Single nucleotide polymorphism discovery from wheat next-generation sequence data
Single nucleotide polymorphism discovery from wheat next-generation sequence data
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DOI：
10.1111/j.1467-7652.2012.00718.x
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发表时间：
2012-08-01
影响因子：
13.8
通讯作者：
Edwards, David
中科院分区：
文献类型：
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作者：
Lai, Kaitao;Duran, Chris;Edwards, David
单核苷酸多态性（snp）是最丰富的分子遗传标记类型，可用于制作高分辨率遗传图谱、标记-性状关联研究和标记辅助育种。大型多倍体基因组，如小麦，对SNP的发现提出了挑战，因为每个基因可能存在多个同源物。AutoSNPdb已经成功地应用于从Sanger序列数据中识别包括大麦、水稻和芸芥在内的几个物种的snp，但是准确调用小麦复杂基因组中的snp所需的数据量阻碍了它在这一重要作物中的应用。随着下一代测序技术的引入，DNA测序技术已经发生了革命性的变化，现在可以及时和经济地产生数百万个序列读取。我们使用454测序技术生成了小麦转录组序列数据，并使用改进的autoSNPdb方法将其应用于SNP发现，该方法将SNP和基因注释信息与图形查看器集成在一起。对3个面包小麦品种的4 694 141个序列进行测序，共鉴定出38 928个候选snp。每个SNP都在一个带有注释的组装中，从而可以在感兴趣的基因中选择多态性。
Single nucleotide polymorphisms (SNPs) are the most abundant type of molecular genetic marker and can be used for producing high-resolution genetic maps, marker-trait association studies and marker-assisted breeding. Large polyploid genomes such as wheat present a challenge for SNP discovery because of the potential presence of multiple homoeologs for each gene. AutoSNPdb has been successfully applied to identify SNPs from Sanger sequence data for several species, including barley, rice and Brassica, but the volume of data required to accurately call SNPs in the complex genome of wheat has prevented its application to this important crop. DNA sequencing technology has been revolutionized by the introduction of next-generation sequencing, and it is now possible to generate several million sequence reads in a timely and cost-effective manner. We have produced wheat transcriptome sequence data using 454 sequencing technology and applied this for SNP discovery using a modified autoSNPdb method, which integrates SNP and gene annotation information with a graphical viewer. A total of 4 694 141 sequence reads from three bread wheat varieties were assembled to identify a total of 38 928 candidate SNPs. Each SNP is within an assembly complete with annotation, enabling the selection of polymorphism within genes of interest.