Isolation and Characterization of Fifteen Microsatellite Loci for the Use in Breeding of Gmelina arborea Roxb. (Lamiaceae)

Main Article Content

Oscar Rocha
Dawa Méndez-Álvarez
Fabiana Rojas Parajeles
Olman Murillo Gamboa

Abstract

Gmelina arborea (melina) is a valuable tree species throughout tropical areas, and there are extensive commercial plantations of this species in Southeast Asia, West Africa, and Latin America. As part of a research program for the genetic improvement and management of G. arborea at Instituto Tecn´ologico de Costa Rica, we developed, validated, and optimized fifteen microsatellite loci. We used 23 clones belonging to five different companies currently using clonal selection to manage their commercial plantations. Our results showed that all fifteen loci were polymorphic and together had 75 alleles (2-7 alleles/locus). We also found that eleven loci showed lower heterozygosity than expected under Hardy-Weinberg equilibrium (HWE). We calculated the genetic similarity among all clone pairs using the number of shared alleles to examine the potential of these loci for clone discrimination. Overall, pairwise similarity among clones ranged from 0.36 to 0.83, and our findings also showed that clones from the same commercial plantation tended to be more similar to each other than to clones from other plantations. These microsatellite loci will contribute toward the characterization of the genetic diversity, the identification of elite clone lines for timber production, and breeding and adequate management of commercial plantations of G. arborea.

Article Details

How to Cite
Rocha, O., Méndez-Álvarez, D., Rojas Parajeles, F. and Murillo Gamboa, O. (2020) “Isolation and Characterization of Fifteen Microsatellite Loci for the Use in Breeding of Gmelina arborea Roxb. (Lamiaceae)”, Genetic Resources, 1(2), pp. 23-28. doi: 10.46265/genresj.LLTJ1737.
Section
Original Articles
Author Biographies

Dawa Méndez-Álvarez, School of Forest Engineering, Instituto Tecnológico de Costa Rica, 159-7050 Cartago, Costa Rica.

Dawa Méndez-Álvarez is an investigator at the School of Forest Engineering, Instituto Tecnológico de Costa Rica, 159-7050 Cartago, Costa Rica.

Fabiana Rojas Parajeles, School of Forest Engineering, Instituto Tecnológico de Costa Rica, 159-7050 Cartago, Costa Rica

Fabiana Rojas Parajeles is an investigator at the School of Forest Engineering, Instituto Tecnológico de Costa Rica, 159-7050 Cartago, Costa Rica

Olman Murillo Gamboa, School of Forest Engineering, Instituto Tecnológico de Costa Rica, 159-7050 Cartago, Costa Rica

Dr. Murillo Gamboa is tree breeder and group leader at the School of Forest Engineering, Instituto Tecnológico de Costa Rica, 159-7050 Cartago, Costa Rica

