Development and Evaluation of High-Density SNP Arrays for the Eastern Oyster Crassostrea virginica
Development and Evaluation of High-Density SNP Arrays for the Eastern Oyster Crassostrea virginica
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DOI：
10.1007/s10126-022-10191-3
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发表时间：
2023-01-09
影响因子：
3
通讯作者：
Wilbur, Ami
中科院分区：
文献类型：
--
作者：
Guo, Ximing;Puritz, Jonathan B.;Wilbur, Ami
东部牡蛎 Crassostrea virginica 是美国的主要水产养殖品种。东部牡蛎养殖业的可持续发展有赖于通过先进的养殖技术不断改良养殖种群。东部牡蛎育种联盟 (EOBC) 的成立是为了促进东部牡蛎的遗传学和育种。为了促进基因组研究和选择所需的高效基因分型，该联盟为东部牡蛎开发了两种单核苷酸多态性 (SNP) 阵列：一种具有 566K SNP 的筛选阵列和一种具有 66K SNP 的育种阵列。 566K 筛查阵列是根据来自大西洋和墨西哥湾种群的 292 个牡蛎的全基因组重测序数据开发的；它包含 566,262 个 SNP，其中来自蛋白质编码基因的 47K 个 SNP，标记转换率为 48.34%。 66K芯片是利用筛选芯片中性能最佳的SNP开发的，其中包含65,893个牡蛎SNP，包括22,984个基因标记，检出率为99.34%，一致性率为99.81%，标记转化率为92.04%，大大提高。在 13.1% 的 SNP 中发现了可归因于大插入缺失的无效等位基因，这表明拷贝数变异是普遍存在的。两种阵列都可以轻松地从野生祖种群中识别和分离选定的种群。该芯片包含 31 个线粒体 SNP，可以明确识别一些大西洋人群中的海湾线粒体基因型。该阵列还包含来自 13 种牡蛎和人类病原体的 756 个探针，用于可能的检测。我们的结果表明，高多态性物种的标记转化率较低，并且阵列开发的两步过程可以极大地提高阵列性能。这两个阵列将通过描绘生产性状的遗传结构和实现基因组选择来推进基因组研究并加速东部牡蛎的遗传改良。该阵列还可用于监测谱系和近交、识别选定种群及其向野生种群的渗入，并评估牡蛎恢复的成功。
The eastern oyster Crassostrea virginica is a major aquaculture species for the USA. The sustainable development of eastern oyster aquaculture depends upon the continued improvement of cultured stocks through advanced breeding technologies. The Eastern Oyster Breeding Consortium (EOBC) was formed to advance the genetics and breeding of the eastern oyster. To facilitate efficient genotyping needed for genomic studies and selection, the consortium developed two single-nucleotide polymorphism (SNP) arrays for the eastern oyster: one screening array with 566K SNPs and one breeders' array with 66K SNPs. The 566K screening array was developed based on whole-genome resequencing data from 292 oysters from Atlantic and Gulf of Mexico populations; it contains 566,262 SNPs including 47K from protein-coding genes with a marker conversion rate of 48.34%. The 66K array was developed using best-performing SNPs from the screening array, which contained 65,893 oyster SNPs including 22,984 genic markers with a calling rate of 99.34%, a concordance rate of 99.81%, and a much-improved marker conversion rate of 92.04%. Null alleles attributable to large indels were found in 13.1% of the SNPs, suggesting that copy number variation is pervasive. Both arrays provided easy identification and separation of selected stocks from wild progenitor populations. The arrays contain 31 mitochondrial SNPs that allowed unambiguous identification of Gulf mitochondrial genotypes in some Atlantic populations. The arrays also contain 756 probes from 13 oyster and human pathogens for possible detection. Our results show that marker conversion rate is low in high polymorphism species and that the two-step process of array development can greatly improve array performance. The two arrays will advance genomic research and accelerate genetic improvement of the eastern oyster by delineating genetic architecture of production traits and enabling genomic selection. The arrays also may be used to monitor pedigree and inbreeding, identify selected stocks and their introgression into wild populations, and assess the success of oyster restoration.