., Maurin, O., Zuntini, A., Arias, T., Serna-Sánchez, A., Gravendeel, B., Torres Jimenez, M. F., Nargar, K., Chomicki, G., Chase, M. W., Leitch, I. J., Forest, F. & Baker, W. J. (2021). Hundreds of nuclear and plastid loci yield novel insights into orchid relationships. American Journal of Botany, 108(7), 1166–1180. doi: 10.1002/ajb2.1702
Qian, X., Li, Q. J., Liu, F., Gong, M. J., Wang, C. X. & Tian, M. (2014). Conservation genetics of an endangered lady’s slipper orchid: Cypripedium japonicum in China. International Journal of Molecular Sciences, 15(7), 11578–11596. doi: 10.3390/ijms150711578
Qian, X., Wang, C.-X. & Tian, M. (2013). Genetic diversity and population differentiation of Calanthe tsoongiana, a rare and endemic orchid in China. International Journal of Molecular Sciences, 14(10), 20399–20413. doi: 10.3390/ijms141020399
R Core Team. (2022). R: a language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing. Retrieved from https://www.r-project.org/.
R Core Team. (2023). R: a language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing. Retrieved from https://www.r-project.org/.
Rambaut, A. (2016). FigTree v1.4.3 software. Institute of Evolutionary Biology, University of Edinburgh. Retrieved from http://tree.bio.ed.ac.uk/software/figtree/
Reis, C. A. M., Brondani, G. E. & De Almeida, M. (2011). Biologia floral, reprodutiva e propagação vegetativa de baunilha. Scientia Agraria Paranaensis, 10(1), 69–82. doi: 10.1818/sap.v10i1.5271
Roldán-Ruiz, I., Dendauw, J., Van Bockstaele, E., Depicker, A. & De Loose, M. (2000). AFLP markers reveal high polymorphic rates in ryegrass (Lolium spp.). Molecular Breeding, 6, 125–134. doi: 10.1023/A:1009680614564
Schlüter, P. M. & Harris, S. A. (2006). Analysis of multilocus fingerprinting data sets containing missing data. Molecular Ecology Notes, 6(2), 569–572. doi: 10.1111/j.1471-8286.2006.01225.x
Shimodaira, H. (2002). An approximately unbiased test of phylogenetic tree selection. Systematic Biology, 51(3), 492–508. doi: 10.1080/10635150290069913
Shimodaira, H. & Hasegawa, M. (1999). Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Molecular Biology and Evolution, 16(8), 1114–1116. doi: 10.1093/oxfordjournals.molbev.a026201
Soltis, P. S., Soltis, D. E. & Smiley, C. J. (1992). An rbcL Sequence from a Miocene Taxodium (Bald Cypress). Proceedings of the National Academy of Sciences of the United States of America, 89(1), 449-451
Soto Arenas, M. A. (2003). Vanilla; tratamiento genérico. In: A. M. Pridgeon, P. M. W. Chase & F. N. Rasmussen (Eds.), Genera Orchidacearum, 3. Orchidoideae (Part two), Vanilloideae (pp. 321-334). Oxford: Oxford University Press.
Soto Arenas, M. A. (2006). La vainilla: retos y perspectivas de su cultivo. Biodiversitas, 66(2), 2–9.
Soto Arenas, M. A. & Cribb, P. (2010). A new infrageneric classification and synopsis of the genus Vanilla Plum. ex Mill. (Orchidaceae: Vanillinae). Lankesteriana, 9(3), 355–398. doi: doi.org/10.15517/lank.v0i0.12071
Soto Arenas, M. A. & Dressler, R. L. (2010). A revision of the Mexican and Central American species of Vanilla plumier ex Miller with a characterization of their ITS region of the nuclear ribosomal DNA. Lankesteriana, 9(3), 285–354. doi: 10.15517/lank.v0i0.12065
Szlachetko, D.L. (ed.) (2016). Orchids of the Guianas (Guyana, Suriname, French Guiana), 1, 1-461. Koeltz Botanical Books
Untergasser, A., Cutcutache, I., Koressaar, T., Ye, J., Faircloth, B. C., Remm, M. & Rozen, S. G. (2012). Primer3--new capabilities and interfaces. Nucleic Acids Research 40(15), e115
Velazco, S.J.E., Galvao, F., Keller, H.A., & Bedrij, N.A. (2015). Floristica e Fitossociologia de uma Floresta Estacional Semidecidual, Reserva Privada Osununú-Misiones, Argentina. Floresta e Ambiente, 22(1),1-12. Doi:10.1590/2179-8087.038513
Verma, P. C., Chakrabarty, D., Jena, S. N., Mishra, D. K., Singh, P. K., Sawant, S. V. & Tuli, R. (2009). The extent of genetic diversity among Vanilla species: Comparative results for RAPD and ISSR. Industrial Crops and Products, 29(2–3), 581–589. doi: 10.1016/j.indcrop.2008.11.006
White, T. J., Bruns, T., Lee, S. & Taylor, J. (1990). Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: M. A. Innis, D. H. Gelfand, J. J. Sninsky & T. J. White (Eds.), PCR protocols: a guide to methods and applications (pp. 315–322). New York: Academic Press, Inc.
Zietkiewicz, E., Rafalski, A. & Labuda, D. (1994). Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction amplification. Genomics, 20(2), 176–183. doi: 10.1006/geno.1994.1151
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