Evidence map›Paper›PMID 31752687›Full record

ArticleBMC genomics2019

Analyses of inter-individual variations of sperm DNA methylation and their potential implications in cattle.

Shuli Liu, Lingzhao Fang, Yang Zhou, Daniel J A Santos, Ruidong Xiang, Hans D Daetwyler, Amanda J Chamberlain, John B Cole, Cong-Jun Li, Ying Yu and 3 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC genomics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.

0numbers the graph read from it
0cells of the map it votes in
21citing papers in PubMed
1.3field-weighted citation impact, top 20% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

21 citing papers in PubMed, 29 citations in OpenAlex.

  1. Article
  2. Article
  3. Emerging opportunities for DNA methylation biomarkers in cattle improvement.The Journal of reproduction and development · 2026
    Review
  4. Article
  5. Article
  6. Review
  7. Review
  8. Article
  9. Article
  10. Article
  11. Review
  12. Article
  13. Harnessing male germline epigenomics for the genetic improvement in cattle.Journal of animal science and biotechnology · 2023
    Review
  14. Article
  15. Article
  16. Article
  17. Article
  18. DNA methylation studies in cattle.Journal of applied genetics · 2021
    Review
  19. Review
  20. Sperm Functional Genome Associated With Bull Fertility.Frontiers in veterinary science · 2021
    Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

13 authors at 7 institutions in 4 countries.

Shuli LiuCollege of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
Lingzhao FangUSDA-ARS, Animal Genomics and Improvement Laboratory, Beltsville, MD, 20705, USA.
Yang ZhouKey Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Education Ministry of China, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
Daniel J A SantosDepartment of Animal and Avian Sciences, University of Maryland, College Park, MD, 20742, USA.
Ruidong XiangFaculty of Veterinary & Agricultural Science, The University of Melbourne, Parkville, Victoria, 3052, Australia.
Hans D DaetwylerAgriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, Victoria, 3083, Australia.
Amanda J ChamberlainAgriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, Victoria, 3083, Australia.
John B ColeUSDA-ARS, Animal Genomics and Improvement Laboratory, Beltsville, MD, 20705, USA.
Cong-Jun LiUSDA-ARS, Animal Genomics and Improvement Laboratory, Beltsville, MD, 20705, USA.
Ying YuCollege of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
Li MaDepartment of Animal and Avian Sciences, University of Maryland, College Park, MD, 20742, USA.
Shengli ZhangCollege of Animal Science and Technology, China Agricultural University, Beijing, 100193, China. zhangslcau@cau.edu.cn.
George E LiuUSDA-ARS, Animal Genomics and Improvement Laboratory, Beltsville, MD, 20705, USA. george.liu@usda.gov.ORCID http://orcid.org/0000-0003-0192-6705
Agricultural Research Service · USChina Agricultural University · CNUniversity of Maryland, College Park · USAgriculture Victoria · AUHuazhong Agricultural University · CNLa Trobe University · AUThe University of Melbourne · AU

Funding

National Institute of Food and Agriculture 2013-67015-20951National Institute of Food and Agriculture 2016-67015-24886National Institute of Food and Agriculture 2019-67015-29321United States - Israel Binational Agricultural Research and Development Fund US-4997-17
6 · The paper itself

Abstract

backgroundDNA methylation has been shown to be involved in many biological processes, including X chromosome inactivation in females, paternal genomic imprinting, and others.

resultsBased on the correlation patterns of methylation levels of neighboring CpG sites among 28 sperm whole genome bisulfite sequencing (WGBS) data (486 × coverage), we obtained 31,272 methylation haplotype blocks (MHBs). Among them, we defined conserved methylated regions (CMRs), variably methylated regions (VMRs) and highly variably methylated regions (HVMRs) among individuals, and showed that HVMRs might play roles in transcriptional regulation and function in complex traits variation and adaptive evolution by integrating evidence from traditional and molecular quantitative trait loci (QTL), and selection signatures. Using a weighted correlation network analysis (WGCNA), we also detected a co-regulated module of HVMRs that was significantly associated with reproduction traits, and enriched for glycosyltransferase genes, which play critical roles in spermatogenesis and fertilization. Additionally, we identified 46 VMRs significantly associated with reproduction traits, nine of which were regulated by cis-SNPs, implying the possible intrinsic relationships among genomic variations, DNA methylation, and phenotypes. These significant VMRs were co-localized (± 10 kb) with genes related to sperm motility and reproduction, including ZFP36L1, CRISP2 and HGF. We provided further evidence that rs109326022 within a predominant QTL on BTA18 might influence the reproduction traits through regulating the methylation level of nearby genes JOSD2 and ASPDH in sperm.

conclusionIn summary, our results demonstrated associations of sperm DNA methylation with reproduction traits, highlighting the potential of epigenomic information in genomic improvement programs for cattle.

Indexed as

DNA MethylationAnimalsBiological Variation, PopulationCattleGenetic VariationHaplotypesMaleQuantitative Trait LociReproductionSpermatozoaCattleMethylation haplotype blocksReproduction traitsSperm DNA methylationVariably methylated regions

Identifiers

PMID31752687
PMCPMC6873545
OpenAlexW2990604430

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.