Evidence map›Paper›PMID 30081822›Full record

ArticleGenetics, selection, evolution : GSE2018

Weighted single-step GWAS and gene network analysis reveal new candidate genes for semen traits in pigs.

Daniele B D Marques, John W M Bastiaansen, Marleen L W J Broekhuijse, Marcos S Lopes, Egbert F Knol, Barbara Harlizius, Simone E F Guimarães, Fabyano F Silva, Paulo S Lopes

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

Article in Genetics, selection, evolution : GSE, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.

0numbers the graph read from it
0cells of the map it votes in
50citing papers in PubMed
12.5field-weighted citation impact, top 1% 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

50 citing papers in PubMed, 108 citations in OpenAlex.

  1. Article
  2. Article
  3. Article
  4. Article
  5. Article
  6. Article
  7. Article
  8. Article
  9. Article
  10. Article
  11. Review
  12. Article
  13. Article
  14. Article
  15. Article
  16. Article
  17. Article
  18. Article
  19. Article
  20. Article
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

9 authors at 3 institutions in 2 countries.

Daniele B D MarquesAnimal Science Department, Universidade Federal de Viçosa, Viçosa, MG, 36.570-000, Brazil.
John W M BastiaansenAnimal Breeding and Genomics, Wageningen University & Research, P.O. Box 338, 6700 AH, Wageningen, The Netherlands. john.bastiaansen@wur.nl.
Marleen L W J BroekhuijseTopigs Norsvin Research Center B.V., P.O. Box 43, 6640 AA, Beuningen, The Netherlands.
Marcos S LopesTopigs Norsvin Research Center B.V., P.O. Box 43, 6640 AA, Beuningen, The Netherlands.
Egbert F KnolTopigs Norsvin Research Center B.V., P.O. Box 43, 6640 AA, Beuningen, The Netherlands.
Barbara HarliziusTopigs Norsvin Research Center B.V., P.O. Box 43, 6640 AA, Beuningen, The Netherlands.
Simone E F GuimarãesAnimal Science Department, Universidade Federal de Viçosa, Viçosa, MG, 36.570-000, Brazil.
Fabyano F SilvaAnimal Science Department, Universidade Federal de Viçosa, Viçosa, MG, 36.570-000, Brazil.
Paulo S LopesAnimal Science Department, Universidade Federal de Viçosa, Viçosa, MG, 36.570-000, Brazil.
Topigs Norsvin (Netherlands) · NLUniversidade Federal de Viçosa · BRWageningen University & Research · NL

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundIn recent years, there has been increased interest in the study of the molecular processes that affect semen traits. In this study, our aim was to identify quantitative trait loci (QTL) regions associated with four semen traits (motility, progressive motility, number of sperm cells per ejaculate and total morphological defects) in two commercial pig lines (L1: Large White type and L2: Landrace type). Since the number of animals with both phenotypes and genotypes was relatively small in our dataset, we conducted a weighted single-step genome-wide association study, which also allows unequal variances for single nucleotide polymorphisms. In addition, our aim was also to identify candidate genes within QTL regions that explained the highest proportions of genetic variance. Subsequently, we performed gene network analyses to investigate the biological processes shared by genes that were identified for the same semen traits across lines.

resultsWe identified QTL regions that explained up to 10.8% of the genetic variance of the semen traits on 12 chromosomes in L1 and 11 chromosomes in L2. Sixteen QTL regions in L1 and six QTL regions in L2 were associated with two or more traits within the population. Candidate genes SCN8A, PTGS2, PLA2G4A, DNAI2, IQCG and LOC102167830 were identified in L1 and NME5, AZIN2, SPATA7, METTL3 and HPGDS in L2. No regions overlapped between these two lines. However, the gene network analysis for progressive motility revealed two genes in L1 (PLA2G4A and PTGS2) and one gene in L2 (HPGDS) that were involved in two biological processes i.e. eicosanoid biosynthesis and arachidonic acid metabolism. PTGS2 and HPGDS were also involved in the cyclooxygenase pathway.

conclusionsWe identified several QTL regions associated with semen traits in two pig lines, which confirms the assumption of a complex genetic determinism for these traits. A large part of the genetic variance of the semen traits under study was explained by different genes in the two evaluated lines. Nevertheless, the gene network analysis revealed candidate genes that are involved in shared biological pathways that occur in mammalian testes, in both lines.

Indexed as

Gene Regulatory NetworksQuantitative Trait LociAnimalsChromosomesDatabases, GeneticGenetic Association StudiesGenome-Wide Association StudyMalePolymorphism, Single NucleotideSemenSus scrofaSwine

Identifiers

PMID30081822
PMCPMC6080523
OpenAlexW2887879627

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.