Effects of ascertainment bias and marker number on estimations of barley diversity from high-throughput SNP genotype data
Effects of ascertainment bias and marker number on estimations of barley diversity from high-throughput SNP genotype data
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DOI：
10.1007/s00122-010-1273-1
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发表时间：
2010-05-01
影响因子：
5.4
通讯作者：
Russell, Joanne R.
中科院分区：
文献类型：
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作者：
Moragues, M.;Comadran, J.;Russell, Joanne R.
分子标记提供遗传结构信息的能力受其数量和选择方式的影响。本研究评价了单核苷酸多态性（SNP）数量和选择策略对大麦品种和地方品种种质多样性和群体结构估计的影响。来自叙利亚和约旦的169个大麦地方品种和171个欧洲大麦品种共获得1536个snp基因型。根据它们在地方品种或栽培大麦中检测多样性的能力，除了相应的随机选择的子集外，还从1536个集合中选择了384个和96个snp的不同子集。除了地方品种优化子集外，所有SNP集都低估了地方品种种质资源中的多样性，所有SNP子集对栽培种质资源的估计都相似。所有标记子集对两个种质集的群体结构给出了质量上相似的估计，但96个SNP集显示的数据分辨率值远低于较大的SNP集。从这些数据中我们推断，就所获得的数据质量而言，根据种质集的多样性预先选择标记是非常值得的。其次，我们认为，适当选择384个SNP子集为种质鉴定提供了良好的功率和经济性组合，而使用1536个SNP的相当适度的收益并不能证明增加的成本是合理的，96个标记的性能低得令人无法接受。最后，我们提出了一个特定的384个SNP子集作为中东地方大麦的标准基因分型工具。
The capability of molecular markers to provide information of genetic structure is influenced by their number and the way they are chosen. This study evaluates the effects of single nucleotide polymorphism (SNP) number and selection strategy on estimates of germplasm diversity and population structure for different types of barley germplasm, namely cultivar and landrace. One hundred and sixty-nine barley landraces from Syria and Jordan and 171 European barley cultivars were genotyped with 1536 SNPs. Different subsets of 384 and 96 SNPs were selected from the 1536 set, based on their ability to detect diversity in landraces or cultivated barley in addition to corresponding randomly chosen subsets. All SNP sets except the landrace-optimised subsets underestimated the diversity present in the landrace germplasm, and all subsets of SNP gave similar estimates for cultivar germplasm. All marker subsets gave qualitatively similar estimates of the population structure in both germplasm sets, but the 96 SNP sets showed much lower data resolution values than the larger SNP sets. From these data we deduce that pre-selecting markers for their diversity in a germplasm set is very worthwhile in terms of the quality of data obtained. Second, we suggest that a properly chosen 384 SNP subset gives a good combination of power and economy for germplasm characterization, whereas the rather modest gain from using 1536 SNPs does not justify the increased cost and 96 markers give unacceptably low performance. Lastly, we propose a specific 384 SNP subset as a standard genotyping tool for middle-eastern landrace barley.