Construction and evaluation of a high-density SNP array for the Pacific oyster (Crassostrea gigas).
Construction and evaluation of a high-density SNP array for the Pacific oyster (Crassostrea gigas).
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太平洋牡蛎 (Crassostrea gigas) 高密度 SNP 阵列的构建和评估
DOI：
10.1371/journal.pone.0174007
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发表时间：
2017
期刊：
影响因子：
3.7
通讯作者：
Zhang G
中科院分区：
文献类型：
--
作者：
Qi H;Song K;Li C;Wang W;Li B;Li L;Zhang G
单核苷酸多态性在遗传学和基因组学研究中有着广泛的应用。太平洋牡蛎（长牡蛎）是一种具有重要经济和生态意义的海洋双壳类动物，是动物物种中基因组DNA变异水平最高的物种之一。太平洋牡蛎的snp已被广泛研究；然而，这些snp以高通量、可转移和经济的方式使用的机制仍有待阐明。本研究利用Affymetrix Axiom基因分型技术构建了一个牡蛎190K SNP阵列。我们在芯片上设计了190,420个snp；这些snp是从中国、日本、韩国和加拿大收集的472种太平洋牡蛎的5400万个snp中挑选出来的。我们的基因分型结果显示，133984个（70.4%）snp是多态性的，并成功转化在芯片上。这些snp在整个牡蛎基因组中分布均匀，分布在3595个长度约为5.094亿的支架中；平均层间距为4210 bp。此外，在21,050个编码基因中分布了111,158个snp，平均每个基因5.3个snp。与重测序获得的基因型相比，~69%的转换snp的一致性率为bb0 0.971；平均一致性率为0.966。基于全同胞家族个体基因型的评估结果显示，平均基因分型准确率为0.975。我们的牡蛎190K SNP阵列携带133 K多态SNP，是第一个商用的软体动物高密度SNP芯片，具有最高的吞吐量。它代表了牡蛎全基因组关联研究、精细连锁定位和群体遗传学的一个有价值的工具。
Single nucleotide polymorphisms (SNPs) are widely used in genetics and genomics research. The Pacific oyster (Crassostrea gigas) is an economically and ecologically important marine bivalve, and it possesses one of the highest levels of genomic DNA variation among animal species. Pacific oyster SNPs have been extensively investigated; however, the mechanisms by which these SNPs may be used in a high-throughput, transferable, and economical manner remain to be elucidated. Here, we constructed an oyster 190K SNP array using Affymetrix Axiom genotyping technology. We designed 190,420 SNPs on the chip; these SNPs were selected from 54 million SNPs identified through re-sequencing of 472 Pacific oysters collected in China, Japan, Korea, and Canada. Our genotyping results indicated that 133,984 (70.4%) SNPs were polymorphic and successfully converted on the chip. The SNPs were distributed evenly throughout the oyster genome, located in 3,595 scaffolds with a length of ~509.4 million; the average interval spacing was 4,210 bp. In addition, 111,158 SNPs were distributed in 21,050 coding genes, with an average of 5.3 SNPs per gene. In comparison with genotypes obtained through re-sequencing, ~69% of the converted SNPs had a concordance rate of >0.971; the mean concordance rate was 0.966. Evaluation based on genotypes of full-sib family individuals revealed that the average genotyping accuracy rate was 0.975. Carrying 133 K polymorphic SNPs, our oyster 190K SNP array is the first commercially available high-density SNP chip for mollusks, with the highest throughput. It represents a valuable tool for oyster genome-wide association studies, fine linkage mapping, and population genetics.