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Title: Comparison of RAPD, ISSR, and AFLP molecular markers to reveal and classify orchardgrass (Dactylis glomerata L.) germplasm variations
Authors: Costa, Ana Rita Pereira da
Pereira, Maria Graça Mendoça
Garrido Carballo, Inmaculada
Sousa, Manuel María Tavares de
Espinosa Borreguero, Francisco
Keywords: Pasto ovillo;Marcadores de repetición de secuencia simple;Polimorfismos en la longitud de fragmentos amplificados;Sistema de detección de polimorfismos en ADN;Dactylis glomerata;Inter Simple Sequence Repeat (ISSR);Amplied Fragment Length Polymorphism (AFLP);Random Amplified Polymorphic DNA (RAPD)
Issue Date: 2016
Publisher: Public Library of Science
Abstract: Three different DNA-based techniques, Random Amplified Polymorphic DNA (RAPD), Inter Simple Sequence Repeat (ISSR) and Amplified Fragment Length Polymorphism (AFLP markers, were used for fingerprinting Dactylis glomerata genotypes and for detecting genetic variation between the three different subspecies. In this study, RAPD assays produced 97 bands, of which 40 were polymorphic (41.2%). The ISSR primers amplified 91 bands, and 54 showed polymorphism (59.3%). Finally, the AFLP showed 100 bands, of which 92 were polymorphic (92%). The fragments were scored as present (1) or absent (0),and those readings were entered in a computer file as a binary matrix (one for each marker). Three cluster analyses were performed to express–in the form of dendrograms–the relationships among the genotypes and the genetic variability detected. All DNA-based techniques used were able to amplify all of the genotypes. There were highly significant correlation coefficients between cophenetic matrices based on the genetic distance for the RAPD, ISSR, AFLP, and combined RAPD-ISSR-AFLP data (0.68, 0.78, 0.70, and 0.70, respectively). Two hypotheses were formulated to explain these results; both of them are in agreement with the results obtained using these three types of molecular markers. We conclude that when we study genotypes close related, the analysis of variability could require more than one DNA-based technique; in fact, the genetic variation present in different sources could interfere or combine with the more or less polymorphic ability, as our results showed for RAPD, ISSR and AFLP markers. Our results indicate that AFLP seemed to be the bestsuited molecular assay for fingerprinting and assessing genetic relationship among genotypes of Dactylis glomerata.
ISSN: 1932-6203
DOI: 10.1371/journal.pone.0152972
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