Single-step genome-wide association study for social genetic effects and direct genetic effects on growth in Landrace pigs

• Published in: Scientific reports Vol. 10; no. 1; p. 14958
• Main Authors: Hong, Joon-Ki, Lee, Jae-Bong, Ramayo-Caldas, Yuliaxis, Kim, Si-Dong, Cho, Eun-Seok, Kim, Young-Sin, Cho, Kyu-Ho, Lee, Deuk-Hwan, Park, Hee-Bok
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 11-09-2020; Nature Publishing Group
• Subjects: 631/208; 631/208/1348; 631/208/205; 631/208/212; 631/208/721; 631/208/729; 631/208/8; 631/553; 631/553/2710; Anatomy; Animal models; Animals; Cadavers; Chromosomes; Gene mapping; Genetic effects; Genome-wide association studies; Genome-Wide Association Study; Genotype; Humanities and Social Sciences; Livestock; Medical students; multidisciplinary; Polymorphism, Single Nucleotide; Quantitative Trait Loci; Science; Science (multidisciplinary); Skull; Social behavior; Swine; Swine - genetics; Swine - growth & development
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-020-71647-x

In livestock social interactions, social genetic effects (SGE) represent associations between phenotype of one individual and genotype of another. Such associations occur when the trait of interest is affected by transmissible phenotypes of social partners. The aim of this study was to estimate SGE and direct genetic effects (DGE, genetic effects of an individual on its own phenotype) on average daily gain (ADG) in Landrace pigs, and to conduct single-step genome-wide association study using SGE and DGE as dependent variables to identify quantitative trait loci (QTLs) and their positional candidate genes. A total of 1,041 Landrace pigs were genotyped using the Porcine SNP 60K BeadChip. Estimates of the two effects were obtained using an extended animal model. The SGE contributed 16% of the total heritable variation of ADG. The total heritability estimated by the extended animal model including both SGE and DGE was 0.52. The single-step genome-wide association study identified a total of 23 QTL windows for the SGE on ADG distributed across three chromosomes (i.e., SSC1, SSC2, and SSC6). Positional candidate genes within these QTL regions included
PRDM13
,
MAP3K7
,
CNR1
,
HTR1E
,
IL4
,
IL5
,
IL13
,
KIF3A
,
EFHD2
,
SLC38A7
,
mTOR
,
CNOT1
,
PLCB2
,
GABRR1
, and
GABRR2
, which have biological roles in neuropsychiatric processes. The results of biological pathway and gene network analyses also support the association of the neuropsychiatric processes with SGE on ADG in pigs. Additionally, a total of 11 QTL windows for DGE on ADG in SSC2, 3, 6, 9, 10, 12, 14, 16, and 17 were detected with positional candidate genes such as
ARL15.
We found a putative pleotropic QTL for both SGE and DGE on ADG on SSC6. Our results in this study provide important insights that can help facilitate a better understanding of the molecular basis of SGE for socially affected traits.