Analysis of gene-derived SNP marker polymorphism in US wheat (Triticum aestivum L.) cultivars
Analysis of gene-derived SNP marker polymorphism in US wheat (Triticum aestivum L.) cultivars
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DOI：
10.1007/s11032-008-9210-6
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发表时间：
2009-01-01
影响因子：
3.1
通讯作者：
Dubcovsky, Jorge
中科院分区：
文献类型：
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作者：
Chao, Shiaoman;Zhang, Wenjun;Dubcovsky, Jorge
在这项研究中，我们针对先前在小麦基因内含子序列中发现的单核苷酸多态性（SNP）开发了359个检测引物，并用它们来评估普通小麦（Triticum aestivum L.）的SNP多态性。这些 SNP 在代表七个市场类别的 20 个美国优质小麦品种中显示出平均多态性信息含量 (PIC) 为 0.18。当在小麦 SNP 发现项目 (http://wheat.pw.usda.gov/SNP) 中使用的 13 个六倍体小麦种质（不包括合成小麦）中预先选择 SNP 的多态性时，该值增加到 0.23。 D 基因组中 SNP 标记的 PIC 值大约是 A 和 B 基因组中的一半。当将美国品种与更加多样化的 13 个小麦品种进行比较时，D 基因组 SNP 也显示出相对于其他基因组更大的 PIC 减少 (P < 0.05)。在这些种质中，D 基因组 SNP 显示出具有低次要等位基因频率 (< 0.125) 的等位基因比例高于其他两个基因组中的比例。这些数据表明，D 基因组中 PIC 值的降低是由于伴随现代商业品种发展的群体规模瓶颈期间低频等位基因的差异丢失引起的。可能需要针对优良小麦种质中的 D 基因组进行额外的 SNP 发现工作，以抵消该基因组较低的多样性。随着SNP发现项目的增加和高通量SNP检测技术的发展，预计SNP标记将在小麦遗传和育种应用中发挥越来越重要的作用。
In this study, we developed 359 detection primers for single nucleotide polymorphisms ( SNPs) previously discovered within intron sequences of wheat genes and used them to evaluate SNP polymorphism in common wheat ( Triticum aestivum L.). These SNPs showed an average polymorphism information content (PIC) of 0.18 among 20 US elite wheat cultivars, representing seven market classes. This value increased to 0.23 when SNPs were pre-selected for polymorphisms among a diverse set of 13 hexaploid wheat accessions ( excluding synthetic wheats) used in the wheat SNP discovery project (http://wheat.pw.usda.gov/SNP). PIC values for SNP markers in the D genome were approximately half of those for the A and B genomes. D genome SNPs also showed a larger PIC reduction relative to the other genomes (P < 0.05) when US cultivars were compared with the more diverse set of 13 wheat accessions. Within those accessions, D genome SNPs show a higher proportion of alleles with low minor allele frequencies (< 0.125) than found in the other two genomes. These data suggest that the reduction of PIC values in the D genome was caused by differential loss of low frequency alleles during the population size bottleneck that accompanied the development of modern commercial cultivars. Additional SNP discovery efforts targeted to the D genome in elite wheat germplasm will likely be required to offset the lower diversity of this genome. With increasing SNP discovery projects and the development of high-throughput SNP assay technologies, it is anticipated that SNP markers will play an increasingly important role in wheat genetics and breeding applications.