Genome-wide scans for detecting the selection signature of the Jeju-island native pig in Korea

Abstract

Objective: The Jeju native pig (JNP) found on the Jeju Island of Korea is a unique black pig known for high-quality meat. To investigate the genetic uniqueness of JNP, we analyzed the selection signature of the JNP in comparison to commercial pigs such as Berkshire and Yorkshire pigs.Methods: We surveyed the genetic diversity to identify the genetic stability of the JNP, using the linkage disequilibrium method. A selective sweep of the JNP was performed to identify the selection signatures. To do so, the population differentiation measure, Weir-Cockerham’s F<sub>st</sub> was utilized. This statistic directly measures the population differentiation at the variant level. Additionally, we investigated the gene ontologies (GOs) and genetic features.Results: Compared to the Berkshire and Yorkshire pigs, the JNP had lower genetic diversity in terms of linkage disequilibrium decays. We summarized the selection signatures of the JNP as GO. In the JNP and Berkshire pigs, the most enriched GO terms were epithelium development and neuron-related. Considering the JNP and Yorkshire pigs, cellular response to oxygen-containing compound and generation of neurons were the most enriched GO.Conclusion: The selection signatures of the JNP were identified through the population differentiation statistic. The genes with possible selection signatures are expected to play a role in JNP’s unique pork quality.

Integration of multi-omics approaches for functional characterization of muscle related selective sweep genes in Nanchukmacdon

“…The Korean peninsula is one of the largest pig consuming country with its Jeju native black pig (JNP) is an indigenous variety of Korean pig with high-quality meat content, redness and nutrition value 4 , 5 . Superior taste leads to an increase in JNP demand with every passing day but less productivity and fertility made it difficult to sustain the demand 6 , 7 .…”

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

“…In JNP, the notable genes containing nsSNPs were Transforming growth factor beta 2 proprotein (TGFB2), glutathione S-transferase kappa 1 (GSTK1) and ATP-binding cassette subfamily A member 8 (ABCA8). In previous study, TGFB2 gene were reported to be related to the developmental growth in JNP in comparison to the Berkshire pigs (Lee, Shin, et al 2020 ). Members of the glutathione S-transferase (GST) family constitute a large class of cytoplasmic, membrane-bound, multigene, and multifunctional enzymes (Hayes et al 2005 ).…”

Detection of Selection Signatures in Anqing Six-End-White Pigs Based on Resequencing Data

“…π ratio analysis is also a common detection method used to focus on the polymorphisms of a specific population based on gene heterozygosity, and a larger π ratio indicates a higher polymorphism [ 27 ]. These methods have been widely used in the selection signal detection of livestock [ 28 , 29 ]. In Zhang’s study, F ST and π ratio analyses were combined; used to define the genomic selection region of the Wannan black pig; and found selected genes associated with growth, immunity, and digestive functions [ 30 ].…”