Cross-species amplification, non-invasive genotyping, and non-Mendelian inheritance of human STRPs in Savannah baboons

Abstract

Twenty-nine human microsatellite primer pairs were screened for their utility in the cross-species amplification of baboon DNA derived from both blood and feces as part of a larger study to identify paternal half sisters in a population of wild baboons (Papio cynocephalus). Forty-one percent (12/29) of the human primers successfully amplified baboon DNA. Of these 12 primers, six amplified fragments that were both polymorphic and heterozygous (mean number of alleles = 6, mean heterozygosity = 87%) and yielded repeatable results. However, only five of these six simple tandem repeat polymorphisms (STRPs) showed patterns of Mendelian inheritance (i.e., mothers and offspring shared at least one allele at each locus), and were therefore useful for determining relatedness between individuals. Analysis of the sixth primer revealed non-Mendelian inheritance, i.e., three of the six known mother-daughter pairs had no shared alleles. This failure was probably due to non-specific fragment amplification, and may have resulted from a different STRP locus being amplified in mother and daughter. This finding highlights the importance of sampling DNA from known parent-offspring pairs when screening microsatellite primers for genetic studies. Multiple, independent replications of genotypes and Mendelian checks are both particularly important when using crossspecies amplification or when using a low-quality source of DNA.

Toward developing a genome‐wide microsatellite marker set for linkage analysis in the rhesus macaque (Macaca mulatta): Identification of 76 polymorphic markers

“…When primers to human markers were tested in the baboon, and optimization of magnesium concentration and annealing temperature was carried out, 24% were successful [Morin et al, 1998]. This is consistent with our 19% success rate, without optimization of PCR conditions; similar results have also been obtained by other groups [Coote & Bruford, 1996;Smith et al, 2000]. Interestingly, five of the markers that were successful and polymorphic in the rhesus macaque were also identified by Morin et al [1998] as successful in the baboon.…”

Toward developing a genome‐wide microsatellite marker set for linkage analysis in the rhesus macaque (Macaca mulatta): Identification of 76 polymorphic markers

“…When primers to human markers were tested in the baboon, and optimization of magnesium concentration and annealing temperature was carried out, 24% were successful [Morin et al, 1998]. This is consistent with our 19% success rate, without optimization of PCR conditions; similar results have also been obtained by other groups [Coote & Bruford, 1996;Smith et al, 2000]. Interestingly, five of the markers that were successful and polymorphic in the rhesus macaque were also identified by Morin et al [1998] as successful in the baboon.…”

Population genetics of the California National Primate Research Center’s (CNPRC) captive Callicebus cupreus colony

“…Other studies have shown that cross-species amplification using common STR markers may pose a greater challenge than was previously appreciated (Smith et al 2000; Chambers et al 2004). In these other studies, cross-species amplification has proven to be successful for a majority of the markers tested, although the allele numbers and frequencies of some loci in the new population of interest are likely to be lower and contribute less statistical power to the analysis of the new species than to analyses of populations in which the loci were originally identified (Chambers et al 2004).…”

Isolation and characterization of polymorphic microsatellite loci in black sea bream (Acanthopagrus schlegeli) by cross-species amplification with six species of the Sparidae family

“…It is increasingly apparent that cross-species amplification using common microsatellite markers may pose a greater challenge than was previously believed (Primmer and Merila 2002;Smith et al 2000). A key difficulty is that while cross species amplification may be possible for a sizable percentage of the markers tested, differences in allele numbers and frequencies in the new population of interest mean that only a few of these cross-amplified markers contribute as much statistical power to the analysis of the new species as they did to the first (Morin et al 1998).…”

Toward developing a genome‐wide microsatellite marker set for linkage analysis in the rhesus macaque (Macaca mulatta): Identification of 76 polymorphic markers

“…When primers to human markers were tested in the baboon, and optimization of magnesium concentration and annealing temperature was carried out, 24% were successful [Morin et al, 1998]. This is consistent with our 19% success rate, without optimization of PCR conditions; similar results have also been obtained by other groups [Coote & Bruford, 1996;Smith et al, 2000]. Interestingly, five of the markers that were successful and polymorphic in the rhesus macaque were also identified by Morin et al [1998] as successful in the baboon.…”

Population genetics of the California National Primate Research Center’s (CNPRC) captive Callicebus cupreus colony

“…Other studies have shown that cross-species amplification using common STR markers may pose a greater challenge than was previously appreciated (Smith et al 2000; Chambers et al 2004). In these other studies, cross-species amplification has proven to be successful for a majority of the markers tested, although the allele numbers and frequencies of some loci in the new population of interest are likely to be lower and contribute less statistical power to the analysis of the new species than to analyses of populations in which the loci were originally identified (Chambers et al 2004).…”

Isolation and characterization of polymorphic microsatellite loci in black sea bream (Acanthopagrus schlegeli) by cross-species amplification with six species of the Sparidae family

“…It is increasingly apparent that cross-species amplification using common microsatellite markers may pose a greater challenge than was previously believed (Primmer and Merila 2002;Smith et al 2000). A key difficulty is that while cross species amplification may be possible for a sizable percentage of the markers tested, differences in allele numbers and frequencies in the new population of interest mean that only a few of these cross-amplified markers contribute as much statistical power to the analysis of the new species as they did to the first (Morin et al 1998).…”

Toward developing a genome‐wide microsatellite marker set for linkage analysis in the rhesus macaque (Macaca mulatta): Identification of 76 polymorphic markers

“…When primers to human markers were tested in the baboon, and optimization of magnesium concentration and annealing temperature was carried out, 24% were successful [Morin et al, 1998]. This is consistent with our 19% success rate, without optimization of PCR conditions; similar results have also been obtained by other groups [Coote & Bruford, 1996;Smith et al, 2000]. Interestingly, five of the markers that were successful and polymorphic in the rhesus macaque were also identified by Morin et al [1998] as successful in the baboon.…”

Population genetics of the California National Primate Research Center’s (CNPRC) captive Callicebus cupreus colony

“…Other studies have shown that cross-species amplification using common STR markers may pose a greater challenge than was previously appreciated (Smith et al 2000; Chambers et al 2004). In these other studies, cross-species amplification has proven to be successful for a majority of the markers tested, although the allele numbers and frequencies of some loci in the new population of interest are likely to be lower and contribute less statistical power to the analysis of the new species than to analyses of populations in which the loci were originally identified (Chambers et al 2004).…”

Isolation and characterization of polymorphic microsatellite loci in black sea bream (Acanthopagrus schlegeli) by cross-species amplification with six species of the Sparidae family

“…It is increasingly apparent that cross-species amplification using common microsatellite markers may pose a greater challenge than was previously believed (Primmer and Merila 2002;Smith et al 2000). A key difficulty is that while cross species amplification may be possible for a sizable percentage of the markers tested, differences in allele numbers and frequencies in the new population of interest mean that only a few of these cross-amplified markers contribute as much statistical power to the analysis of the new species as they did to the first (Morin et al 1998).…”