Evidence map›Paper›PMID 31890201›Full record

ArticleJournal of animal science and biotechnology2019

Fine mapping of genomic regions associated with female fertility in Nellore beef cattle based on sequence variants from segregating sires.

Gerson A Oliveira Júnior, Daniel J A Santos, Aline S M Cesar, Solomon A Boison, Ricardo V Ventura, Bruno C Perez, José F Garcia, José Bento S Ferraz, Dorian J Garrick

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

Article in Journal of animal science and biotechnology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
0.9field-weighted citation impact, top 21% 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

4 citing papers in PubMed, 13 citations in OpenAlex.

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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 5 institutions in 5 countries.

Gerson A Oliveira Júnior1Department of Veterinary Medicine, University of São Paulo (USP), Faculty of Animal Science and Food Engineer, Pirassununga, SP Brazil.ORCID 0000-0002-4228-2910
Daniel J A Santos3Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland, USA.
Aline S M Cesar4Department of Animal Science, University of São Paulo (USP), Piracicaba, SP Brazil.
Solomon A Boison5Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences, Vienna, Austria.
Ricardo V Ventura2Department of Animal Bioscience, Center for Genetic Improvement of Livestock, University of Guelph, Guelph, ON Canada.
Bruno C Perez1Department of Veterinary Medicine, University of São Paulo (USP), Faculty of Animal Science and Food Engineer, Pirassununga, SP Brazil.
José F Garcia7Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University (Unesp), Araçatuba, SP Brazil.
José Bento S Ferraz1Department of Veterinary Medicine, University of São Paulo (USP), Faculty of Animal Science and Food Engineer, Pirassununga, SP Brazil.
Dorian J Garrick8School of Agriculture, Massey University, Ruakura Ag Centre, Hamilton, New Zealand.
Universidade de São Paulo · BRBOKU University · ATMassey University · NZUniversidade Estadual Paulista (Unesp) · BRUniversity of Maryland, College Park · US

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundImpaired fertility in cattle limits the efficiency of livestock production systems. Unraveling the genetic architecture of fertility traits would facilitate their improvement by selection. In this study, we characterized SNP chip haplotypes at QTL blocks then used whole-genome sequencing to fine map genomic regions associated with reproduction in a population of Nellore (

methodsThe dataset comprised of 1337 heifers genotyped using a GeneSeek® Genomic Profiler panel (74677 SNPs), representing the daughters from 78 sires. After performing marker quality control, 64800 SNPs were retained. Haplotypes carried by each sire at six previously identified QTL on BTAs 5, 14 and 18 for heifer pregnancy and BTAs 8, 11 and 22 for antral follicle count were constructed using

resultsA total of six (BTA 5), six (BTA 14) and five (BTA 18) sires were heterozygous for heifer pregnancy QTL whereas six (BTA 8), fourteen (BTA 11), and five (BTA 22) sires were heterozygous for number of antral follicles' QTL. Due to inadequate representation of many haplotype alleles in the sequenced animals, fine mapping analysis could only be reliably performed for the QTL on BTA 5 and 14, which had 641 and 3733 concordant candidate sequence variants, respectively. The KEGG "Circadian rhythm" and "Neurotrophin signaling pathway" were significantly associated with the genes in the QTL on BTA 5 whereas 32 MeSH terms were associated with the QTL on BTA 14. Among the concordant sequence variants, 0.2% and 0.3% were classified as missense variants for BTAs 5 and 14, respectively, highlighting the genes

conclusionsThe identification of heterozygous sires by positionally phasing SNP chip data and contrasting haplotype effects for previously detected QTL can be used for fine mapping to identify potential causal mutations and candidate genes. Genomic variants on genes

Indexed as

Antral folliclesCausal variantsHaplotypeHeifer pregnancyWGS

Identifiers

PMID31890201
PMCPMC6913038
OpenAlexW2994760266

What OpenQuestion holds

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Registered trials

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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.