Genome-wide association studies and meta-analysis uncovers new candidate genes for growth and carcass traits in pigs
| Autor: | Jens Tetens, Iulia Blaj, Jörn Bennewitz, Georg Thaller, Siegfried Preuß |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2018 |
| Předmět: |
0301 basic medicine
Male Linkage disequilibrium Candidate gene Swine Sus scrofa lcsh:Medicine Genome-wide association study Biochemistry Linkage Disequilibrium Fats Geographical Locations Mathematical and Statistical Techniques Skeletal Joints Medicine and Health Sciences lcsh:Science Musculoskeletal System 2. Zero hunger Mammals education.field_of_study Multidisciplinary Statistics Eukaryota 04 agricultural and veterinary sciences Genomics Metaanalysis Lipids Europe Phenotype Physical Sciences Vertebrates Female Anatomy Research Article Meat Population Quantitative Trait Loci Single-nucleotide polymorphism Biology Quantitative trait locus Research and Analysis Methods Polymorphism Single Nucleotide Molecular Genetics 03 medical and health sciences Species Specificity Genome-Wide Association Studies Genetics Animals Statistical Methods education Molecular Biology Genetic association lcsh:R 0402 animal and dairy science Organisms Biology and Life Sciences Computational Biology Human Genetics Genome Analysis 040201 dairy & animal science 030104 developmental biology Evolutionary biology Genetic Loci Amniotes People and Places lcsh:Q Mathematics Genome-Wide Association Study Selective Breeding |
| Zdroj: | PLoS ONE, Vol 13, Iss 10, p e0205576 (2018) PLoS ONE |
| ISSN: | 1932-6203 |
| Popis: | Genome-wide association studies (GWAS) have been widely used in the genetic dissection of complex traits. As more genomic data is being generated within different commercial or resource pig populations, the challenge which arises is how to collectively investigate the data with the purpose to increase sample size and implicitly the statistical power. This study performs an individual population GWAS, a joint population GWAS and a meta-analysis in three pig F2 populations. D1 is derived from European type breeds (Pietrain, Large White and Landrace), D2 is obtained from an Asian breed (Meishan) and Pietrain, and D3 stems from a European Wild Boar and Pietrain, which is the common founder breed. The traits investigated are average daily gain, backfat thickness, meat to fat ratio and carcass length. The joint and the meta-analysis did not identify additional genomic clusters besides the ones discovered via the individual population GWAS. However, the benefit was an increased mapping resolution which pinpointed to narrower clusters harboring causative variants. The joint analysis identified a higher number of clusters as compared to the meta-analysis; nevertheless, the significance levels and the number of significant variants in the meta-analysis were generally higher. Both types of analysis had similar outputs suggesting that the two strategies can complement each other and that the meta-analysis approach can be a valuable tool whenever access to raw datasets is limited. Overall, a total of 20 genomic clusters that predominantly overlapped at various extents, were identified on chromosomes 2, 7 and 17, many confirming previously identified quantitative trait loci. Several new candidate genes are being proposed and, among them, a strong candidate gene to be taken into account for subsequent analysis is BMP2 (bone morphogenetic protein 2). |
| Databáze: | OpenAIRE |
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