Towards the detection of copy number variation from single sperm sequencing in cattle
Liu Yang,
Yahui Gao,
Adam Oswalt,
Lingzhao Fang,
Clarissa Boschiero,
Mahesh Neupane,
Charles G. Sattler,
Cong-jun Li,
Eyal Seroussi,
Lingyang Xu,
Lv Yang,
Li Li,
Hongping Zhang,
Benjamin D. Rosen,
Curtis P. Van Tassell,
Yang Zhou,
Li Ma,
George E. Liu
Affiliations
Liu Yang
Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA
Yahui Gao
Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA
Adam Oswalt
Select Sires Inc
Lingzhao Fang
MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh
Clarissa Boschiero
Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA
Mahesh Neupane
Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA
Charles G. Sattler
Select Sires Inc
Cong-jun Li
Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA
Eyal Seroussi
Agricultural Research Organization (ARO), Institute of Animal Science
Lingyang Xu
Innovation Team of Cattle Genetic Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences
Lv Yang
Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University
Li Li
College of Animal Science and Technology, Sichuan Agricultural University
Hongping Zhang
College of Animal Science and Technology, Sichuan Agricultural University
Benjamin D. Rosen
Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA
Curtis P. Van Tassell
Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA
Yang Zhou
Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University
Li Ma
Department of Animal and Avian Sciences, University of Maryland
George E. Liu
Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA
Abstract Background Copy number variation (CNV) has been routinely studied using bulk-cell sequencing. However, CNV is not well studied on the single-cell level except for humans and a few model organisms. Results We sequenced 143 single sperms of two Holstein bulls, from which we predicted CNV events using 14 single sperms with deep sequencing. We then compared the CNV results derived from single sperms with the bulk-cell sequencing of one bull’s family trio of diploid genomes. As a known CNV hotspot, segmental duplications were also predicted using the bovine ARS-UCD1.2 genome. Although the trio CNVs validated only some single sperm CNVs, they still showed a distal chromosomal distribution pattern and significant associations with segmental duplications and satellite repeats. Conclusion Our preliminary results pointed out future research directions and highlighted the importance of uniform whole genome amplification, deep sequence coverage, and dedicated software pipelines for CNV detection using single cell sequencing data.
