Abstract
While Simple Sequence Repeats (SSRs) are extremely useful genetic markers, recent advances in technology have produced a shift toward use of single nucleotide polymorphisms (SNPs). The different mutational properties of these two classes of markers result in differences in heterozygosities and allele frequencies that may have implications for their use in assessing relatedness and evaluation of genetic diversity. We compared analyses based on 89 SSRs (primarily dinucleotide repeats) to analyses based on 847 SNPs in individuals from the same 259 inbred maize lines, which had been chosen to represent the diversity available among current and historic lines used in breeding. The SSRs performed better at clustering germplasm into populations than did a set of 847 SNPs or 554 SNP haplotypes, and SSRs provided more resolution in measuring genetic distance based on allele-sharing. Except for closely related pairs of individuals, measures of distance based on SSRs were only weakly correlated with measures of distance based on SNPs. Our results suggest that 1) large numbers of SNP loci will be required to replace highly polymorphic SSRs in studies of diversity and relatedness and 2) relatedness among highly-diverged maize lines is difficult to measure accurately regardless of the marker system.
Highlights
Until recently, Simple Sequence Repeats (SSRs), called microsatellites, have been the genetic markers of choice, because they are economical to score, have high allelic diversity, and are usually selectively neutral [1]
We found that a set of 89 highly polymorphic SSRs performed better at clustering germplasm into populations than did a set of 847 single nucleotide polymorphism (SNP) or 554 SNP haplotypes, and that SSRs provided more resolution in measuring genetic distance based on allele-sharing
Our analysis showed that most maize lines in a diverse sample are separated by a large genetic distance and, consistent with the results of Jones et al [19], that measures of distance based on different markers were well-correlated only for the small subset of individuals that were closely related
Summary
Simple Sequence Repeats (SSRs), called microsatellites, have been the genetic markers of choice, because they are economical to score, have high allelic diversity, and are usually selectively neutral [1]. While re-sequencing studies can detect large numbers of singleton SNPs in many population samples (depending on population history), the selection of informative SNPs for genotyping studies (i.e., ascertainment) ensures that most SNP marker alleles will segregate at intermediate frequency, exaggerating the difference in frequency spectrum that already exists between SNPs and SSRs [3,4]. This ascertainment bias must be corrected if SNP data are to be used in estimation of population genetic parameters
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