Development of new microsatelite loci for Geoffroea decorticans (Gillies ex Hook. & Arn.) Burkart
DOI:
https://doi.org/10.31055/1851.2372.v56.n4.32721Keywords:
Atacama desert, genetic diversity, Geoffroea decorticans, next-generation sequencing, SSR markersAbstract
Background and aims: One of the few tree species adapted to the ecologically limiting conditions of the Atacama Desert is Geoffroea decorticans, known as chañar. It is a valuable multipurpose resource used as a food and medicinal product. However, for the purpose of genetic studies, codominant DNA markers specific for this species have not yet been developed. The objective of this work is to develop and validate microsatellite markers (SSR) for G. decorticans, in order to perform future studies of genetic diversity and genetic structure of populations.
M&M: SSR markers were searched in the G. decorticans genome using the Next-Generation Sequencing (NGS) method, and they were validated through thirty individuals distributed in different localities in northern Chile.
Results: A total of ~ 144,117 microsatellite loci were identified and a set of 41 primer pairs was used for validation. The amplified fragments ranged from 106 bp to 225 bp, the number of alleles ranged from 2 to 9, and the PIC value of the 41 SSR loci ranged between 0.32 and 0.86, with an average of 0.64.
Conclusions: For the first time, putative neutral SSR markers specific to the G. decorticans species have been developed in order to promote genetic studies for the conservation of the species. The present study provides a set of 38 new polymorphic SSR markers, which could serve as an effective tool to estimate genetic diversity, genetic structure and to be used in breeding programs.
References
ALEKSIC, J. M., D. STOJANOVIĆ, B. BANOVIĆ & R. JANČIĆ. 2012. A simple and efficient DNA isolation method for Salvia officinalis. Biochem. Genet. 50: 881-892. https://doi.org/10.1007/s10528-012-9528-y
BESNARD, G., C. GARCIA-VERDUGO, R. R. DE CASAS, U. A. TREIER, N. GALLAND & P. VARGAS. 2008. Polyploidy in the olive complex (Olea europaea): evidence from flow cytometry and nuclear microsatellite analyses. Ann. Bot. 101: 25-30. https://doi.org/10.1093/aob/mcm275
BESSEGA, C., C. POMETTI, R. FORTUNATO, F. GREENE, C. M. SANTORO & V. MCROSTIE. 2021. Genetic studies of various Prosopis species (Leguminosae, Section Algarobia) co-occurring in oases of the Atacama Desert (northern Chile). Ecol. Evol. 11: 2375– 2390. https://doi.org/10.1002/ece3.7212
BOTSTEIN, D., R. D. WHITE, M. SKOLNICK & R. W. DAVIS. 1980. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am. J. Hum. Genet. 32: 314-331.
BURKART, A. 1949. La posición sistemática del "chañar" y las especies del género Geoffroea (Leguminosae-Dalbergieae). Darwiniana 9: 9-23. http://www.jstor.org/stable/23211719
CAETANO, S., M. CURRAT, R. T. PENNINGTON, D. E. PRADO, L. EXCOFFIER & Y. NACIRI. 2012. Recent colonization of the Galapagos by the tree Geoffroea spinosa Jacq. (Leguminosae). Mol. Ecol. 21: 2743–2760. https://doi.org/10.1111/j.1365-294X.2012.05562.x
CASTRO, L. C. 2020. El bosque de la Pampa del Tamarugal y la industria salitrera: el problema de la deforestación, los proyectos para su manejo sustentable y el debate político (Tarapacá, Perú-Chile 1829-1941). Scr. Nova 24: 1-37.
CITTADINI, M. C., I. GARCÍA-ESTÉVEZ, M. T. ESCRIBANO-BAILÓN, R. M. BODOIRA, D. BARRIONUEVO & D. MAESTRI. 2021. Nutritional and nutraceutical compounds of fruits from native trees (Ziziphus mistol and Geoffroea decorticans) of the dry chaco forest. J. Food Compost. Anal. 97: 103775. https://doi.org/10.1016/j.jfca.2020.103775
CONTRERAS, R., V. PORCILE & F. AGUAYO. 2018. Genetic diversity of Geoffroea decorticans, a native woody leguminous species from Atacama Desert in Chile. Bosque 39: 321-332. https://doi.org/10.4067/S0717-92002018000200321
CONTRERAS, R, V. PORCILE & F. AGUAYO. 2019. Microsatellites reveal a high genetic differentiation among native Geoffroea decorticans populations in Chilean Atacama Desert Bol. Soc. Argent. Bot. 54: 225-240. https://doi.org/10.31055/1851.2372.v54.