References

Ávila-Arias, Carlos et al. (2014). “Desarrollo juvenil de clones de Gmelina arborea Roxb. de dos procedencias, en sitios planos del Pacífico Sur de Costa Rica”. Revista Forestal Mesoamericana Kurú 12(28). (in Spanish), pp. 23–23. DOI: 10.18845/rfmk.v12i28.2097. URL: https://dx.doi.org/10.18845/rfmk.v12i28.2097.
Ávila-Arias, Carlos, Murillo-Cruz, Rafael, and Murillo-Gamboa, Olmán (2015). “Selección de clones superiores de dos conjuntos genéticos de Gmelina arborea en el Pacífico Sur de Costa Rica”. Revista de Ciencias Ambientales 49(1). (in Spanish), pp. 17–35. DOI: 10.15359/rca.49-1.2. URL: https://dx.doi.org/10.15359/rca.49-1.2.
Ávila-Arias, Carlos et al. (2015). “Interacción genotipo sitio para dos conjuntos clonales de Gmelina arborea Roxb., en sitios planos del Pacífico Sur de Costa Rica”. Revista Forestal Mesoamericana Kurú 12(29), pp. 02–14. URL: https://revistas.tec.ac.cr/index.php/kuru/article/view/2250/2033.
Cardle, Linda et al. (2000). “Computational and experimental characterization of physically clustered simple sequence repeats in plants”. Genetics 156, pp. 847–854.
Cullings, K. W. (1992). “Design and testing of a plant-specific PCR primer for ecological and evolutionary studies”. Molecular Ecology 1(4), pp. 233–240. DOI: 10.1111/j.1365-294x.1992.tb00182.x. URL: https://dx.doi.org/10.1111/j.1365-294x.1992.tb00182.x.
Dice, Lee R. (1945). “Measures of the Amount of Ecologic Association Between Species”.
Ecology 26(3), pp. 297–302. DOI: 10.2307/1932409. URL: https://dx.doi.org/10.2307/1932409.
Doyle, Jeff J. and Doyle, Jane L. (1987). “A rapid DNA isolation procedure for small quantities of fresh leaf tissue”. Phytochemical Bulletin 19, pp. 11–15. URL: https://webpages.uncc.edu/~jweller2/pages/BINF8350f2011/BINF8350_Readings/Doyle_plantDNAextractCTAB_1987.pdf.
Dvorak, W. S. (2004). “World view of Gmelina arborea: opportunities and challenges”. New Forests 28(2/3), pp. 111–126. DOI: 10.1023/b:nefo.0000040940.32574.22. URL: https://dx.doi.org/10.1023/b:nefo.0000040940.32574.22.
Glenn, Travis C and Schable, Nancy A (2005). “Isolating microsatellite DNA loci”. In: Molecular Evolution: Producing the Biochemical Data. Ed. by Elizabeth A. Zimmer and Eric H. Roalson. Vol. 395. Methods in Enzymology. Academic Press, pp. 202–222. DOI: 10.1016/S0076-6879(05)95013-1. URL: https://doi.org/10.1016/S0076-6879(05)95013-1.
Lauridsen, E B and Kjaer, E D (2002). “Provenance research in Gmelina arborea Linn., Roxb. A summary of results from three decades of research and a discussion of how to use them”. The International Forestry Review 4(1), pp. 20–29. URL: https://www.jstor.org/stable/43740942.
Li, Shou-Hsien, Huang, Yi-Jiun and Brown, J. L. (1997). “Isolation of tetranucleotide microsatellites from the Mexican jay Aphelocoma ultramarina”. Molecular Ecology 6(5), pp. 499–501. DOI: 10.1046/j.1365-294x.1997.00215.x. URL: https://dx.doi.org/10.1046/j.1365-294x.1997.00215.x.
Liao, M et al. (2010). “Isolation and characterization of 11 polymorphic microsatellite loci for Gmelina arborea”. Molecular Ecology Resources 10, pp. 1106–1108. DOI: https://doi.org/10.1111/j.1755-0998.2010.02916.x.
Lodhi, Muhammad A. et al. (1994). “A simple and efficient method for DNA extraction from grapevine cultivars and Vitis species”. Plant Molecular Biology Reporter 12(1), pp. 6–13. DOI: 10.1007/bf02668658. URL: https://dx.doi.org/10.1007/bf02668658.
Murillo-Gamboa, Olman et al. (2016). “Tasa de avance de la pudrición del tronco en melina Gmelina arborea Roxb. y posibilidades de manejo”. Revista Forestal Mesoamericana Kurú 13(32), pp. 40–40. DOI: 10.18845/rfmk.v0i0.2551. URL: https://dx.doi.org/10.18845/rfmk.v0i0.2551.
Oosterhout, Cock van et al. (2004). “micro-checker: software for identifying and correcting genotyping errors in microsatellite data”. Molecular Ecology Notes 4(3), pp. 535–538. DOI: 10.1111/j.1471-8286.2004.00684.x. URL: https://dx.doi.org/10.1111/j.1471-8286.2004.00684.x.
Peakall, Rod and Smouse, Peter E. (2006). “genalex 6: genetic analysis in Excel. Population genetic software for teaching and research”. Molecular Ecology Notes 6(1), pp. 288–295. DOI: 10.1111/j.1471-8286.2005.01155.x. URL: https://dx.doi.org/10.1111/j.1471-8286.2005.01155.x.
Rohlf, F J (1993). NTSYS-pc : numerical taxonomy and multivariate analysis system. New York, USA.
Rosero, Carolina et al. (2011). “A drought stress transcriptome profiling as the first genomic resource for white teak - Gamhar - (Gmelina arborea Roxb) and related species”. BMC Proceedings 5(Suppl 7), P178–P178. DOI: 10.1186/1753-6561-5-s7-p178. URL: https://dx.doi.org/10.1186/1753-6561-5-s7-p178.
Rounda, Francisco F. Lega (1988). Estudios de la forma de Gmelina arborea (Roxb). Análisis de las plantaciones de Manila. (in Spanish). Turrialba (Costa Rica). URL: http://orton.catie.ac.cr/repdoc/A1645e/A1645e00.pdf.
Rozen, Steve and Skaletsky, Helen J (2000). “Primer3 on the WWW for general users and for biologist programmers”. In: Bioinformatics Methods and Protocols. Ed. by S. Misener and S. Kravetz. Vol. 132. Methods in Molecular BiologyTM. Totowa, NJ: Humana Press, pp. 365–386. DOI: 10.1385/1-59259-192-2:365. URL: https://doi.org/10.1385/1-59259-192-2:365.
Schuelke, Markus (2000). “An economic method for the fluorescent labeling of PCR fragments”. Nature Biotechnology 18(2), pp. 233–234. DOI: 10.1038/72708. URL: https://dx.doi.org/10.1038/72708.
Vergara, A et al. (2017). “Requerimiento Hídrico de Gmelina arborea en Etapa de Vivero Bajo Condiciones Controladas (Water Requirement of Gmelina arborea on Nursery Stage Under Controlled Conditions)”. Floresta e Ambiente 24. (in Spanish), e20150129. DOI: 10.1590/2179-8087.012915. URL: http://dx.doi.org/10.1590/2179-8087.012915.
Wee, Alison K. S. et al. (2012). “Genetic diversity in natural populations of Gmelina arborea: implications for breeding and conservation”. New Forests 43(4), pp. 411–428. DOI: 10.1007/s11056-011-9288-2. URL: https://dx.doi.org/10.1007/s11056-011-9288-2.