A genome-wide association study of social genetic effects in Landrace pigs

Hong, Joon Ki; Jeong, Yong Dae; Cho, Eun Seok; Choi, Tae-Jeong; Kim, Yong Min; Cho, Kyu Ho; Lee, Jae Bong; Lim, Hyun‐Tae; Lee, Deukhwan

doi:10.5713/ajas.17.0440

Cited by 11 publications

(12 citation statements)

References 29 publications

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“…5) The associated gene in bold in this column represent these genes were associated with traits based on annotation. 6) down/up = the location of SNP in downstream/upstream of the nearest gene.…”

Section: Discussionmentioning

confidence: 99%

“…Over the past 20 years, the dense genome coverage provided by high-throughput chip genotyping makes it possible to exploit the linkage disequilibrium (LD) between single nucleotide polymorphisms (SNPs) and quantitative trait locus (QTL) through genome-wide association study (GWAS) to identify genes related to traits of interest. Several GWAS have been revealed significant associations for economically important traits such as reproduction traits [5], growth traits [6], meat traits [7], and feed conversion [8].…”

Section: Introductionmentioning

confidence: 99%

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A genome-wide association study of reproduction traits in four pig populations with different genetic backgrounds

Jiang

Tang

Xiao

et al. 2020

Asian-Australas J Anim Sci

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Objective: Genome-wide association study and two meta-analysis based on GWAS performed to explore the genetic mechanism underlying variation in pig number born alive (NBA) and total number born (TNB). Methods: Single trait GWAS and two meta-analysis (single-trait meta analysis and multitrait meta analysis) were used in our study for NBA and TNB on 3,121 Yorkshires from 4 populations, including three different American Yorkshire populations (n = 2,247) and one British Yorkshire populations (n = 874). Results: The result of single trait GWAS showed that no significant associated single nucleotide polymorphisms (SNPs) were identified. Using single-trait meta analysis and multi-trait meta analysis within populations, 11 significant loci were identified associated with target traits. Spindlin 1, vascular endothelial growth factor A, forkhead box Q1, msh homeobox 1, and LHFPL tetraspan submily member 3 are five functionally plausible candidate genes for NBA and TNB. Compared to the single population GWAS, single-trait Meta analysis can improve the detection power to identify SNPs by integrating information of multiple populations. The multiple-trait analysis reduced the power to detect trait-specific loci but enhanced the power to identify the common loci across traits. Conclusion: In total, our findings identified novel genes to be validated as candidates for NBA and TNB in pigs. Also, it enabled us to enlarge population size by including multiple populations with different genetic backgrounds and increase the power of GWAS by using meta analysis.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

A genome-wide association study of reproduction traits in four pig populations with different genetic backgrounds

Jiang

Tang

Xiao

et al. 2020

Asian-Australas J Anim Sci

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“…Based on the Illumina PorcineSNP60 v2 BeadChip panel, Hong et al . 24 identified several genomic regions and candidate genes associated with SGE for ADG in Landrace pigs. In their study, the individual ADG and the average ADG of unrelated pen-mates were directly used as DGE and SGE, respectively.…”

Section: Discussionmentioning

confidence: 99%

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

Wang

Zhou

et al. 2019

Sci Rep

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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.

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“…A total of 1,041 Landrace pigs were genotyped using the Illumina PorcineSNP60 v2 BeadChip panel, which included 61,565 SNP markers 56 . This population was previously used in GWAS for the naïve SGE 45 . The quality control process of the genotype data included the removal of individuals with pedigree errors, omission of monomorphic SNP genotypes, SNPs on sex chromosomes or SNPs with minor allele frequencies (< 0.95), genotype call rate of < 0.90, animal missing rate of > 0.90, Hardy-Weinberg equilibrium of 0.15, and the SNPs with displaced segregation distortion 57,58 .…”

Section: Methodsmentioning

confidence: 99%

“…We previously reported the identification of several QTLs for SGE and DGE using a standard GWAS approach 45 . In the previous study, the mean phenotypic value of ADG for unrelated pen partners and the phenotypic value of individual ADG were used as the naïve SGE and DGE for the GWAS, respectively.…”

Section: Dge On Adgmentioning

confidence: 99%

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

Hong

Lee

Ramayo-Caldas

et al. 2020

Sci Rep

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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.

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A genome-wide association study of social genetic effects in Landrace pigs

Cited by 11 publications

References 29 publications

A genome-wide association study of reproduction traits in four pig populations with different genetic backgrounds

A genome-wide association study of reproduction traits in four pig populations with different genetic backgrounds

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

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

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