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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 #326427

Research Project: ENHANCING GENETIC MERIT OF RUMINANTS THROUGH GENOME SELECTION AND ANALYSIS

Location: Animal Genomics and Improvement Laboratory

Title: Initial analysis of sperm DNA methylome in Holstein bulls

Author
item Liu, Ge - George

Submitted to: International Society for Animal Genetics (ISAG)
Publication Type: Abstract Only
Publication Acceptance Date: 7/23/2016
Publication Date: 7/23/2016
Citation: Liu, G. 2016. Initial analysis of sperm DNA methylome in Holstein bulls. In: Proceedings of the 35th International Society for Animal Genetics (ISAG) Conference. 7/23-27/16, Salt Lake City, Utah. P2009.

Interpretive Summary:

Technical Abstract: Aberrant DNA methylation patterns have been associated with abnormal semen parameters, idiopathic male infertility and early embryonic loss in mammals. Using Holstein bulls with high (Bull1) or low (Bull2) fertility rates, we created two representative sperm DNA methylomes at a single-base resolution using the whole genome bisulfite sequencing (WGBS). Totally, 442 million reads (~44 Gb, 15× coverage) and 612 million reads (~61 Gb, 23× coverage) were obtained for Bull1 and Bull2, respectively. We anchored these reads onto the cattle reference genome by filtering monoclonal reads and allowing multiple mapping reads, and then determined the methylation status of each cytosine site. With these two sperm genomes have high coverage of methylation, we observed that the methylation status of individual CpG sites can vary even when in very close proximity to apparently invariable methylated cytosines. We also performed differentially methylated region (DMR) analyses and identified 392 DMRs ranging from 123 bp to 3,973 bp (mean 436bp, total 268,582 bp) in Bull1 and 690 DMRs ranging from 148 bp to 6,639 bp (mean 620bp, total 722,822 bp) in Bull2, respectively. We evaluated the functional impacts of these DMRs on genomic features including functional genes, regulatory elements and common repeats. We are processing 20 more similar genome-wide DNA methylation maps and designing high-throughput DNA methylation assays for semen quality control, which will facilitate a full assessment of the impact of sperm DNA methylation on male fertility in dairy cattle.