Weighted single-step genome-wide association study to reveal new candidate genes for productive traits of Landrace pig in Korea

• Published in: Journal of animal science and technology 2024-07, Vol.66 (4), p.702-716
• Main Authors: Park, Jun, Na, Chong-Sam
• Format: Article
• Language: English
• Subjects: Gene ontology; Kyoto Encyclopedia of Genes and Genomes; Landrace pigs; Productive traits; Weighted single-step genome-wide association studies
• ISSN: 2055-0391; 2672-0191; 2055-0391; 2093-6281
• DOI: 10.5187/jast.2023.e104

The objective of this study was to identify genomic regions and candidate genes associated with productive traits using a total of 37,099 productive records and 6,683 single nucleotide polymorphism (SNP) data obtained from five Great-Grand-Parents (GGP) farms in Landrace. The estimated of heritabilities for days to 105 kg (AGE), average daily gain (ADG), backfat thickness (BF), and eye muscle area (EMA) were 0.49, 0.49, 0.56, and 0.23, respectively. We identified a genetic window that explained 2.05%-2.34% for each trait of the total genetic variance. We observed a clear partitioning of the four traits into two groups, and the most significant genomic region for AGE and ADG were located on the chromosome (SSC) 1, while BF and EMA were located on SSC 2. We conducted Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), which revealed results in three biological processes, four cellular component, three molecular function, and six KEGG pathway. Significant SNPs can be used as markers for quantitative trait loci (QTL) investigation and genomic selection (GS) for productive traits in Landrace pig.