Detection and assessment of copy number variation using PacBio long-read and Illumina sequencing in New Zealand dairy cattle

Couldrey, C., Keehan, M., Johnson, T., Tiplady, K., Winkelman, A., Littlejohn, M. D., Scott, A., Kemper, K. E., Hayes, B., Davis, S. R. and Spelman, R. J. (2017) Detection and assessment of copy number variation using PacBio long-read and Illumina sequencing in New Zealand dairy cattle. Journal of Dairy Science, 100 7: 5472-5478. doi:10.3168/jds.2016-12199

Author Couldrey, C.
Keehan, M.
Johnson, T.
Tiplady, K.
Winkelman, A.
Littlejohn, M. D.
Scott, A.
Kemper, K. E.
Hayes, B.
Davis, S. R.
Spelman, R. J.
Title Detection and assessment of copy number variation using PacBio long-read and Illumina sequencing in New Zealand dairy cattle
Journal name Journal of Dairy Science   Check publisher's open access policy
ISSN 1525-3198
Publication date 2017-07-01
Sub-type Article (original research)
DOI 10.3168/jds.2016-12199
Open Access Status DOI
Volume 100
Issue 7
Start page 5472
End page 5478
Total pages 7
Place of publication New York, NY, United States
Publisher Elsevier
Language eng
Subject 1106 Food Science
1103 Animal Science and Zoology
1311 Genetics
Abstract 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; 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.
Keyword Cattle
Copy number variant
Genomic selection
Structural variant
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: HERDC Pre-Audit
Queensland Alliance for Agriculture and Food Innovation
Institute for Molecular Bioscience - Publications
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