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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 #381292

Research Project: Enhancing Genetic Merit of Ruminants Through Improved Genome Assembly, Annotation, and Selection

Location: Animal Genomics and Improvement Laboratory

Title: Genome-wide recombination map construction from single sperm sequencing in cattle

item YANG, LIU - Sichuan Agricultural University
item GAO, YAHUI - University Of Maryland
item LI, MINGXUN - Yangzhou University
item PARK, KI-EUN - University Of Maryland
item LIU, SHULI - China Agricultural University
item KANG, XIAOLONG - Lanzhou University
item LIU, MEI - Hunan Agricultural University
item OSWALT, ADAM - Select Sires, Inc
item FANG, LINGZHAO - University Of Edinburgh
item TELUGU, BHANU - University Of Maryland
item SATTLER, CHARLES - Select Sires, Inc
item Cole, John
item SEROUSSI, EYAL - Volcani Center (ARO)
item XU, LINGYANG - Chinese Agricultural University
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: 10/29/2021
Publication Date: 5/3/2022
Citation: Yang, L., Gao, Y., Li, M., Park, K., Liu, S., Kang, X., Liu, M., Oswalt, A., Fang, L., Telugu, B.P., Sattler, C.G., Cole, J.B., Seroussi, E., Xu, L., Li, C., Li, L., Zhang, H., Rosen, B.D., Van Tassell, C.P., Ma, L., Liu, G. 2022. Genome-wide recombination map construction from single sperm sequencing in cattle. BMC Genomics. 23(1):181.

Interpretive Summary: Comprehensive analyses of tissues at single-cell level will benefit our understanding of genetic bases for complex traits. We provided the first single-cell analysis of recombination, de novo mutation and genome instability in bovine sperm. 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: Meiotic recombination, de novo mutation, genome instability like structural variation (SV), large copy number variation (CNV) and/or aneuploidy are important phenomena contributing to gamete genome diversity. However, except for human and a few model organisms, they are not well studied in other mammals including cattle. Results: To investigate how the cattle genome is impacted by these processes, we sequenced 143 single sperms from two Holstein bulls, phased their genomes. ; and mapped recombination events at high resolution. In the absence of evolutionary selection pressure in fertilization and survival, recombination in sperm is enriched near distal chromosomal ends and noncoding regions, revealing that such a pattern is intrinsic to the molecular mechanism of meiosis. From single sperms with uniform sequencing coverage, we observed a similar distal chromosomal distribution for genome instability (SV, CNV and/or aneuploidy) on a global per-sperm basis. Using deep sequencing of ten single sperms, we found that de novo mutations were similarly but unevenly distributed across the individual sperm chromosomes with a rate ranging from 2.05e-08 to 7.63e-08. Furthermore, we were able to validate these findings in single sperms by comparing them with results derived from sequencing a family of trio diploid genomes and our previous studies of recombination in cattle pedigree. Conclusion: We reported patterns of distal chromosomal distributions for recombination, de novo mutation, SV, and large CNV in bovine sperms. To our knowledge, this is the first large-scale single sperm cell sequencing effort in livestock, which provides useful information for future studies of recombination, genome instability, and male infertility.