Evidence map›Paper›PMID 36451102›Full record

SynthesisBMC genomics2022

Meta-analysis of genome-wide association studies uncovers shared candidate genes across breeds for pig fatness trait.

Haonan Zeng, Zhanming Zhong, Zhiting Xu, Jinyan Teng, Chen Wei, Zitao Chen, Wenjing Zhang, Xiangdong Ding, Jiaqi Li, Zhe Zhang

Open access · goldAbstract readMeta-Analysis
PubMed Full text at PMC Publisher
In one paragraph

Synthesis in BMC genomics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers, 3 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
16citing papers in PubMed, 3 pooled it
4.7field-weighted citation impact, top 5% 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

16 citing papers in PubMed, 3 syntheses or guidelines pooled it, 27 citations in OpenAlex.

  1. Pooled it
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  13. Application of GWAS and mGWAS in Livestock and Poultry Breeding.Animals : an open access journal from MDPI · 2024
    Review
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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

10 authors at 3 institutions in 1 country.

Haonan ZengGuangdong Provincial Key Lab of Agro-animal Genomics and Molecular Breeding, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, 510642, Guangzhou, China.
Zhanming ZhongGuangdong Provincial Key Lab of Agro-animal Genomics and Molecular Breeding, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, 510642, Guangzhou, China.
Zhiting XuGuangdong Provincial Key Lab of Agro-animal Genomics and Molecular Breeding, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, 510642, Guangzhou, China.
Jinyan TengGuangdong Provincial Key Lab of Agro-animal Genomics and Molecular Breeding, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, 510642, Guangzhou, China.
Chen WeiGuangdong Provincial Key Lab of Agro-animal Genomics and Molecular Breeding, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, 510642, Guangzhou, China.
Zitao ChenDepartment of Animal Science, College of Animal Science, Zhejiang University, 310058, Hangzhou, China.
Wenjing ZhangGuangdong Provincial Key Lab of Agro-animal Genomics and Molecular Breeding, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, 510642, Guangzhou, China.
Xiangdong DingKey Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China.
Jiaqi LiGuangdong Provincial Key Lab of Agro-animal Genomics and Molecular Breeding, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, 510642, Guangzhou, China.
Zhe ZhangGuangdong Provincial Key Lab of Agro-animal Genomics and Molecular Breeding, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, 510642, Guangzhou, China. zhezhang@scau.edu.cn.
South China Agricultural University · CNMinistry of Agriculture and Rural Affairs · CNZhejiang University · CN

Funding

The earmarked fund for China Agriculture Research System CARS-35The National Natural Science Foundation of China 32022078
6 · The paper itself

Abstract

backgroundAverage backfat thickness (BFT) is a critical complex trait in pig and an important indicator for fat deposition and lean rate. Usually, genome-wide association study (GWAS) was used to discover quantitative trait loci (QTLs) of BFT in a single population. However, the power of GWAS is limited by sample size in a single population. Alternatively, meta-analysis of GWAS (metaGWAS) is an attractive method to increase the statistical power by integrating data from multiple breeds and populations. The aim of this study is to identify shared genetic characterization of BFT across breeds in pigs via metaGWAS. 

resultsIn this study, we performed metaGWAS on BFT using 15,353 pigs (5,143 Duroc, 7,275 Yorkshire, and 2,935 Landrace) from 19 populations. We detected 40 genome-wide significant SNPs (Bonferroni corrected P < 0.05) and defined five breed-shared QTLs in across-breed metaGWAS. Markers within the five QTL regions explained 7 ~ 9% additive genetic variance and showed strong heritability enrichment. Furthermore, by integrating information from multiple bioinformatics databases, we annotated 46 candidate genes located in the five QTLs. Among them, three important (MC4R, PPARD, and SLC27A1) and seven suggestive candidate genes (PHLPP1, NUDT3, ILRUN, RELCH, KCNQ5, ITPR3, and U3) were identified.

conclusionQTLs and candidate genes underlying BFT across breeds were identified via metaGWAS from multiple populations. Our findings contribute to the understanding of the genetic architecture of BFT and the regulating mechanism underlying fat deposition in pigs.

Indexed as

Genome-Wide Association StudyQuantitative Trait LociAdipose TissueAnimalsCD36 AntigensPhenotypeSwineCD36 AntigensBackfat thicknessGWASmeta-analysisPigQTL

Identifiers

PMID36451102
PMCPMC9714057
OpenAlexW4310476603

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.