PS3-14. Parent-specific DNA Methylation in the Developing Bovine Placenta.

Abstract

Pregnancy loss contributes over a billion dollars in economic losses per year in the dairy and beef cattle industries in the United States alone. Several factors are involved in successful pregnancy, from fertilization to the birth of a live calf, including placental development. In many species, including humans and mice, parent-of-origin-specific DNA methylation patterns and gene expression important for placental development have been identified; however, sire and dam contributions to placental development in cattle are not well understood. The objective of this study was to determine the parent-of-origin specific DNA methylation patterns in the developing bovine placenta. Cotyledon tissue was collected at day 50 of gestation from reciprocal crosses of one Holstein sire X Angus dams (n = 2) and one Angus sire X Holstein dams (n = 3). Cotyledon DNA was extracted, then sequenced to 30X coverage using PacBio Hifi sequencing, and parent DNA was sequenced to 30X coverage using an Illumina NovaSeq 6000 platform. Variants were called using GATK HaplotypeCaller and Deepvariant, and pedigree phasing and haplotagging was completed for each trio using Whatshap, to identify sire and dam haplotypes. Pb-cpg-tools was used to call methylation, then differential methylation was determined with MethBat. Annotation of differentially methylated regions (DMRs) to the reference genome was completed using HOMER. A total of 333 significant (P < 0.05) DMRs were discovered, within or in cis-regulatory regions relative to 252 candidate genes. There was a total of 224 hypomethylated sire DMRs compared to 109 hypomethylated dam DMRs. Forty-one percent of DMRs were located in intronic regions, 36% in intergenic regions, 13% in promoters, 9% in exons, and 1% in transcription termination sites. Candidate genes hypomethylated in the sire haplotypes included PEG10, PEG3, KBTBD6, MEST, NAP1L5, PLAGL1, and VEGFA which all have previous implications in aspects of mammalian pregnancy. Pregnancy related genes hypomethylated on the dam haplotype included TWIST2, PGF, and PAPPA. Overall, these results identified parent-specific DNA methylation patterns in the developing bovine placenta. The majority of hypomethylated regions are specific to the sire, suggesting that the sire may drive much of placental development in cattle. Understanding parent-specific mechanisms of placental development will allow for more precise selection strategies specific to sires and dams and ultimately improve reproductive outcomes in cattle.