CONTRERAS, R., F. S. CAREVIC, V. PORCILE & M. ARIAS. 2020a. Development of SSR loci in Prosopis tamarugo Phillipi and assessment of their transferability to species of the Strombocarpa section. For. Syst. 29: e012. https://doi.org/10.5424/fs/2020292-16706
CONTRERAS, R., L. VAN DEN BRINK, B. BURGOS, M. GONZÁLEZ & S. GACITÚA. 2020b. Genetic Characterization of an Endangered Chilean Endemic Species, Prosopis burkartii Muñoz, Reveals its Hybrids Parentage. Plants 9: 744. https://doi.org/10.3390/plants9060744
COSTAMAGNA, M. S., R. M. ORDOÑEZ, I. C. ZAMPINI, J. E. SAYAGO & M. I. ISLA. 2013. Nutritional and antioxidant properties of Geoffroea decorticans, an Argentinean fruit, and derived products (flour, arrope, decoction and hydroalcoholic beverage). Food Res. Int. 54: 160-168. https://doi.org/10.1016/j.foodres.2013.05.038
COTABARREN, J., D. J. BROITMAN, E. QUIROGA & W. D. OBREGÓN. 2020. GdTI, the first thermostable trypsin inhibitor from Geoffroea decorticans seeds. A novel natural drug with potential application in biomedicine. Int. J. Biol. Macromol. 148: 869-879. https://doi.org/10.1016/j.ijbiomac.2020.01.214
DAÏNOU, K., C. BLANC-JOLIVET, B. DEGEN, P. KIMANI, D. NDIADE-BOUROBOU, A. S. DONKPEGAN, F. TOSSO, E. KAYMAK, N. BOURLAND, J. L. DOUCET & O. J. HARDY. 2016. Revealing hidden species diversity in closely related species using nuclear SNPs, SSRs and DNA sequences - a case study in the tree genus Milicia. BMC Evol. Biol. 16: 259. https://doi.org/10.1186/s12862-016-0831-9
DEMEKE, T. & G. R. JENKINS. 2010. Influence of DNA extraction methods, PCR inhibitiors and quantification methods on real-time PCR assay of biotechnology-derived traits. Anal. Bioanal. Chem. 396: 1977-1990. https://doi.org/10.1007/s00216-009-3150-9
ECHEVERRÍA, J., N. Y. PANIAGUA-ZAMBRANA & R. W. BUSSMANN. 2020. Geoffroea decorticans (Gillies ex Hook. & Arn.) Burkart Fabaceae. In: N. PANIAGUA-ZAMBRANA & R. BUSSMANN (eds.), Ethnobotany of the Andes. Ethnobotany of Mountain Regions. Springer, Cham.
https://doi.org/10.1007/978-3-319-77093-2_128-1
EXCOFFIER, L., G. LAVAL & S. SCHNEIDER. 2005. Arlequín ver. 3.0: An integrated software package for population genetics data analysis. Evol. Bioinform. Online 1: 47-50. https://doi.org/10.1177/117693430500100003
EYNARD, C. & L. GALETTO. 2002. Pollination ecology of Geoffroea decorticans (Fabaceae) in central Argentine dry forest. J. Arid Environ. 51: 79-88. https://doi.org/10.1006/jare.2001.0923
FOX, G., R. F. PREZIOSI, R. E. ANTWIS, M. BENAVIDES‐SERRATO, F. J. COMBE, W. E. HARRIS, I. R. HARTLEY, A. C. KITCHENER, S. R. DE KORT, A. I. NEKARIS et al. 2019. Multi-individual microsatellite identification: A multiple genome approach to microsatellite design (MiMi). Mol. Eco.l Resour. 19: 1672– 1680.
https://doi.org/10.1111/1755-0998.13065
GIMÉNEZ, A. M. & J. G. MOGLIA. 2003. Arboles del Chaco Argentino, Guía para el reconocimiento dendrológico [online]. Disponible en: https://fcf.unse.edu.ar/archivos/publicaciones/libro-arboles-del-chaco/libro-arboles-del-chaco-argentino-GIMENEZ-MOGLIA.pdf. [Acceso: 04 de abril de 2021].
