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Journal of Animal Science and Technology
Korean Society of Animal Science and Technology

J Anim Sci Technol

pISSN: 2055-0391, eISSN: 2672-0191

DOI: https://doi.org/10.5187/jast.2023.e104

Article

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

Jun Park1, Chong-Sam Na1,*
1Department of Animal Biotechnology, Jeonbuk National University, Jeonju 54896, Korea.
*Corresponding Author: Chong-Sam Na, Department of Animal Biotechnology, Jeonbuk National University, Jeonju 54896, Korea, Republic of. Phone: +82-63-270-2614. E-mail: csna@jbnu.ac.kr.

© Copyright 2023 Korean Society of Animal Science and Technology. This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Received: Jul 14, 2023; Revised: Sep 12, 2023; Accepted: Oct 04, 2023

Published Online: Oct 04, 2023

Abstract

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 SNP data obtained from five Great-Grand-Parents (GGP) farms in Landrace. The estimated of heritabilities for days to 105kg (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 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.

Keywords: Gene ontology; Kyoto Encyclopedia of Genes and Genomes; Landrace pigs; Productive traits; Weighted single-step GWAS