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Genes 2019, 10(4), 293; https://doi.org/10.3390/genes10040293

Bayes Factor-Based Regulatory Gene Network Analysis of Genome-Wide Association Study of Economic Traits in a Purebred Swine Population

1,†, 2,† and 3,*
1
Jung P&C Institute, Inc., 1504 U-TOWER, Yongin-si, Gyeonggi-do 16950, Korea
2
Research & Development Center, PatentPia Inc., Seoul 06223, Korea
3
Department of Animal Science and Technology, Chung-Ang University, Anseong-si, Gyeonggi-do 17546, Korea
*
Author to whom correspondence should be addressed.
These authors contributed equally to this work.
Received: 3 February 2019 / Revised: 8 March 2019 / Accepted: 1 April 2019 / Published: 10 April 2019
(This article belongs to the Section Animal Genetics and Genomics)
PDF [1672 KB, uploaded 10 April 2019]

Abstract

: Early stage prediction of economic trait performance is important and directly linked to profitability of farm pig production. Genome-wide association study (GWAS) has been applied to find causative genomic regions of traits. This study established a regulatory gene network using GWAS for critical economic pig characteristics, centered on easily measurable body fat thickness in live animals. We genotyped 2,681 pigs using Illumina Porcine SNP60, followed by GWAS to calculate Bayes factors for 47,697 single nucleotide polymorphisms (SNPs) of seven traits. Using this information, SNPs were annotated with specific genes near genome locations to establish the association weight matrix. The entire network consisted of 226 nodes and 6,921 significant edges. For in silico validation of their interactions, we conducted regulatory sequence analysis of predicted target genes of transcription factors (TFs). Three key regulatory TFs were identified to guarantee maximum coverage: AT-rich interaction domain 3B (ARID3B), glial cell missing homolog 1 (GCM1), and GLI family zinc finger 2 (GLI2). We identified numerous genes targeted by ARID3B, associated with cellular processes. GCM1 and GLI2 were involved in developmental processes, and their shared target genes regulated multicellular organismal process. This system biology-based function analysis might contribute to enhancing understanding of economic pig traits.
Keywords: Association weight matrix; Bayes factor; economic trait; single nucleotide polymorphism Association weight matrix; Bayes factor; economic trait; single nucleotide polymorphism
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).
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Lee, J.; Kang, J.-H.; Kim, J.-M. Bayes Factor-Based Regulatory Gene Network Analysis of Genome-Wide Association Study of Economic Traits in a Purebred Swine Population. Genes 2019, 10, 293.

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