Comparison of microsatellites and isozymes in genetic diversity studies of Oryza glumaepatula (Poaceae) populations
The study of the genetic structure of wild plant populations is essential for their management and conservation. Several DNA markers have been used in such studies, as well as isozyme markers. In order to provide a better comprehension of the results obtained and a comparison between markers which w...
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| Format: | Article |
| Language: | English |
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Vicerractoría Investigación
2012-12-01
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| Series: | Revista de Biología Tropical |
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| Online Access: | http://www.scielo.sa.cr/scielo.php?script=sci_arttext&pid=S0034-77442012000400005 |
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| author | Marines M. G Karasawa Roland Vencovsky Cynthia M Silva Daruska C Cardim Eduardo de A Bressan Giancarlo C.X Oliveira Elizabeth A. Veasey |
| author_facet | Marines M. G Karasawa Roland Vencovsky Cynthia M Silva Daruska C Cardim Eduardo de A Bressan Giancarlo C.X Oliveira Elizabeth A. Veasey |
| author_sort | Marines M. G Karasawa |
| collection | DOAJ |
| description | The study of the genetic structure of wild plant populations is essential for their management and conservation. Several DNA markers have been used in such studies, as well as isozyme markers. In order to provide a better comprehension of the results obtained and a comparison between markers which will help choose tools for future studies in natural populations of Oryza glumaepatula, a predominantly autogamous species, this study used both isozymes and microsatellites to assess the genetic diversity and genetic structure of 13 populations, pointing to similarities and divergences of each marker, and evaluating the relative importance of the results for studies of population genetics and conservation. A bulk sample for each population was obtained, by sampling two to three seeds of each plant, up to a set of 50 seeds. Amplified products of eight SSR loci were electrophoresed on non-denaturing polyacrylamide gels, and the fragments were visualized using silver staining procedure. Isozyme analyses were conducted in polyacrylamide gels, under a discontinuous system, using six enzymatic loci. SSR loci showed higher mean levels of genetic diversity (A=2.83, p=0.71, A P=3.17, Ho=0.081, He=0.351) than isozyme loci (A=1.20, p=0.20, A P=1.38, Ho=0.006, He=0.056). Interpopulation genetic differentiation detected by SSR loci (R ST=0.631, equivalent to F ST=0.533) was lower than that obtained with isozymes (F ST=0.772). However, both markers showed high deviation from Hardy-Weinberg expectations (F IS=0.744 and 0.899, respectively for SSR and isozymes). The mean apparent outcrossing rate for SSR ( =0.14) was higher than that obtained using isozymes ( =0.043), although both markers detected lower levels of outcrossing in Amazonia compared to the Pantanal. The migrant number estimation was also higher for SSR (Nm=0.219) than isozymes (Nm=0.074), although a small number for both markers was expected due to the mode of reproduction of this species, defined as mixed with predominance of self fertilization. No correlation was obtained between genetic and geographic distances with SSR, but a positive correlation was found between genetic and geographic distances with isozymes. We conclude that these markers are divergent in detecting genetic diversity parameters in O. glumaepatula and that microsatellites are powerful for detecting information at the intra-population level, while isozymes are more powerful for inter-population diversity, since clustering of populations agreed with the expectations based on the geographic distribution of the populations using this marker<br>El estudio de la estructura genética de poblaciones de plantas silvestres es esencial para su manejo y conservación. Varios marcadores de ADN e isoenzimas se han utilizado en este tipo de análisis. Con el fin de proporcionar una mejor comprensión de los resultados obtenidos y saber que marcador codominante elegir para futuros estudios en poblaciones naturales de Oryza glumaepatula, este trabajo busco evaluar y comparar dos marcadores de ADN, isoenzimas y microsatélites, en la diversidad y estructura genética de 13 poblaciones, destacando las similitudes y divergencias de cada