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Genome size and microsatellites: the effect of nuclear size on amplification potential

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Abstract:

Although the frequency of microsatellite DNA regions generally increases with increasing genome size, genome size has a negative effect on polymerase chain reaction (PCR) amplification. Thus, researchers developing sets of PCR primers, as is commonly done for microsatellite DNA regions, may encounter greater difficulty when working with species that have larger genomes. I investigated the effect of genome size on overall amplification success using data from nine different metazoan taxa. The proportion of primer sets that did not amplify PCR products was strongly and positively correlated with the haploid C value of the target species. Increasing genome size may affect amplification success negatively because of a decrease in target:nontarget DNA or by dilution of the available primer pool by nonspecific binding.Key words: microsatellites, genome size, amplification success.

Bien que la fréquence des microsatellites augmente généralement avec la taille du génome, la taille du génome a un effet négatif sur la réaction d'amplification à la polymérase (PCR). Ainsi, des chercheurs qui développent des amorces PCR, tel que cela se fait communément pour les microsatellites, peuvent rencontrer de plus grandes difficultés lorsqu'ils travaillent sur des espèces à grand génome. L'auteur a examiné l'effet de la taille du génome sur le taux de succès des amplifications en employant les données provenant de neuf taxons de métazoaires. La proportion des jeux d'amorces qui n'ont pas produit des amplicons était fortement et positivement corrélée avec le contenu en ADN de l'espèce à l'étude. L'accroissement de la taille du génome pourrait influencer négativement l'amplification en raison d'un accroissement de l'ADN non-cible par rapport à l'ADN cible ou encore par une diminution de la concentration d'amorces disponibles en raison de l'appariement non-spécifique.Mots clés : microsatellites, taille du génome, succès de l'amplification.[Traduit par la Rédaction]

Keywords: amplification success; genome size; microsatellites; succès de l'amplification; taille du génome

Document Type: Research Article

Publication date: February 1, 2002

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  • From its inception in 1957, this international cytogenetics journal has catered to the research areas of the members of the Genetics Society of Canada; traditionally, these have included agriculture, entomology, genetics/cytogenetics, and evolutionary mechanisms. The contents of the journal have evolved as contributors developed new technologies and interests. A 20-member Editorial Board is composed of scientists from around the world. Reviews and commentary from respected experts are often featured.
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