Comparison of SNPs and microsatellites for assessing the genetic structure of chicken populations
Comparison of SNPs and microsatellites for assessing the genetic structure of chicken populations
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DOI：
10.1111/j.1365-2052.2011.02284.x
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发表时间：
2012-08-01
期刊：
影响因子：
2.4
通讯作者：
Simianer, H.
中科院分区：
文献类型：
--
作者：
Gaerke, C.;Ytournel, F.;Simianer, H.
人类遗传学的许多研究比较了单核苷酸多态性（SNP）和微卫星（单序列重复; SSR）在基因组扫描中的信息量，但由于不同的群体结构，很难将结果直接转移到牲畜身上。本研究的目的是确定获得与给定标准微卫星组相同的分化能力所需的SNP数量。对8个鸡品种进行了29个SSR和9216个SNPs的基因分型。过滤后，仅剩下2931个SNP。使用两种方法评估区分能力：基于主成分分析（PCA）和基于贝叶斯模型的聚类方法的欧氏距离矩阵的分区。通常，使用基于PCA的划分，70个SNP提供与29个SSR相当的分辨率。在基于模型的聚类中，与SSR相比，SNP的重复运行之间的相似性系数显示出显著更高的值。对于隶属系数，反映了基因组的一部分片段属于第i个聚类的比例，分别获得了29个SSR和100个SNPs的最高值。由于基因座数量较少（29个SSR或=100个SNP），两种标记类型都无法检测到戈多洛Nhx群体中的混合物。使用超过250个SNP可以更详细地了解遗传结构。因此，可以检测混合种群。它的结论是，品种分化研究将大大增加权力，即使有中等数量的SNPs。
Many studies in human genetics compare informativeness of single-nucleotide polymorphisms (SNPs) and microsatellites (single sequence repeats; SSR) in genome scans, but it is difficult to transfer the results directly to livestock because of different population structures. The aim of this study was to determine the number of SNPs needed to obtain the same differentiation power as with a given standard set of microsatellites. Eight chicken breeds were genotyped for 29 SSRs and 9216 SNPs. After filtering, only 2931 SNPs remained. The differentiation power was evaluated using two methods: partitioning of the Euclidean distance matrix based on a principal component analysis (PCA) and a Bayesian model-based clustering approach. Generally, with PCA-based partitioning, 70 SNPs provide a comparable resolution to 29 SSRs. In model-based clustering, the similarity coefficient showed significantly higher values between repeated runs for SNPs compared to SSRs. For the membership coefficients, reflecting the proportion to which a fraction segment of the genome belongs to the ith cluster, the highest values were obtained for 29 SSRs and 100 SNPs respectively. With a low number of loci (29 SSRs or =100 SNPs), neither marker types could detect the admixture in the Godollo Nhx population. Using more than 250 SNPs allowed a more detailed insight into the genetic architecture. Thus, the admixed population could be detected. It is concluded that breed differentiation studies will substantially gain power even with moderate numbers of SNPs.