Hamblin Martha T, Warburton Marilyn L, Buckler Edward S
Institute for Genomic Diversity, Cornell University, Ithaca, New York, United States of America.
PLoS One. 2007 Dec 26;2(12):e1367. doi: 10.1371/journal.pone.0001367.
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.
虽然简单序列重复（SSRs）是极其有用的遗传标记，但技术的最新进展已导致向单核苷酸多态性（SNPs）的使用转变。这两类标记不同的突变特性导致杂合性和等位基因频率的差异，这可能对它们在评估亲缘关系和遗传多样性评估中的应用产生影响。我们将基于89个SSRs（主要是二核苷酸重复）的分析与基于来自相同259个自交玉米品系个体的847个SNP的分析进行了比较，这些品系被选来代表当前和历史上用于育种的品系中可用的多样性。与一组847个SNP或554个SNP单倍型相比，SSRs在将种质聚类到群体方面表现更好，并且在基于等位基因共享测量遗传距离时，SSRs提供了更高的分辨率。除了亲缘关系密切的个体对之外，基于SSRs的距离测量与基于SNP的距离测量之间仅存在弱相关性。我们的结果表明：1）在多样性和亲缘关系研究中，需要大量的SNP位点才能取代高度多态的SSRs；2）无论使用何种标记系统，高度分化的玉米品系之间的亲缘关系都难以准确测量。
