Journal
GENES
Volume 10, Issue 4, Pages -Publisher
MDPI
DOI: 10.3390/genes10040293
Keywords
Association weight matrix; Bayes factor; economic trait; single nucleotide polymorphism
Categories
Funding
- Ministry of Education of the Republic of Korea
- National Research Foundation of Korea [NRF-2019R1A6A1A03025159]
- Korea Institute of Planning and Evaluation for Technology in Food, Agriculture, Forestry and Fisheries through the Golden Seed Project, Ministry of Agriculture, Food, and Rural Affairs [213010-05-2-SB510]
- Cooperative Research Program for Agriculture Science & Technology Development, of the Rural Development Administration, Republic of Korea [PJ012817012019]
- Rural Development Administration (RDA), Republic of Korea [PJ012817012019] Funding Source: Korea Institute of Science & Technology Information (KISTI), National Science & Technology Information Service (NTIS)
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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.
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