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

doi:10.1186/s12864-022-08441-8

Towards the detection of copy number variation from single sperm sequencing in cattle

BMC Genomics. 2022 Mar 17;23(1):215. doi: 10.1186/s12864-022-08441-8.

Authors

Liu Yang^#^{1

2}, Yahui Gao^#^{1

3}, Adam Oswalt⁴, Lingzhao Fang⁵, Clarissa Boschiero¹, Mahesh Neupane¹, Charles G Sattler⁴, Cong-Jun Li¹, Eyal Seroussi⁶, Lingyang Xu⁷, Lv Yang⁸, Li Li², Hongping Zhang², Benjamin D Rosen¹, Curtis P Van Tassell¹, Yang Zhou⁸, Li Ma⁹, George E Liu¹⁰

Affiliations

¹ Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA.
² College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
³ Department of Animal and Avian Sciences, University of Maryland, College Park, MD, 20742, USA.
⁴ Select Sires Inc, 11740 U.S. 42 North, Plain City, OH, 43064, USA.
⁵ MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, EH4 2XU, UK.
⁶ Agricultural Research Organization (ARO), Institute of Animal Science, HaMaccabim Road, P.O.B 15159, 7528809, Volcani CenterRishon LeTsiyon, Israel.
⁷ Innovation Team of Cattle Genetic Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
⁸ Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
⁹ Department of Animal and Avian Sciences, University of Maryland, College Park, MD, 20742, USA. lima@umd.edu.
¹⁰ Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA. George.Liu@ars.usda.gov.

^# Contributed equally.

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.

Keywords: Cattle; Copy number variation; Single sperm sequencing.

MeSH terms

Animals
Cattle / genetics
DNA Copy Number Variations*
Genome*
Male
Segmental Duplications, Genomic
Sequence Analysis, DNA / methods
Spermatozoa

Abstract

MeSH terms

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