Ag Data Commons
Browse

File(s) stored somewhere else

Please note: Linked content is NOT stored on Ag Data Commons and we can't guarantee its availability, quality, security or accept any liability.

Comparative sperm methylome analysis provide insights into complex phenotypes and epigenome evolution

dataset
posted on 2024-01-27, 05:04 authored by Animal Genomics and Improvement Laboratory, ARS, USDA
Using whole-genome bisulfite sequencing (WGBS), we profiled 18 DNA methylomes of cattle sperms that were collected from 18 representative age-matched Holstein bulls with high reliable phenotypes on many complex traits, including sire-conception rate (SCR), gestation length (GL), sire calving ease (SCE), cow conception rate (CCR) and body depth (BDE). Through comparison with human sperm methylome, we observed that genomic regions with differetial DNA methylation levels were enriched for GWAS signals and had important evolutionary impact. By comparing animals with extreme SCR, we showed that differentially methylated regions (DMR) associated with SCR and aging were significantly and selectively enriched for GWAS signals of male fertility traits in cattle. In addition, we detected ans compared DMRs assocaited with GL, CCR, SCE and BDE. We integrated GWAS signals of 37 complex traits with DMRs associated with GL to provide insights into genetic basis of GL. Overall design: Genomic DNA of sperm was isolated according to the QIAamp DNA Mini Kit protocol (QIAGEN, Valencia, CA, USA). The quality of DNA samples was evaluated using the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) including degradation, and potential RNA contamination, and purity (OD260/OD280), and concentration using a spectrophotometer (NanoDrop Technologies, Rockland, DE) to meet the requirements for library construction. The qualified sperm genomic DNA were used to construct a library. The library different lanes of a HiSeq X Ten (Illumina, San Diego, CA, USA) to generate 150-bp paired-end reads by Novogene (Novogene, Beijing, China).

History

Data contact name

BioProject Curation Staff

Publisher

National Center for Biotechnology Information

Temporal Extent Start Date

2018-08-30

Theme

  • Non-geospatial

ISO Topic Category

  • biota

National Agricultural Library Thesaurus terms

epigenetics; genome; genomics

Pending citation

  • No

Public Access Level

  • Public

Accession Number

PRJNA488627

Usage metrics

    Categories

    Exports

    RefWorks
    BibTeX
    Ref. manager
    Endnote
    DataCite
    NLM
    DC