Abstract

LOPEZ-ARDILA, Iván Yesid; MARTINEZ-PEREZ, Francisco José  and  RONDON-GONZALEZ, Fernando. Application of the model of DNA loss for desing of primers in Potamotrygon magdalenae (Potamotrygonidae). Acta biol.Colomb. [online]. 2022, vol.27, n.1, pp.97-103.  Epub Feb 18, 2022. ISSN 0120-548X.  https://doi.org/10.15446/abc.v27n1.87401.

The primer design is critical for amplifying gene regions because the specificity that primer-sequence maintain can cause success or failure in the PCR reaction. Concerning Potamotrygon magdalenae (a species of interest according to the PAN Tiburones-Colombia), there is little information available about aspects related to population genetics of this river stingray. This study aimed to design primers under DNA Loss Model (DNA-LM) criteria, which will allow assessing the genetics status of populations of P. magdalenae. We aligned sequences from the superfamily Dayastoidea, available in the NCBI, of the mitochondrial genes Cytochrome C Oxidase 1 (MT-CO1) and Cytochromeb (MT-CYB). We followed the parameters Gap open penalty (5), Gap extension penalty (0.2) and Terminal gap penalties (0.1) and selected two pairs of primers according to the DNA-LM. We calculated the amplified product of the MT-CO1 gene in 916 pb and the MT-CYB gene in 774 pb in samples from different swamps of the middle Magdalena. We discussed the results from the perspective of validating the specificity of the primers designed, considering the correspondence and identity of gene sequences considered. The primers reported here will contribute to broadening the knowledge of population genetics, biogeography and phylogenetic of the river stingray P. magdalenae.

Keywords : Elasmobranchii; genetics; population; Polymerase Chain Reaction; sequence alignment.

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