Genome-wide investigation of a Korean synthetic breed, Woori-Heukdon using the Illumina PorcineSNP60K BeadChip
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Genes & Genomics https://doi.org/10.1007/s13258-020-01008-5
RESEARCH ARTICLE
Genome‑wide investigation of a Korean synthetic breed, Woori‑Heukdon using the Illumina PorcineSNP60K BeadChip Yong‑Min Kim1,2 · Ha‑Seung Seong2 · Jung‑Jae Lee3 · Da‑Hye Son4 · Jin‑Su Kim2 · Soo‑Jin Sa1 · Young‑Sin Kim1 · Tae‑Jeong Choi1 · Kyu‑Ho Cho1 · Joon‑Ki Hong1 · Jung‑Woo Choi2 · Eun‑Seok Cho1 Received: 30 July 2020 / Accepted: 25 September 2020 © The Genetics Society of Korea 2020
Abstract Background Woori-Heukdon (KWH) is a Korean synthetic pig breed generated using Chookjin-Duroc (KCD), ChookjinChamdon (KCC), and their crossbreds. Currently, there is a severe lack of studies investigating the Korean breed populations including wild boars (KWB) throughout the genome. Objective This study was performed to investigate the genetic characteristics of Korean pig populations at the genome-wide level. Methods Using the SNP dataset derived from genotyped and downloaded datasets using the Illumina PorcineSNP60K BeadChip, we compared the genomes of 532 individuals derived from 23 pig breeds to assess the genetic diversity, inbreeding coefficient, genetic differentiation, and population structure. Results KWB showed the lowest average expected heterozygosity (HE = 0.1904), while KWH showed the highest genetic diversity (HE = 0.02859) among Korean populations. We verified that the genetic composition of KWH, showing USD of 74.8% and KCC of 25.2% in ADMIXTURE analysis. In population structure analyses, KCC was consistently shown to be separated from other pig populations. In addition, we observed gene flow from Western pigs to a part of Chinese populations. Conclusion This study showed that Korean native pigs, KCC have genetic differences in comparison with Chinese and Western pigs; despite some historical records and recent genetic studies, we could not find any clear evidence that KCC was significantly influenced by Chinese or Western breeds in this study. We also verified the theoretical genomic composition of KWH at the molecular level in structure analyses. To our knowledge, this is the first genomic study to investigate the genomic characteristics of KWH and KCC. Keywords Woori-heukdon · Chookjin-chamdon · Chookjin-duroc · Genotyping · Population structure
Introduction
Yong-Min Kim, Ha-Seung Seong and Jung-Jae Lee contributed equally to this work. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s13258-020-01008-5) contains supplementary material, which is available to authorized users. * Joon‑Ki Hong [email protected] * Jung‑Woo Choi [email protected] * Eun‑Seok Cho [email protected] Extended author information available on the last page of the article
Korean native pigs are known to have been introduced from northern China and spread throughout Korean peninsula approximately 3000 years ago according to historical records (Chung and Ko 2006; Kim 2002; Kim et al. 2005). This historical account is also supported by a previous genomic study using microsatellite markers, whic
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