Development of single nucleotide polymorphism (SNP) markers for use in commercial maize (Zea mays L.) germplasm
Development of single nucleotide polymorphism (SNP) markers for use in commercial maize (Zea mays L.) germplasm
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DOI：
10.1007/s11032-009-9281-z
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发表时间：
2009-09-01
影响因子：
3.1
通讯作者：
Smith, Stephen
中科院分区：
文献类型：
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作者：
Jones, Elizabeth;Chu, Wen-Chy;Smith, Stephen
玉米单核苷酸多态性（SNP）标记的开发为利用DNA标记在群体遗传学、基因发现、植物育种和种质鉴定等许多新领域提供了机会。然而，从测序和SNP发现到SNP标记设计和验证的步骤是漫长而昂贵的。获得一组经过验证的SNP标记对于希望将SNP应用于科学探究的玉米研究人员来说是一个显著的优势。我们在北美和欧洲用于玉米育种的60个公共近交系中挖掘了1088个基因座序列。然后，我们使用通用标记设计标准选择了640个SNP，使其能够与几种SNP化学物质结合使用。在1088个玉米基因序列中，平均每43个碱基发现一个snp，平均每623个碱基发现一个适合标记设计的snp；仅占已发现snp总数的7%。我们还描述了在Illumina(a(R)) BeadArray （TM）平台上使用的768标记多重检测的开发。利用IBM2分离群体或多亲代三胞胎分离，在IBM2杂交B73 x Mo17高分辨率遗传图谱上定位SNP标记。与遗传嵌套关联图谱有高度的共线性。对于每个SNP，我们给出了地图位置、不同杂种优势群体的多态性率以及在Illumina（A (R)）平台上的表现。
The development of single nucleotide polymorphism (SNP) markers in maize offers the opportunity to utilize DNA markers in many new areas of population genetics, gene discovery, plant breeding and germplasm identification. However, the steps from sequencing and SNP discovery to SNP marker design and validation are lengthy and expensive. Access to a set of validated SNP markers is a significant advantage to maize researchers who wish to apply SNPs in scientific inquiry. We mined 1,088 loci sequenced across 60 public inbreds that have been used in maize breeding in North America and Europe. We then selected 640 SNPs using generalized marker design criteria that enable utilization with several SNP chemistries. While SNPs were found on average every 43 bases in 1,088 maize gene sequences, SNPs that were amenable to marker design were found on average every 623 bases; representing only 7% of the total SNPs discovered. We also describe the development of a 768 marker multiplex assay for use on the Illumina(A (R)) BeadArray (TM) platform. SNP markers were mapped on the IBM2 intermated B73 x Mo17 high resolution genetic map using either the IBM2 segregating population, or segregation in multiple parent-progeny triplets. A high degree of colinearity was found with the genetic nested association map. For each SNP presented we give information on map location, polymorphism rates in different heterotic groups and performance on the Illumina(A (R)) platform.