Detection and assessment of copy number variation using PacBio long-read and Illumina sequencing in New Zealand dairy cattle
Detection and assessment of copy number variation using PacBio long-read and Illumina sequencing in New Zealand dairy cattle
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DOI：
10.3168/jds.2016-12199
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发表时间：
2017-07-01
影响因子：
3.5
通讯作者：
Spelman, R. J.
中科院分区：
文献类型：
--
作者：
Couldrey, C.;Keehan, M.;Spelman, R. J.
单核苷酸多态性已成为基因组预测的DNA变体的选择，主要是因为单核苷酸多态性基因型收集的容易性。相比之下，包括拷贝数变异（CNV）、易位、插入和倒位的结构变异（SV）难以检测和表征，特别是在非人类物种中。然而，越来越多的证据表明，SV不仅贡献了相当大比例的遗传变异，但也有显着的影响表型。在这里，我们介绍了使用长读PacBio（Pacific Biosciences，门洛帕克，CA）测序技术和Sniffles SV发现工具（版本0.0.1; https：//github.com/fritzsedlazeck/Sniffies）在新西兰一头著名奶牛中发现CNV。将从长读段鉴定的CNV与使用CNVnator（基于读段深度的工具; Illumina Inc.，San Diego，CA）作为验证手段。随后，使用全基因组Illumina测序对代表更广泛的新西兰奶牛群体的556头牛进行了进一步验证。在从2个测序平台发现的CNV中观察到非常有限的重叠，部分原因是检测到的CNV大小的差异。因此，只有少数CNV能够使用这种方法进行验证。然而，使用CNVnator对557头牛的拷贝数进行基因分型的能力在所有地区被确定为推定的CNV，允许基于系谱对拷贝数的传播水平进行全基因组评估。观察到假定的CNV区域的传播性越高，拷贝数分布在557只测序动物中越可能是多峰的。此外，高传播性CNV区域的视觉评估提供了支持在测序动物中存在CNV的证据。这种基于传播的方法能够确认在新西兰奶牛群体中分离的CNV子集。CNV的全基因组鉴定和验证是将其纳入基因组选择策略的重要一步。
Single nucleotide polymorphisms have been the DNA variant of choice for genomic prediction, largely because of the ease of single nucleotide polymorphism genotype collection. In contrast, structural variants (SV), which include copy number variants (CNV), translocations, insertions, and inversions, have eluded easy detection and characterization, particularly in nonhuman species. However, evidence increasingly shows that SV not only contribute a substantial proportion of genetic variation but also have significant influence on phenotypes. Here we present the discovery of CNV in a prominent New Zealand dairy bull using long-read PacBio (Pacific Biosciences, Menlo Park, CA) sequencing technology and the Sniffles SV discovery tool (version 0.0.1; https://github.com/fritzsedlazeck/Sniffies). The CNV identified from long reads were compared with CNV discovered in the same bull from Illumina sequencing using CNVnator (read depth based tool; Illumina Inc., San Diego, CA) as a means of validation. Subsequently, further validation was undertaken using whole-genome Illumina sequencing of 556 cattle representing the wider New Zealand dairy cattle population. Very limited overlap was observed in CNV discovered from the 2 sequencing platforms, in part because of the differences in size of CNV detected. Only a few CNV were therefore able to be validated using this approach. However, the ability to use CNVnator to genotype the 557 cattle for copy number across all regions identified as putative CNV allowed a genome-wide assessment of transmission level of copy number based on pedigree. The more highly transmissible a putative CNV region was observed to be, the more likely the distribution of copy number was multimodal across the 557 sequenced animals. Furthermore, visual assessment of highly transmissible CNV regions provided evidence supporting the presence of CNV across the sequenced animals. This transmission-based approach was able to confirm a subset of CNV that segregates in the New Zealand dairy cattle population. Genome-wide identification and validation of CNV is an important step toward their inclusion in genomic selection strategies.