Development of a Medium Density Combined-Species SNP Array for Pacific and European Oysters (Crassostrea gigas and Ostrea edulis).
Development of a Medium Density Combined-Species SNP Array for Pacific and European Oysters (Crassostrea gigas and Ostrea edulis).
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DOI：
10.1534/g3.117.041780
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发表时间：
2017-07-05
期刊：
影响因子：
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通讯作者：
Houston RD
中科院分区：
文献类型：
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作者：
Gutierrez AP;Turner F;Gharbi K;Talbot R;Lowe NR;Peñaloza C;McCullough M;Prodöhl PA;Bean TP;Houston RD
SNP阵列是高分辨率研究养殖和野生动物复杂性状遗传基础的工具。从生态和经济的角度来看，牡蛎在许多地区都至关重要，牡蛎水产养殖构成了全球粮食安全的一个关键组成部分。本研究的目的是为太平洋牡蛎(Crassostrea Gigas)和欧洲平贝(Ostrea Edulis)设计一个物种组合、中等密度的SNP阵列，并测试该阵列在多个地点的养殖和野生种群上的性能，重点是欧洲种群。SNP的发现是通过对8个群体的基因组DNA样本进行全基因组测序(WGS)和对11个地理上不同的群体进行限制性内切酶相关DNA测序(RAD-Seq)来实现的。根据几个标准发现和筛选了近1200万个候选SNPs，包括偏爱在多个群体中分离的SNPs和具有单态侧翼区域的SNPs。创建了Affymetrix Axiom定制阵列，并在一组不同的样本(n=219)上进行了测试，显示了在这些种群中分离的∼27K高质量SNP和∼11K高质量SNP。在每个群体中都有很高比例的SNP被分离，该阵列被用来检测群体结构和连锁不平衡(LD)水平。对三个千年虫核心家族(n=165)的进一步测试表明，该阵列可用于基于按州身份(IBS)分类的父母分配软件清楚地区分这两个家族。这种中等密度的组合物种阵列将通过Affymetrix公开提供，并将用于全基因组关联和进化遗传学研究，以及牡蛎育种计划中的基因组选择。
SNP arrays are enabling tools for high-resolution studies of the genetic basis of complex traits in farmed and wild animals. Oysters are of critical importance in many regions from both an ecological and economic perspective, and oyster aquaculture forms a key component of global food security. The aim of our study was to design a combined-species, medium density SNP array for Pacific oyster (Crassostrea gigas) and European flat oyster (Ostrea edulis), and to test the performance of this array on farmed and wild populations from multiple locations, with a focus on European populations. SNP discovery was carried out by whole-genome sequencing (WGS) of pooled genomic DNA samples from eight C. gigas populations, and restriction site-associated DNA sequencing (RAD-Seq) of 11 geographically diverse O. edulis populations. Nearly 12 million candidate SNPs were discovered and filtered based on several criteria, including preference for SNPs segregating in multiple populations and SNPs with monomorphic flanking regions. An Affymetrix Axiom Custom Array was created and tested on a diverse set of samples (n = 219) showing ∼27 K high quality SNPs for C. gigas and ∼11 K high quality SNPs for O. edulis segregating in these populations. A high proportion of SNPs were segregating in each of the populations, and the array was used to detect population structure and levels of linkage disequilibrium (LD). Further testing of the array on three C. gigas nuclear families (n = 165) revealed that the array can be used to clearly distinguish between both families based on identity-by-state (IBS) clustering parental assignment software. This medium density, combined-species array will be publicly available through Affymetrix, and will be applied for genome-wide association and evolutionary genetic studies, and for genomic selection in oyster breeding programs.