Comparative analysis of genetic diversity in Prunus L. as revealed by RAPD and SSR markers

Baránek, Miroslav; Raddová, Jana; Pidra, M.

doi:10.1016/j.scienta.2006.01.023

Cited by 18 publications

(12 citation statements)

References 25 publications

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“…Interestingly, the first axis of PCA permitted the separation of wild-type from cultivated species. Additionally, an important homogeneity between introduced and local accessions was observed, confirming the results of previous studies (Casas et al, 1999;Shimada et al, 1999;Baránek et al, 2006;Ayanoglu et al, 2007;Ben Tamarzizt et al, 2009). …”

Section: Genetic Diversity Between Cultivated and Wild-type Plumssupporting

confidence: 89%

“…In fact, these primers generated 226 polymorphic bands of 234 fragments, with a mean of 15.6 per primer pair. This is significantly higher than values reported in other studies based on RAPD markers in plum cultivars (Casas et al, 1999;Shimada et al, 1999;Baránek et al, 2006) and AFLP markers (Ayanoglu et al, 2007). Similar results were also observed for Tunisian plum shrubs using the RAPD technique (Ben Tamarzizt et al, 2009).…”

Section: Discussionsupporting

confidence: 62%

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Assessment of genetic diversity and relationships among wild and cultivated Tunisian plums (Prunus spp) using random amplified microsatellite polymorphism markers

Tamarzizt¹,

Mustapha²,

Baraket³

et al. 2015

Genet. Mol. Res.

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ABSTRACT. The usefulness of random amplified microsatellite polymorphism markers to study the genetic diversity and relationships among cultivars belonging to Prunus salicina and P. domestica and their wild relatives (P. insititia and P. spinosa) was investigated. A total of 226 of 234 bands were polymorphic (96.58%). The 226 random amplified microsatellite polymorphism markers were screened using 15 random amplified polymorphic DNA and inter-simple sequence repeat primers combinations for 54 Tunisian plum accessions. The percentage of polymorphic bands (96.58%), the resolving power of primers values (135.70), and the polymorphic information content demonstrated the efficiency of the primers used in this study. The genetic distances between accessions ranged from 0.18 to 0.79 with a mean of 0.24, suggesting a high level of genetic diversity at the intra-and interspecific levels. The unweighted pair group with arithmetic mean dendrogram 1942-1956 (2015) Genetic diversity of Tunisian plums using RAMPO markers and principal component analysis discriminated cultivars efficiently and illustrated relationships and divergence between spontaneous, locally cultivated, and introduced plum types. These procedures showed continuous variation that occurs independently of the status of the species and geographical origin of the plums. In this study, random amplified microsatellite polymorphism was found to be as a reliable molecular marker for fingerprinting and for examining the diversity study of the plum and its relatives.

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Section: Genetic Diversity Between Cultivated and Wild-type Plumssupporting

confidence: 89%

Section: Discussionsupporting

confidence: 62%

Assessment of genetic diversity and relationships among wild and cultivated Tunisian plums (Prunus spp) using random amplified microsatellite polymorphism markers

Tamarzizt¹,

Mustapha²,

Baraket³

et al. 2015

Genet. Mol. Res.

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“…Random amplified polymorphic DNA (RAPD) technique has been used to study the genetic diversity of Prunus, including almonds, in several studies (Gogorcena et al, 1993;Casas et al, 1999;Mir Ali and Nabulsi, 2003;Gouta et al, 2008;Shiran et al, 2007) and is considered as a quick, inexpensive and less laborious approach for studying genetic diversity. Previous studies showed that results of RAPD analysis are reliable and comparable to markers like SSR (Baránek et al, 2006;Shiran et al, 2007;Bouhadida et al, 2009;Gouta et al, 2010) and AFLP (Sorkheh et al, 2009a).…”

Section: Introductionmentioning

confidence: 83%

Morphological and molecular variability in some Iranian almond genotypes and related Prunus species and their potentials for rootstock breeding

