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

Madjid Delghandi*, Marit Pedersen Delghandi, Stephen Goddard

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingChapter

1 Citation (Scopus)


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.

Original languageEnglish
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Number of pages13
Publication statusPublished - 2022

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029


  • Genetic markers
  • Marine species
  • Microsatellite markers
  • Molecular tools
  • Oligonucleotide design
  • Polymerase Chain Reaction
  • Population genetics studies
  • SNP markers

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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