Empirical comparison of Simple Sequence Repeats and single nucleotide polymorphisms in assessment of maize diversity and relatedness - PubMed (original) (raw)

Comparative Study

Empirical comparison of Simple Sequence Repeats and single nucleotide polymorphisms in assessment of maize diversity and relatedness

Martha T Hamblin et al. PLoS One. 2007.

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.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1

Figure 1. Allele frequency spectra for different classes of markers.

Note that the scale on the x axis is different for total SNPs, because only this class is biallelic.

Figure 2

Figure 2. Estimated ln(probability of the data) and Var[ln(probability of the data)] for k from 2 to 5.

Values are from STRUCTURE run three times at each value of k, using A) 89 SSRs; B) 847 SNPs; C) 554 SNP haplotypes; D) 89 SSRs+847 SNPs. The blue diamonds are ln(probability of the data) and the pink squares are var[ln(probability of the data)].

Figure 3

Figure 3. Comparison of membership in population clusters based on marker class.

Each point represents one individual's proportion of ancestry in the NSS (top panel) or TS (bottom panel) cluster, based on SSR (x axis) or SNP (y axis) data assuming three populations. The arrows indicate line F2834T (see text).

Figure 4

Figure 4. Correlation between genetic distance based on SSRs and SNPs.

Each point represents the genetic distance between a pair of individuals, based on sharing of SSR (x axis) or SNP (y axis) alleles. The top panel shows the relationship for pairs of individuals whose SSR distance is <0.65; the bottom panel shows the relationship for pairs of individuals whose SSR distance is ≥0.65.

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