Elucidating breed-specific variants of native pigs in Korea: insights into pig breeds’ genomic characteristics

Abstract

Although conserving native pig breeds is important in Korea, research on the genomic aspects to identify breed-specific variations in native pig breeds is uncommon. Single nucleotide polymorphisms (SNPs) can be a powerful source for identifying breed-specific variants. We used whole genome sequencing data, including Jeju Native Pig (JNP), Korean Native Pig (KNP), Korean Wild Boar (KWB), and other western commercial pig breeds to determine native pig breed-specific SNPs. Furthermore, the goal was not only to determine the genomic specificity of native pig breeds but also to identify SNPs that carry breed-specific information (breed-informative SNPs) that can be related to breed characteristics. The representative characteristics of native pigs are their unique meat quality and disease resistance. We surveyed the gene ontology (GO) of native pigs with breed-specific SNPs. Examining the genes associated with GO may contribute to revealing the reasons for the unique characteristics of native pig breeds. The enriched GOs terms were neuron projection development, cell surface receptor signaling pathway, ion homeostasis in JNP, cell adhesion and wound healing in KNP, and DNA repair and reproduction in KWB. We expect that this study of breed-specific SNPs will enable us to gain a deeper understanding of native pigs in Korea.

Identification of Breed-Specific SNPs of Danish Large White Pig in Comparison with Four Chinese Local Pig Breed Genomes

“…In the present study, most variations were in the intergenic and intronic regions of the genomes of all five pig breeds, which is consistent with previous reports. Breed-specific SNPs can elucidate the genomic landscape related to the unique characteristics of a breed compared with other breeds, which implies that they may be excellent genetic markers [13].…”

A genomic estimated breeding value-assisted reduction method of single nucleotide polymorphism sets: a novel approach for determining the cutoff thresholds in genome-wide association studies and best linear unbiased prediction

“…Genome-wide association studies (GWAS) aim to detect variants of genomic loci associated with complex traits in the population, and common single nucleotide polymorphisms (SNPs) are the main source of these variants. SNPs are used to describe genetic variability and identify candidate genes, and GWAS examine significant SNPs (Lee et al 2021 ; Lee et al 2022 ). Attempts to use linkage analysis for mapping genomic loci that affect complex traits are ubiquitous.…”