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

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.

A Genetic and Cytogenetic Map for the Duck (Anas platyrhynchos)

“…One is that the procedure used to construct the library is different. The second is that the frequency of microsatellite DNA regions generally increases with increasing genome sizes (Gibbs et al 1997;Garner 2002). In our enriched library, 41.37% of the clones, which contain microsatellite repeats, are not suitable to develop PCR primers because of the short flanking sequence.…”

Evaluación de la variabilidad genética del tomate de árbol (<em>Solanum betaceum</em> Cav.) en los cultivos de tres provincias del Ecuador por medio de marcadores microsatélites

“…Por otro lado, se ha reportado que el tamaño del genoma tiene incidencia en la eficiencia de la amplificación de los loci microsatélites. La tendencia es que mientras más grande sea el genoma de una especie, mayor es la proporción de primers que no logran producir una amplificación exitosa del ADN [16]. Los genomas del tomate de árbol y de sus especies relacionadas sobresalen por su tamaño: incluso el menor de ellos tiene más ADN que otro taxón de igual número cromosómico (24) dentro de las solanáceas [17].…”

Analysis of transferability of microsatellite primers (SSR) in wild Passiflora species and intraspecific genetic diversity in Passiflora alata

“…The lack of conservation of primer annealing sites may have prevented the amplification of microsatellite loci, namely null alleles (Garner, 2002), and this condition is mostly observed in the event of primer transfer between different species, which usually affects all individuals to the same degree. In the germplasm of Triticum dicoccon Schrank, it was noted that 10 of the 29 SSR primers that were used resulted in null alleles (Teklu et al, 2007).…”