Skip to main content
ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #232665

Title: Empirical Comparison of Simple Sequence Repeats and Single Nucleotide Polymorphisms in Assessment of Maize Diversity and Relatedness

item Buckler, Edward - Ed

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/2/2008
Publication Date: 12/26/2008
Citation: Buckler Iv, E.S., Hamblin, M.T., Warburton, M.L. 2008. Empirical Comparison of Simple Sequence Repeats and Single Nucleotide Polymorphisms in Assessment of Maize Diversity and Relatedness. PLoS One. 2(12):e1367.

Interpretive Summary: Simple Sequence Repeats (SSRs), also called microsatellites, have been the genetic markers of choice because they are economical to score, have high allelic diversity and are usually selectively neutral. Recent advances in technology, however, have produced a shift toward single nucleotide polymorphism (SNP) markers, particularly for model organisms with substantial genomic resources. The different properties of SNP and SSR markers arise from inherent differences in their mutational processes as well as from biased sampling practices that intensify the different effects on population mapping and estimates of relatedness.

Technical 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.