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Meta-analysis of genome-wide association studies for loin muscle area and loin muscle depth in two Duroc pig populations
- Source :
- PLoS ONE, PLoS ONE, Vol 14, Iss 6, p e0218263 (2019)
- Publication Year :
- 2019
- Publisher :
- Public Library of Science, 2019.
-
Abstract
- Loin muscle area (LMA) and loin muscle depth (LMD) are important traits influencing the production performance of breeding pigs. However, the genetic architecture of these two traits is still poorly understood. To discern the genetic architecture of LMA and LMD, a material consisting of 6043 Duroc pigs belonging to two populations with different genetic backgrounds was collected and applied in genome-wide association studies (GWAS) with a genome-wide distributed panel of 50K single nucleotide polymorphisms (SNPs). To improve the power of detection for common SNPs, we conducted a meta-analysis in these two pig populations and uncovered additional significant SNPs. As a result, we identified 75 significant SNPs for LMA and LMD on SSC6, 7, 12, 16, and 18. Among them, 25 common SNPs were associated with LMA and LMD. One pleiotropic quantitative trait locus (QTL), which was located on SSC7 with a 283 kb interval, was identified to affect LMA and LMD. Marker ALGA0040260 is a key SNP for this QTL, explained 1.77% and 2.48% of the phenotypic variance for LMA and LMD, respectively. Another genetic region on SSC16 (709 kb) was detected and displayed prominent association with LMA and the peak SNP, WU_10.2_16_35829257, contributed 1.83% of the phenotypic variance for LMA. Further bioinformatics analysis determined eight promising candidate genes (GCLC, GPX8, DAXX, FGF21, TAF11, SPDEF, NUDT3, and PACSIN1) with functions in glutathione metabolism, adipose and muscle tissues development and lipid metabolism. This study provides the first GWAS for the LMA and LMD of Duroc breed to analyze the underlying genetic variants through a large sample size. The findings further advance our understanding and help elucidate the genetic architecture of LMA, LMD and growth-related traits in pigs.
- Subjects :
- 0301 basic medicine
Candidate gene
Heredity
Fibroblast Growth Factor
Swine
Physiology
Population genetics
Genome-wide association study
Breeding
Mathematical and Statistical Techniques
Endocrinology
Medicine and Health Sciences
Adiposity
Genetics
Mammals
Multidisciplinary
Muscles
Statistics
Eukaryota
04 agricultural and veterinary sciences
Genomics
Metaanalysis
Phenotype
Vertebrates
Physical Sciences
Medicine
Research Article
Genotype
Science
Quantitative Trait Loci
Single-nucleotide polymorphism
Biology
Quantitative trait locus
Research and Analysis Methods
Polymorphism, Single Nucleotide
Molecular Genetics
03 medical and health sciences
Growth Factors
Genome-Wide Association Studies
SNP
Animals
Statistical Methods
Molecular Biology
Genetic association
Evolutionary Biology
Population Biology
Endocrine Physiology
0402 animal and dairy science
Organisms
Biology and Life Sciences
Computational Biology
Human Genetics
Genome Analysis
040201 dairy & animal science
Genetic architecture
030104 developmental biology
Genetic Loci
Amniotes
Mathematics
Population Genetics
Genome-Wide Association Study
Subjects
Details
- Language :
- English
- ISSN :
- 19326203 and 35829257
- Volume :
- 14
- Issue :
- 6
- Database :
- OpenAIRE
- Journal :
- PLoS ONE
- Accession number :
- edsair.doi.dedup.....15f2cf46769fcff688bc3a23ed8784f8