GIMÉNEZ, A. M. 2004. Anatomía comparada de leño y corteza de Geoffroea striata y Geoffroea decorticans. Madera y bosques 10: 55-68. https://doi.org/10.21829/myb.2004.1011279
GROOM, A. 2012. Geoffroea decorticans. En: The IUCN Red List of Threatened Species 2012 [online]. Disponible en: https://www.iucnredlist.org/species/62502/20075550 [Acceso:10 de abril de 2021].
IRELAND & PENNIGNTON. 1999. A revision of Geoffroea (Leguminosae-Papilionoide). Edinb. J. Bot. 56: 329-347.
JIMÉNEZ-ASPEE, F., C. THEODULOZ, M. D. P. C. SORIANO, M. UGALDE-ARBIZU, M. R. ALBERTO, I. C. ZAMPINI, M. I. ISLA, M. J. SIMIRGIOTIS & G. SCHMEDA-HIRSCHMANN. 2017. The Native Fruit Geoffroea decorticans from Arid Northern Chile: Phenolic Composition, Antioxidant Activities and In Vitro Inhibition of Pro-Inflammatory and Metabolic Syndrome-Associated Enzymes. Molecules 22: 2-18. https://doi.org/10.3390/molecules22091565
LAMARQUE, A., D. LABUCKAS, J. GREPPI & R. FORTUNATO. 2009. Electrophoretic analysis of Geoffroea (Leguminosae, Papilionoideae): taxonomic inferences in Argentinean populations. Austral. Syst. Bot. 22: 137-142. https://doi.org/10.1071/SB08022
LAWSON, S. & A. EBRAHIMI. 2018. Development and validation of Acacia koa and A. koaia nuclear SSRs using Illumina sequencing. Silvae Genet. 67: 20-25. https://doi.org/10.2478/sg-2018-0003
LIU, F. M., Z. HONG, Z. J. YANG, N. N. ZHANG, X. J. LIU & D. P. XU. 2019. De novo transcriptome analysis of Dalbergia odorifera and transferability of SSR markers developed from the transcriptome. Forests 10: 98. https://doi.org/10.3390/f10020098
MAESTRI, D. M., R. H. FORTUNATO, J. A. GREPPI & A. L. LAMARQUE. 2001. Compositional studies of seeds and fruits from two varieties of Geoffroea decorticans. Int. J. Biol. Macromol. 14: 585-590. https://doi.org/10.1006/jfca.2001.1020
MMA (Ministerio de Medio Ambiente). 2021. Ficha de Antecedente de la especie Geoffroea decorticans [online]. Disponible en: https://clasificacionespecies.mma.gob.cl/wp-content/uploads/2020/09/Geoffroea_decorticans_17RCE_INICIO.pdf. [Acceso: 04 de abril de 2021].
MONCADA, X., D. PLAZA, A. STOLL, C. PAYACAN, D. SEELENFREUND, E. MARTÍNEZ, A. BERTIN & F. A. SQUEO. 2019. Genetic diversity and structure of the vulnerable species Prosopis chilensis (Molina) Stuntz in the Coquimbo Region, Chile. Gayana Bot.76: 91–104. http://dx.doi.org/10.4067/S0717-66432019000100091
NACIRI-GRAVEN, Y., S. CAETANO, D. PRADO, R. T. PENNINGTON & R. SPICHIGER. 2005. Development and characterization of 11 microsatellite markers in a widespread Neotropical seasonally dry forest tree species, Geoffroea spinosa Jacq. (Leguminosae). Mol. Ecol. 5: 542-545. https://doi.org/10.1111/j.1471-8286.2005.00982.x
NÚÑEZ, L., V. MCROSTIE & I. CARTAJENA. 2009. Consideraciones sobre la recolección vegetal y horticultura durante el Formativo temprano en el Sureste de la Cuenca de Atacama. Darwiniana 47: 56-75. https://doi.org/10.14522/darwiniana.2014.471.41
ORRABALIS, C. J. 2014. Aprovechamiento Integral de los Frutos de Geoffroea decorticans (chañar), de la Región Fitogeográfica de la Provincia de Formosa. Tesis Doctoral. Universidad Nacional de Córdoba, Argentina.
PEAKALL, R. & P. E. SMOUSE. 2012. GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research—an update. Bioinformatics 28: 2537-2539. https://doi.org/10.1093/bioinformatics/bts460
PLANT LIST. 2021. Species of the genus Geoffroea [online]. Disponible en: http://www.theplantlist.org/1.1/browse/A/Leguminosae/Geoffroea/. [Acceso: 29 de marzo de 2021].
