Genome-wide detection of genetic markers associated with growth and fatness in four pig populations using four approaches
2017
Guo, Yuanmei | Huang, Yixuan | Hou, Lijuan | Ma, Junwu | Chen, Congying | Ai, Huashui | Huang, Lusheng | Ren, Jun
BACKGROUND: Genome-wide association studies (GWAS) have been extensively used to identify genomic regions associated with a variety of phenotypic traits in pigs. Until now, most GWAS have explored single-trait association models. Here, we conducted both single- and multi-trait GWAS and a meta-analysis for nine fatness and growth traits on 2004 pigs from four diverse populations, including a White Duroc × Erhualian F₂ intercross population and Chinese Sutai, Laiwu and Erhualian populations. RESULTS: We identified 44 chromosomal regions that were associated with the nine traits, including four genome-wide significant single nucleotide polymorphisms (SNPs) on SSC2 (SSC for Sus scrofa chromosome), 4, 7 and X. Compared to the single-population GWAS, the meta-analysis was less powerful for the identification of SNPs with population-specific effects but more powerful for the detection of SNPs with population-shared effects. Multiple-trait analysis reduced the power to detect trait-specific SNPs but significantly enhanced the power to identify common SNPs across traits. The SNP on SSC7 had pleiotropic effects on the nine traits in the F₂ and Erhualian populations. Another pleiotropic SNP was observed on SSCX for these traits in the F₂ and Sutai populations. Both population-specific and shared SNPs were identified in this study, thus reflecting the complex genetic architecture of pig growth and fatness traits. CONCLUSIONS: We demonstrate that the multi-trait method and the meta-analysis on multiple populations can be used to increase the power of GWAS. The two significant SNPs on SSC7 and X had pleiotropic effects in the F₂, Erhualian and Sutai populations.
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