marcador, así como la importancia relativa de los resultados en genética de poblaciones y conservación. Para los SSR, ocho loci SSR fueron evaluados, y los fragmentos se visualizaron utilizando el procedimiento de coloración con plata. Los análisis de isoenzimas se realizaron en geles de poliacrilamida, en los seis loci enzimáticos. Los loci SSR mostraron mayores niveles de diversidad genética que los loci isoenzimáticos, en promedio. La diferenciación genética entre los loci SSR (R ST=0.631, equivalente a F ST=0.533) fue inferior a la obtenida con las isoenzimas (F ST=0.772). Ambos marcadores mostraron alta desviación del equilibrio de Hardy-Weinberg (F IS=0.744 y 0.899, respectivamente, para SSR e isoenzimas). La tasa media aparente de cruzamiento para SSR ( =0.14) fue mayor que la obtenida con isoenzimas ( =0.043), aunque ambos marcadores detectaron niveles más bajos en la tasa de fecundación cruzada para la Amazonia, en comparación con la región del Pantanal. La estimación de número de migrantes también fue mayor para los SSR (Nm=0.219) que en isoenzimas (Nm=0.074). No se obtuvo ninguna correlación entre las distancias genéticas y geográficas para los SSR, y para las isoenzimas se obtuvo una correlación positiva entre las distancias genéticas y geográficas. Llegamos a la conclusión de que estos marcadores son divergentes en la detección de los parámetros de la diversidad genética en O. glumaepatula y que los microsatélites son más eficientes para detectar la información a nivel intra-poblacional, mientras que las isoenzimas son más potentes para detectar la diversidad entre poblaciones. |
| first_indexed | 2024-03-12T07:41:18Z |
| format | Article |
| id | doaj.art-24c9e78531ea45c2a39287ed60e28d3e |
| institution | Directory Open Access Journal |
| issn | 0034-7744 2215-2075 |
| language | English |
| last_indexed | 2024-03-12T07:41:18Z |
| publishDate | 2012-12-01 |
| publisher | Vicerractoría Investigación |
| record_format | Article |
| series | Revista de Biología Tropical |
| spelling | doaj.art-24c9e78531ea45c2a39287ed60e28d3e2023-09-02T21:18:13ZengVicerractoría InvestigaciónRevista de Biología Tropical0034-77442215-20752012-12-0160414631478Comparison of microsatellites and isozymes in genetic diversity studies of Oryza glumaepatula (Poaceae) populationsMarines M. G KarasawaRoland VencovskyCynthia M SilvaDaruska C CardimEduardo de A BressanGiancarlo C.X OliveiraElizabeth A. VeaseyThe study of the genetic structure of wild plant populations is essential for their management and conservation. Several DNA markers have been used in such studies, as well as isozyme markers. In order to provide a better comprehension of the results obtained and a comparison between markers which will help choose tools for future studies in natural populations of Oryza glumaepatula, a predominantly autogamous species, this study used both isozymes and microsatellites to assess the genetic diversity and genetic structure of 13 populations, pointing to similarities and divergences of each marker, and evaluating the relative importance of the results for studies of population genetics and conservation. A bulk sample for each population was obtained, by sampling two to three seeds of each plant, up to a set of 50 seeds. Amplified products of eight SSR loci were electrophoresed on non-denaturing polyacrylamide gels, and the fragments were visualized using silver staining procedure. Isozyme analyses were conducted in polyacrylamide gels, under a discontinuous system, using six enzymatic loci. SSR loci showed higher mean levels of genetic diversity (A=2.83, p=0.71, A P=3.17, Ho=0.081, He=0.351) than isozyme loci (A=1.20, p=0.20, A P=1.38, Ho=0.006, He=0.056). Interpopulation genetic differentiation detected by SSR loci (R ST=0.631, equivalent to F ST=0.533) was lower than that obtained with isozymes (F ST=0.772). However, both markers showed high deviation from Hardy-Weinberg expectations (F IS=0.744 and 0.899, respectively for SSR and isozymes). The mean apparent outcrossing rate for SSR ( =0.14) was higher than that obtained using isozymes ( =0.043), although both markers detected lower levels of outcrossing in Amazonia compared to the Pantanal. The migrant number estimation was also higher for SSR (Nm=0.219) than isozymes (Nm=0.074), although a small number for both markers was expected due to the mode of reproduction of this species, defined as mixed with predominance of self fertilization. No correlation was