RITTER, B., V. WENNRICH, A. MEDIALDEA, D. BRILL, G. KING, S. SCHNEIDERWIND, K. NIEMANN, E. FERNÁNDEZ-GALEGO, J. DIEDERICH, C. ROLF, R. BAO, M. MELLES & T. J. DUNAI. 2019. “Climatic fluctuations in the hyperarid core of the Atacama Desert during the past 215 ka”. Sci. Rep. 9: 1-13. https://doi.org/10.1038/s41598-019-41743-8
RODRÍGUEZ, R., C. MARTICORENA, D. ALARCÓN, C. BAEZA, L. CAVIERES, V. L. FINOT, N. FUENTES, A. KIESSLING, M. MIHOC, A. PAUCHARD, E. RUIZ, P. SANCHEZ & A. MARTICORENA. 2018. Catálogo de las plantas vasculares de Chile. Gayana Botánica 75: 1- 430. http://doi.org/10.4067/S0717-66432018000100001
ROZEN, S. & H. SKALETSKY. 2000. Primer3 on the WWW for general users and for biologist programmers. Methods Mol. Biol. 132: 365-386. http://doi.org/10.1385/1-59259-192-2:365
SAIKI, F. A., A. P. BERNARDI, M. S. REIS, H. FAORO, E. M. SOUZA, F. O. PEDROSA, A. MANTOVANI & A. F. GUIDOLIN. 2017. Development and validation of the first SSR markers for Mimosa scabrella Benth. Genet. Mol. Res. 16: gmr16019571. https://doi.org/10.4238/gmr16019571
SALINAS F., R. VARDANEGA, C. ESPINOSA-ÁLVAREZ, D. JIMENÉZ, W. BUGUEÑO, M. C. RUIZ-DOMÍNGUEZ, M. A. A. MEIRELES & P. CEREZAL- MEZQUITA. 2020. Supercritical fluid extraction of chañar (Geoffroea decorticans) almond oil: Global yield, kinetics and oil characterization. J. Supercrit. Fluids 161: 104824. https://doi.org/10.1016/j.supflu.2020.104824
SCHUELKE, M. 2000. An economic method for the fluorescent labeling of PCR fragments. Nat. Biotechnol. 18: 233-4. https://doi.org/10.1038/72708.
STOLL, A., D. HARPKE, C. SCHÜTTE, L. JIMENEZ, L. LETELIER, F. R. BLATTNER & D. QUANDT. 2020. Landscape genetics of the endangered Atacama Desert shrub Balsamocarpon brevifolium in the context of habitat fragmentation Glob. Planet. Chang. 184: 103059. https://doi.org/10.1016/j.gloplacha.2019.103059
THIEL, T., W. MICHALEK, R. K. VARSHNEY & 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: 411-422. https://doi.org/10.1007/s00122-002-1031-0
UGALDE, P. C., V. MCROSTIE, E. M. GAYO, M. GARCÍA, C. LATORRE & C. M. SANTORO. 2020. 13,000 years of sociocultural plant use in the Atacama Desert of northern Chile. Veg. Hist. Archaeobot. 30: 1-18. https://doi.org/10.1007/s00334-020-00783-1
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. 4: 535-538. https://doi.org/10.1111/j.1471-8286.2004.00684.x
VARELA, M. C., M. GONZÁLEZ, E. VILLALOBOS, S. GACITÚA & J. MONTENEGRO. 2019. Producción y Comercialización de Productos del Chañar (Geoffroea decorticans (Gillies ex Hook. & Arn.) Burkart) por descendientes de pueblos originarios de la Comuna de Copiapó. Región de Atacama. Chile. Idesia 37: 131-137. http://dx.doi.org/10.4067/S0718-34292019000300131.
VIEIRA, M. L., L. SANTINI, A. L. DINIZ & C. DE F. MUNHOZ. 2016. Microsatellite markers: what they mean and why they are so useful. Genet. Mol. Biol. 39: 312-328. https://doi.org/10.1590/1678-4685-GMB-2016-0027
ZHANG, J., K. KOBERT, T. FLOURI & A. STAMATAKIS. 2014. PEAR: a fast and accurate Illumina paired-end read merger. Bioinformatics 30: 614-620. https://doi.org/10.1093/bioinformatics/btt593
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