Australian Centre for Plant Functional Genomics, School of Agriculture and Food Science, University of Queensland, Brisbane, QLD 4072, Australia.
Centre for Integrative Legume Research, School of Agriculture and Food Science, University of Queensland, Brisbane, QLD 4072, Australia.
Biology (Basel). 2012 Aug 27;1(2):370-82. doi: 10.3390/biology1020370.
Single nucleotide polymorphisms (SNPs) are becoming the dominant form of molecular marker for genetic and genomic analysis. The advances in second generation DNA sequencing provide opportunities to identify very large numbers of SNPs in a range of species. However, SNP identification remains a challenge for large and polyploid genomes due to their size and complexity. We have developed a pipeline for the robust identification of SNPs in large and complex genomes using Illumina second generation DNA sequence data and demonstrated this by the discovery of SNPs in the hexaploid wheat genome. We have developed a SNP discovery pipeline called SGSautoSNP (Second-Generation Sequencing AutoSNP) and applied this to discover more than 800,000 SNPs between four hexaploid wheat cultivars across chromosomes 7A, 7B and 7D. All SNPs are presented for download and viewing within a public GBrowse database. Validation suggests an accuracy of greater than 93% of SNPs represent polymorphisms between wheat cultivars and hence are valuable for detailed diversity analysis, marker assisted selection and genotyping by sequencing. The pipeline produces output in GFF3, VCF, Flapjack or Illumina Infinium design format for further genotyping diverse populations. As well as providing an unprecedented resource for wheat diversity analysis, the method establishes a foundation for high resolution SNP discovery in other large and complex genomes.
单核苷酸多态性（SNPs）正成为遗传和基因组分析中分子标记的主要形式。第二代 DNA 测序技术的进步为在多种物种中识别大量 SNP 提供了机会。然而，由于其大小和复杂性，SNP 的识别仍然是大型和多倍体基因组的一个挑战。我们已经开发了一种使用 Illumina 第二代 DNA 测序数据在大型和复杂基因组中稳健识别 SNP 的管道，并通过在六倍体小麦基因组中发现 SNP 来证明这一点。我们开发了一种称为 SGSautoSNP（第二代测序自动 SNP）的 SNP 发现管道，并将其应用于在染色体 7A、7B 和 7D 上的四个六倍体小麦品种之间发现超过 800,000 个 SNP。所有 SNP 都可在公共 GBrowse 数据库中下载和查看。验证表明，超过 93%的 SNP 代表小麦品种之间的多态性，因此对于详细的多样性分析、标记辅助选择和测序基因分型非常有价值。该管道以 GFF3、VCF、Flapjack 或 Illumina Infinium 设计格式生成输出，用于对不同群体进行进一步基因分型。该方法不仅为小麦多样性分析提供了前所未有的资源，还为其他大型和复杂基因组中高分辨率 SNP 发现奠定了基础。
