Evidence map›Paper›PMID 31810463›Full record

ArticleBMC genomics2019

Combining information from genome-wide association and multi-tissue gene expression studies to elucidate factors underlying genetic variation for residual feed intake in Australian Angus cattle.

Sara de Las Heras-Saldana, Samuel A Clark, Naomi Duijvesteijn, Cedric Gondro, Julius H J van der Werf, Yizhou Chen

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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 18 papers.

0numbers the graph read from it
0cells of the map it votes in
18citing papers in PubMed
–field-weighted citation impact
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

18 citing papers in PubMed.

  1. Genome-wide association study of mature cow size traits in American Angus cattle.Mammalian genome : official journal of the International Mammalian Genome Society · 2026
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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

6 authors.

Sara de Las Heras-SaldanaSchool of Environmental and Rural Science, University of New England, Armidale, NSW, Australia. sdelash2@une.edu.au.ORCID http://orcid.org/0000-0002-8665-6160
Samuel A ClarkSchool of Environmental and Rural Science, University of New England, Armidale, NSW, Australia.
Naomi DuijvesteijnSchool of Environmental and Rural Science, University of New England, Armidale, NSW, Australia.
Cedric GondroSchool of Environmental and Rural Science, University of New England, Armidale, NSW, Australia.
Julius H J van der WerfSchool of Environmental and Rural Science, University of New England, Armidale, NSW, Australia.
Yizhou ChenDepartment of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, NSW, Australia.

Funding

Meat and Livestock Australia B.SBP.0089 and PSH.0528
6 · The paper itself

Abstract

backgroundGenome-wide association studies (GWAS) are extensively used to identify single nucleotide polymorphisms (SNP) underlying the genetic variation of complex traits. However, much uncertainly often still exists about the causal variants and genes at quantitative trait loci (QTL). The aim of this study was to identify QTL associated with residual feed intake (RFI) and genes in these regions whose expression is also associated with this trait. Angus cattle (2190 steers) with RFI records were genotyped and imputed to high density arrays (770 K) and used for a GWAS approach to identify QTL associated with RFI. RNA sequences from 126 Angus divergently selected for RFI were analyzed to identify the genes whose expression was significantly associated this trait with special attention to those genes residing in the QTL regions.

resultsThe heritability for RFI estimated for this Angus population was 0.3. In a GWAS, we identified 78 SNPs associated with RFI on six QTL (on BTA1, BTA6, BTA14, BTA17, BTA20 and BTA26). The most significant SNP was found on chromosome BTA20 (rs42662073) and explained 4% of the genetic variance. The minor allele frequencies of significant SNPs ranged from 0.05 to 0.49. All regions, except on BTA17, showed a significant dominance effect. In 1 Mb windows surrounding the six significant QTL, we found 149 genes from which OAS2, STC2, SHOX, XKR4, and SGMS1 were the closest to the most significant QTL on BTA17, BTA20, BTA1, BTA14, and BTA26, respectively. In a 2 Mb windows around the six significant QTL, we identified 15 genes whose expression was significantly associated with RFI: BTA20) NEURL1B and CPEB4; BTA17) RITA1, CCDC42B, OAS2, RPL6, and ERP29; BTA26) A1CF, SGMS1, PAPSS2, and PTEN; BTA1) MFSD1 and RARRES1; BTA14) ATP6V1H and MRPL15.

conclusionsOur results showed six QTL regions associated with RFI in a beef Angus population where five of these QTL contained genes that have expression associated with this trait. Therefore, here we show that integrating information from gene expression and GWAS studies can help to better understand the genetic mechanisms that determine variation in complex traits.

Indexed as

EatingQuantitative Trait LociAnimalsCattleChromosome MappingFemaleGene Expression ProfilingGene Expression RegulationGene FrequencyGenome-Wide Association StudyMaleOligonucleotide Array Sequence AnalysisPolymorphism, Single NucleotideSequence Analysis, RNAAngusBeef cattleGene expressionGWASQTLResidual feed intakeRNA-seq

Identifiers

PMID31810463
PMCPMC6898931

What Socratic holds

Textmetadata
LicenceCC BY
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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 Socratic graph.