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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Genomics and Improvement Laboratory » Research » Publications at this Location » Publication #385859
Research Project: Enhancing Genetic Merit of Ruminants Through Improved Genome Assembly, Annotation, and Selection

Location: Animal Genomics and Improvement Laboratory

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

Author
item YANG, LIU - Sichuan Agricultural University
item GAO, YAHUI - University Of Maryland
item OSWALT, ADAM - Select Sires, Inc
item FANG, LINGZHAO - University Of Edinburgh
item Boschiero, Clarissa
item Neupane, Mahesh
item SATTLER, CHARLES - Select Sires, Inc
item SEROUSSI, EYAL - Agricultural Research Organization Of Israel
item XU, LINGYANG - Chinese Academy Of Agricultural Sciences
item Li, Congjun - Cj
item LI, LI - Sichuan Agricultural University
item ZHANG, HONGPING - Sichuan Agricultural University
item Rosen, Benjamin - Ben
item Van Tassell, Curtis - Curt
item MA, LI - University Of Maryland
item Liu, Ge - George

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/15/2021
Publication Date: 3/17/2022
Citation: Yang, L., Gao, Y., Oswalt, A., Fang, L., Boschiero, C., Neupane, M., Sattler, C.G., Seroussi, E., Xu, L., Li, C., Li, L., Zhang, H., Rosen, B.D., Van Tassell, C.P., Ma, L., Liu, G. 2022. Towards the detection of copy number variation from single sperm sequencing in cattle. BMC Genomics. 23(1):215. https://doi.org/10.1186/s12864-022-08441-8.
DOI: https://doi.org/10.1186/s12864-022-08441-8

Interpretive Summary: Comprehensive analyses of tissues at single-cell level will benefit our understanding of genetic bases for complex traits. We sequenced 143 single sperms of two Holstein bulls, from which we predicted CNV events using 14 single sperms with deep sequencing. These results fill our knowledge gaps and provide the foundation for incorporating new knowledge into the future animal breeding program. Farmers, scientist, and policy planners who need improve animal health and production based on genome-enabled animal selection will benefit from this study.

Technical Abstract: Background: Copy number variation (CNV) has been routinely studied using bulk-cell sequencing. However, except for humans and a few model organisms, CNV is not well studied on the single-cell level. 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 results derived from 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 only some single sperm CNVs were validated by the trio 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.