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The Significance of PCR Primer Design in Genetic Diversity Studies: Exemplified by Recent Research into the Genetic Structure of Marine Species

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PCR Primer Design

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2392))

Abstract

Genetic markers are widely applied in the study of genetic diversity for many species. The approach incorporates a Polymerase Chain Reaction (PCR) amplification of targeted sequences in the genome. Crucial for the overall success of a PCR experiment is the careful design of synthetic oligonucleotide primers. Ideally designed primer pairs will ensure the efficiency and specificity of the amplification reaction, resulting in a high yield of the desired amplicon. Important criteria such as primer-sequence, −length, and -melting temperature (Tm) are fundamental for the selection of primers and amplification of targeted nucleotide sequences from a DNA template. There are many computational tools available to assist with critical bioinformatics issues related to primer design. These resources allow the user to define parameters and criteria that need to be taken into account when designing primers. Following the initial in silico selection, a primer pair should be further tested in vivo for their amplification efficiency and robustness.

Using examples taken from genetic diversity studies in a marine crustacean, this chapter provides outlines for the application of PCR technology and discusses details for the design of primers for the development and characterization of microsatellite and SNP-markers.

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Acknowledgments

This work was supported by the Research Council of Oman (TRC) (ORG/SQU/EBR/13/027) and by the Deanship of Research at the Sultan Qaboos University (IG/DVC/CEMB/14/01). We acknowledge all researchers, students, and members of the research group for their contributions to these projects.

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Authors and Affiliations

  1. Centre of Excellence in Marine Biotechnology, Sultan Qaboos University, Al-Khoud, Sultanate of Oman

    Madjid Delghandi

  2. College of Medicine & Health Sciences, Sultan Qaboos University, Al-Khoud, Sultanate of Oman

    Marit Pedersen Delghandi

  3. Water Farmers, Hatrival, Belgium

    Stephen Goddard

Authors
  1. Madjid Delghandi
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  2. Marit Pedersen Delghandi
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  3. Stephen Goddard
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Corresponding author

Correspondence to Madjid Delghandi .

Editor information

Editors and Affiliations

  1. Department of Biology, California State University, Northridge, Los Angeles, CA, USA

    Chhandak Basu

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Delghandi, M., Delghandi, M.P., Goddard, S. (2022). The Significance of PCR Primer Design in Genetic Diversity Studies: Exemplified by Recent Research into the Genetic Structure of Marine Species. In: Basu, C. (eds) PCR Primer Design. Methods in Molecular Biology, vol 2392. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1799-1_1

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  • DOI: https://doi.org/10.1007/978-1-0716-1799-1_1

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1798-4

  • Online ISBN: 978-1-0716-1799-1

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