Estimate of nucleotide diversity in dogs with a pool-and-sequence method
Estimate of nucleotide diversity in dogs with a pool-and-sequence method
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DOI：
10.1007/s003350010220
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发表时间：
2000-12-01
期刊：
影响因子：
2.5
通讯作者：
Venta, PJ
中科院分区：
文献类型：
--
作者：
Brouillette, JA;Andrew, JR;Venta, PJ
核苷酸多样性（pi）是指从群体中随机选择的两个同源序列在每个位点上的碱基差异的平均值，是了解群体结构和历史的重要参数。这对于确定从单核苷酸多态性（SNPs）开发物种遗传图谱的可行性也很重要。从未对狗的核苷酸多样性进行过估计。采用池-序列法对来自10个不同犬种的12个犬基因片段进行核苷酸变异分析。我们在编码区（2501 bp）鉴定了3个snp，在内含子（2953 bp）鉴定了11个snp。每个假定的snp都通过限制性内切酶分析进行了测试，并且都得到了验证。在一个基因中含有的单个SINE中鉴定出6个额外的snp。利用这些数据，估计犬种之间的序列多样性在内含子区和编码区分别为0.001和0.0004，SNPs平均间隔为400bp。在12个基因中发现了7个有用的snp，这表明用目前的技术可以完成犬类snp图谱的构建。在猫、马、牛和猪的5847 bp中发现了13个多态性snp，使用了4个相同的基因，估计了犬的核苷酸多样性。这些结果表明，这些物种可能具有相似数量的核苷酸多样性。
Nucleotide diversity (pi), the average number of base differences per site for two homologous sequences randomly selected from a population, is an important parameter used to understand the structure and history of populations. It is also important for determining the feasibility of developing a genetic map for a species from single nucleotide polymorphisms (SNPs). Nucleotide diversity has never been estimated for dogs. Segments of twelve canine genes from ten diverse dog breeds were examined for nucleotide variation by using a pool-and-sequence method. We identified three SNPs in the coding regions (2501 bp) and 11 SNPs in the introns (2953 bp). Each of these putative SNPs was tested by restriction enzyme analysis, and all were verified. Six additional SNPs were identified in a single SINE contained in one gene. Using these data, canine sequence diversity across breeds was estimated to be 0.001 and 0.0004 in intronic and coding regions, respectively, with SNPs spaced every 400 bp on average. Discovery of useful SNPs in 7 of the 12 genes suggests that construction of a canine SNP-based map can be accomplished with current technology. Thirteen polymorphic SNPs were also found in 5847 bp in the cat, horse, ox, and pig, by using four of the same genes from which canine nucleotide diversity was estimated. These results suggest that these species may have similar amounts of nucleotide diversity.