Nikoumanesh

Ebadi

Zeinalabedini

et al. 2011

Scientia Horticulturae

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In this study, in order to know the variability for a rootstock breeding program genetic diversity and relationships among 55 Iranian almond genotypes and seven related Prunus species were investigated. Morphological and molecular analyses were used. Principal component analysis showed that three components explained 67.6% of the total morphological variation for the first year and 68.06% for the second year of the study. Leaf traits were predominant in the first component and contributed most of the total variation. Leaf length and width, as well as, leaf area were highly correlated with each other and correlated to vigor. Also a negative correlation was found among leaf length/width ratio and vigor. Ward's method was used to construct cluster from morphological data which allocated individuals into their respective species. Out of 100 pre-screened RAPD primers, 16 with reproducible bands and maximum polymorphism were selected. Two-hundred and sixty bands were scored which 250 of them were polymorphic. Average value of polymorphism per primer was 95.81% and maximum value for polymorphism (100%) was obtained from TIBMBA-14, TIBMBA-17, TIBMBB-05, TIBMBB-08, TIBMBD-09, TIBMBD-10. On the other hand, the minimum value was obtained from TIBMBB-16 (86%). Primer TIBMBB-5 gave the maximum number of bands (25 fragments) and the minimum obtained from TIBMBE-18 (11 fragments). Genetic similarity based on Jaccard's coefficient ranged from 0.28 to 0.79 with an average of 0.53. Molecular analysis revealed a high degree of separation among samples regarding their geographical origin. Correlation between two approaches was low (R=-0.38). High molecular and morphological variability indicated that this collection includes rich and valuable plant materials for almond rootstock breeding.

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“…Although, RAPD and SSR primers were able to amplify all DNA templates, each type of marker detected different types of genetic variation. RAPD markers may detect mutations at many locations within an entire genome, but microsatellites typically detect mutation at particular loci, often within repetitive DNA (Baranek et al, 2006). SSR and RAPD markers have similar marker index values but contrasting data for fig discrimination.…”

Section: Combined Rapd and Ssr Analysismentioning

confidence: 99%

Molecular characterization of autochthonous Turkish fig accessions

Çalışkan

Polat

Celikkol

et al. 2012

Span. j. agric. res.

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Turkey is one of the main genetic centers for fig tree, Ficus carica L. The genetic variabilities of 76 fig accessions from Hatay province of Turkey were evaluated by analysis of 10 simple sequence repeats (SSR) loci. The number of alleles revealed by SSR analysis ranged from 3 to 12 alleles per locus with a mean value of 6.8. A total of 68 alleles were detected by SSR and the average heterozygosity was higher than the expected one. In addition, seven random amplified polymorphic DNA (RAPD) primers detected a total of 68 clear and reproducible bands, 55 of which were polymorphic, so it was possible to effectively characterize these fig accessions with either marker techniques. In both marker systems, Mantel's correlation between similarity scores and cophenetic values was moderately high (0.90 for RAPD and 0.87 for SSR), which demonstrated that the clustering patterns fitted the data well. The clusters obtained using these types of markers were independent. This study indicated that there is great genetic variability among local fig accessions, making them a valuable genetic source for incorporation into potential breeding programs especially for table fig selections.Additional key words: Ficus carica; genetic diversity; RAPD; SSR. Resumen Caracterización molecular de accesiones autóctonas de higo de TurquíaTurquía es uno de los principales centros genéticos de la higuera, Ficus carica L. Se evaluó, mediante análisis de 10 loci de microsatélites o repeticiones de secuencias simples (SSR), la variabilidad genética de 76 accesiones de higuera muestreadas en la provincia Hatay de Turquía. El número de alelos revelados por análisis SSR varió de 3 a 12 por locus con una media de 6,8; se detectaron en total 68 alelos y la heterocigosidad promedio fue mayor que la heterocigosidad esperada. Además, siete cebadores RAPD detectaron un total de 68 bandas claras y reproducibles, de las cuales 55 fueron polimórficas, por lo que estas accesiones de higuera pudieron ser eficazmente caracterizadas utilizando ambas técnicas. Tanto con SSRs como con RAPDs, la similitud y las correlaciones cofenéticas mediante la prueba de Mantel fueron moderadamente altas (0,90 para RAPD y 0,87 para SSR), lo que demuestra que los patrones de agrupamiento se ajustan bien a los datos. Los grupos obtenidos con este tipo de marcadores fueron independientes. Este estudio encontró una gran variabilidad genética entre accesiones autóctonas de higuera, lo que las hace una fuente valiosa para su incorporación potencial en programas de mejora, especialmente para higos de mesa.

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Comparative analysis of genetic diversity in Prunus L. as revealed by RAPD and SSR markers

Cited by 18 publications

References 25 publications

Assessment of genetic diversity and relationships among wild and cultivated Tunisian plums (Prunus spp) using random amplified microsatellite polymorphism markers

Assessment of genetic diversity and relationships among wild and cultivated Tunisian plums (Prunus spp) using random amplified microsatellite polymorphism markers

Morphological and molecular variability in some Iranian almond genotypes and related Prunus species and their potentials for rootstock breeding

Molecular characterization of autochthonous Turkish fig accessions

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