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