Soybean Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland, United States of America.
PLoS One. 2013;8(1):e54985. doi: 10.1371/journal.pone.0054985. Epub 2013 Jan 25.
The objective of this research was to identify single nucleotide polymorphisms (SNPs) and to develop an Illumina Infinium BeadChip that contained over 50,000 SNPs from soybean (Glycine max L. Merr.). A total of 498,921,777 reads 35-45 bp in length were obtained from DNA sequence analysis of reduced representation libraries from several soybean accessions which included six cultivated and two wild soybean (G. soja Sieb. et Zucc.) genotypes. These reads were mapped to the soybean whole genome sequence and 209,903 SNPs were identified. After applying several filters, a total of 146,161 of the 209,903 SNPs were determined to be ideal candidates for Illumina Infinium II BeadChip design. To equalize the distance between selected SNPs, increase assay success rate, and minimize the number of SNPs with low minor allele frequency, an iteration algorithm based on a selection index was developed and used to select 60,800 SNPs for Infinium BeadChip design. Of the 60,800 SNPs, 50,701 were targeted to euchromatic regions and 10,000 to heterochromatic regions of the 20 soybean chromosomes. In addition, 99 SNPs were targeted to unanchored sequence scaffolds. Of the 60,800 SNPs, a total of 52,041 passed Illumina's manufacturing phase to produce the SoySNP50K iSelect BeadChip. Validation of the SoySNP50K chip with 96 landrace genotypes, 96 elite cultivars and 96 wild soybean accessions showed that 47,337 SNPs were polymorphic and generated successful SNP allele calls. In addition, 40,841 of the 47,337 SNPs (86%) had minor allele frequencies ≥ 10% among the landraces, elite cultivars and the wild soybean accessions. A total of 620 and 42 candidate regions which may be associated with domestication and recent selection were identified, respectively. The SoySNP50K iSelect SNP beadchip will be a powerful tool for characterizing soybean genetic diversity and linkage disequilibrium, and for constructing high resolution linkage maps to improve the soybean whole genome sequence assembly.
本研究的目的是鉴定单核苷酸多态性（SNP），并开发一种包含超过 50,000 个大豆（Glycine max L. Merr.）SNP 的 Illumina Infinium BeadChip。从六个栽培大豆和两个野生大豆（G. soja Sieb. et Zucc.）基因型的简化基因组文库的 DNA 序列分析中获得了总计 498,921,777 个 35-45bp 的读取。这些读取被映射到大豆全基因组序列上，鉴定出了 209,903 个 SNP。应用几种过滤器后，从 209,903 个 SNP 中确定了 146,161 个 SNP 作为 Illumina Infinium II BeadChip 设计的理想候选物。为了使所选 SNP 之间的距离相等，提高检测成功率，并最小化具有低次要等位基因频率的 SNP 数量，开发了一种基于选择指数的迭代算法，并用于选择 60,800 个 SNP 用于 Infinium BeadChip 设计。在 60,800 个 SNP 中，有 50,701 个 SNP 靶向 20 个大豆染色体的常染色质区域，有 10,000 个 SNP 靶向异染色质区域。此外，有 99 个 SNP 靶向未锚定序列支架。在 60,800 个 SNP 中，共有 52,041 个 SNP 通过了 Illumina 的制造阶段，生成了 SoySNP50K iSelect BeadChip。用 96 个地方品种、96 个优良品种和 96 个野生大豆品系对 SoySNP50K 芯片进行验证，结果显示 47,337 个 SNP 具有多态性，并产生了成功的 SNP 等位基因调用。此外，在地方品种、优良品种和野生大豆品系中，有 40,841 个 SNP（86%）的次要等位基因频率≥10%。分别鉴定到 620 个和 42 个候选区域，这些区域可能与驯化和近期选择有关。SoySNP50K iSelect SNP 珠芯片将成为一种强大的工具，用于描述大豆遗传多样性和连锁不平衡，并用于构建高分辨率连锁图谱，以提高大豆全基因组序列组装。
