Empirical comparison of Simple Sequence Repeats and single nucleotide polymorphisms in assessment of maize diversity and relatedness.
Empirical comparison of Simple Sequence Repeats and single nucleotide polymorphisms in assessment of maize diversity and relatedness.
复制标题
在评估玉米多样性和相关性评估中简单序列重复和单核苷酸多态性的经验比较。
DOI：
10.1371/journal.pone.0001367
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发表时间：
2007-12-26
期刊：
影响因子：
3.7
通讯作者：
Buckler, Edward S.
中科院分区：
文献类型：
--
作者：
Hamblin, Martha T.;Warburton, Marilyn L.;Buckler, Edward S.
虽然简单序列重复（SSRs）是非常有用的遗传标记，但最近的技术进步已经产生了使用单核苷酸多态性（snp）的转变。这两类标记的不同突变特性导致了杂合度和等位基因频率的差异，这可能对它们在评估亲缘性和遗传多样性方面的应用产生影响。我们将基于89个ssr（主要是二核苷酸重复序列）的分析结果与基于相同259个自交系个体的847个snp的分析结果进行了比较，这些自交系被选择来代表育种中使用的当前和历史系之间可用的多样性。与847个SNP或554个SNP单倍型相比，SSRs在将种质聚类成群体方面表现更好，并且SSRs在基于等位基因共享的遗传距离测量中提供了更高的分辨率。除了密切相关的个体对外，基于ssr的距离测量与基于snp的距离测量仅呈弱相关。我们的研究结果表明，1)在多样性和亲缘性研究中，需要大量的SNP位点来取代高度多态性的SSRs； 2)无论采用何种标记系统，高度分化的玉米品系之间的亲缘性都难以准确测量。
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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