Journal Article

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

Song, Ki-Duk, Kim, Dae Cheol, Shin, Donghyun, Young-Sup, Lee, Won, Kyeong-Hye, Lee, Sang Chul

2020

Overview

ObjectiveThe 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.MethodsWe 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 Fst was utilized. This statistic directly measures the population differentiation at the variant level. Additionally, we investigated the gene ontologies (GOs) and genetic features.ResultsCompared 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.ConclusionThe 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.

• Publisher: 아세아·태평양축산학회
• Subject: Disequilibrium / Epithelium / Expected values / Genes / Genetic diversity / Genomes / Haplotypes / Hogs / Linkage disequilibrium / Meat quality / Neurogenesis / Ontology / Population differentiation / Pork / Proteins / Quality control / Sample variance / 축산학