obtained between genetic and geographic distances with SSR, but a positive correlation was found between genetic and geographic distances with isozymes. We conclude that these markers are divergent in detecting genetic diversity parameters in O. glumaepatula and that microsatellites are powerful for detecting information at the intra-population level, while isozymes are more powerful for inter-population diversity, since clustering of populations agreed with the expectations based on the geographic distribution of the populations using this marker<br>El estudio de la estructura genética de poblaciones de plantas silvestres es esencial para su manejo y conservación. Varios marcadores de ADN e isoenzimas se han utilizado en este tipo de análisis. Con el fin de proporcionar una mejor comprensión de los resultados obtenidos y saber que marcador codominante elegir para futuros estudios en poblaciones naturales de Oryza glumaepatula, este trabajo busco evaluar y comparar dos marcadores de ADN, isoenzimas y microsatélites, en la diversidad y estructura genética de 13 poblaciones, destacando las similitudes y divergencias de cada marcador, así como la importancia relativa de los resultados en genética de poblaciones y conservación. Para los SSR, ocho loci SSR fueron evaluados, y los fragmentos se visualizaron utilizando el procedimiento de coloración con plata. Los análisis de isoenzimas se realizaron en geles de poliacrilamida, en los seis loci enzimáticos. Los loci SSR mostraron mayores niveles de diversidad genética que los loci isoenzimáticos, en promedio. La diferenciación genética entre los loci SSR (R ST=0.631, equivalente a F ST=0.533) fue inferior a la obtenida con las isoenzimas (F ST=0.772). Ambos marcadores mostraron alta desviación del equilibrio de Hardy-Weinberg (F IS=0.744 y 0.899, respectivamente, para SSR e isoenzimas). La tasa media aparente de cruzamiento para SSR ( =0.14) fue mayor que la obtenida con isoenzimas ( =0.043), aunque ambos marcadores detectaron niveles más bajos en la tasa de fecundación cruzada para la Amazonia, en comparación con la región del Pantanal. La estimación de número de migrantes también fue mayor para los SSR (Nm=0.219) que en isoenzimas (Nm=0.074). No se obtuvo ninguna correlación entre las distancias genéticas y geográficas para los SSR, y para las isoenzimas se obtuvo una correlación positiva entre las distancias genéticas y geográficas. Llegamos a la conclusión de que estos marcadores son divergentes en la detección de los parámetros de la diversidad genética en O. glumaepatula y que los microsatélites son más eficientes para detectar la información a nivel intra-poblacional, mientras que las isoenzimas son más potentes para detectar la diversidad entre poblaciones.http://www.scielo.sa.cr/scielo.php?script=sci_arttext&pid=S0034-77442012000400005estructura genéticaflujo de genesisoenzimasSSRsistema de cruzamientogenetic structuregene flowisozymesmating systemSSR |
| spellingShingle | Marines M. G Karasawa Roland Vencovsky Cynthia M Silva Daruska C Cardim Eduardo de A Bressan Giancarlo C.X Oliveira Elizabeth A. Veasey Comparison of microsatellites and isozymes in genetic diversity studies of Oryza glumaepatula (Poaceae) populations Revista de Biología Tropical estructura genética flujo de genes isoenzimas SSR sistema de cruzamiento genetic structure gene flow isozymes mating system SSR |
| title | Comparison of microsatellites and isozymes in genetic diversity studies of Oryza glumaepatula (Poaceae) populations |
| title_full | Comparison of microsatellites and isozymes in genetic diversity studies of Oryza glumaepatula (Poaceae) populations |
| title_fullStr | Comparison of microsatellites and isozymes in genetic diversity studies of Oryza glumaepatula (Poaceae) populations |
| title_full_unstemmed | Comparison of microsatellites and isozymes in genetic diversity studies of Oryza glumaepatula (Poaceae) populations |
| title_short | Comparison of microsatellites and isozymes in genetic diversity studies of Oryza glumaepatula (Poaceae) populations |
| title_sort | comparison of microsatellites and isozymes in genetic diversity studies of oryza glumaepatula poaceae populations |
| topic | estructura genética flujo de genes isoenzimas SSR sistema de cruzamiento genetic structure gene flow isozymes mating system SSR |
| url | http://www.scielo.sa.cr/scielo.php?script=sci_arttext&pid=S0034-77442012000400005 |
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