Whole-genome re-sequencing association study for direct genetic effects and social genetic effects of six growth traits in Large White pigs

Abstract

Socially affected traits are affected by direct genetic effects (DGE) and social genetic effects (SGE). DGE and SGE of an individual directly quantify the genetic influence of its own phenotypes and the phenotypes of other individuals, respectively. In the current study, a total of 3,276 Large White pigs from different pens were used, and each pen contained 10 piglets. DGE and SGE were estimated for six socially affected traits, and then a GWAS was conducted to identify SNPs associated with DGE and SGE. Based on the whole-genome re-sequencing, 40 Large White pigs were genotyped and 10,501,384 high quality SNPs were retained for single-locus and multi-locus GWAS. For single-locus GWAS, a total of 54 SNPs associated with DGE and 33 SNPs with SGE exceeded the threshold (P < 5.00E-07) were detected for six growth traits. Of these, 22 SNPs with pleiotropic effects were shared by DGE and SGE. For multi-locus GWAS, a total of 72 and 110 putative QTNs were detected for DGE and SGE, respectively. Of these, 5 SNPs with pleiotropic effects were shared by DGE and SGE. It is noteworthy that 2 SNPs (SSC8: 16438396 for DGE and SSC17: 9697454 for SGE) were detected in single-locus and multi-locus GWAS. Furthermore, 15 positional candidate genes shared by SGE and DGE were identified because of their roles in behaviour, health and disease. Identification of genetic variants and candidate genes for DGE and SGE for socially affected traits will provide a new insight to understand the genetic architecture of socially affected traits in pigs.

Figure 1

Manhattan plots of genome-wide association analysis results associated to DGE for six growth traits using GEMMA software. The threshold for genome-wide and suggestive significance was set at P = 5.00 × 10⁻⁸ and P = 5.00 × 10⁻⁷, respectively.

Figure 2

Manhattan plots of genome-wide association analysis results associated to SGE for six growth traits using GEMMA software. The threshold for genome-wide and suggestive significance was set at P = 5.00 × 10⁻⁸ and P = 5.00 × 10⁻⁷, respectively.