Genome-wide investigation of a Korean synthetic breed, Woori-Heukdon using the Illumina PorcineSNP60K BeadChip

Kim, Yongmin; Seong, Ha-Seung; Lee, Jung-Jae; Son, Da‐Hye; Kim, Jin-Su; Sa, Soo-Jin; Kim, Young-Sin; Choi, Tae-Jeong; Cho, Kyu-Ho; Hong, Joon-Ki; Choi, Jung‐Woo; Cho, Eun Seok

doi:10.1007/s13258-020-01008-5

Cited by 3 publications

(1 citation statement)

References 23 publications

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“…Haplotypes 9, 23, 52, and 110, which were connected to Chinese pigs to some extent, were of pigs of Okinawa, Japan. According to historical records, Korean pigs were reported from North China approximately 3000 years ago (Chung & Ko, 2006; Kim et al, 2005, 2020). In the present study, we found that Korean wild boars formed haplotypes 111 and 113, which were closer to South China pigs, whereas native Korean pigs formed haplotypes 59–66, which were linked to the haplotypes of the pigs from North China, Vietnam, and Thailand.…”

Section: Resultsmentioning

confidence: 99%

Comprehensive analysis of mitogenome of native Henan pig breeds with 58 worldwide pig breeds

Zhang

et al. 2022

Animal Genetics

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Mitochondria follow non‐Mendelian maternal inheritance, and thus can be used to compare genetic diversity and infer the expansion and migration between animal populations. Based on the mitochondrial DNA sequences of 58 pig breeds from Asia, Europe, Oceania, and America, we observed a distinct division of Eurasian pig species into two main Haplogroups (A and B), with the exception of the Berkshire and Yorkshire breeds. Oceanian pigs were much more similar to European and American pigs in Haplogroup A. Additionally, native Chinese pigs exhibited the most abundant genetic polymorphisms and occupied the centre of Haplogroup B. Miyazaki (Japan) and Siberia (Russia) are two distant and disconnected regions; however, most pigs from these regions were clustered into a subcluster, while native pigs from Korea clustered into a second subcluster. This study is the first to report that pigs from Thailand and Vietnam had haplotypes similar to those of Henan, where the earliest evidence of domestic pigs was found from the Yellow River Basin of North China. Local Henan pig breeds are related to many Asian breeds while still having their own mutation identity, such as g.314 delins T>AC/AT/C of the 12S rRNA gene in Yuxi. Some pigs from Palawan, Itbayat, and Batan Islands of the Philippines and Lanyu Island of China were distinct from other Asian pigs and clustered together into Haplogroup C. These findings show that the complexity of domestication of worldwide pig breeds and mitochondria could reflect genetic communication between pig breeds due to geographical proximity and human activities.

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Section: Resultsmentioning

confidence: 99%

Comprehensive analysis of mitogenome of native Henan pig breeds with 58 worldwide pig breeds

Zhang

et al. 2022

Animal Genetics

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Genome-Wide Assessment of a Korean Composite Pig Breed, Woori-Heukdon

et al. 2022

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A Korean synthetic pig breed, Woori-Heukdon (WRH; F3), was developed by crossing parental breeds (Korean native pig [KNP] and Korean Duroc [DUC]) with their crossbred populations (F1 and F2). This study in genome-wide assessed a total of 2,074 pigs which include the crossbred and the parental populations using the Illumina PorcineSNP60 BeadChip. After quality control of the initial datasets, we performed population structure, genetic diversity, and runs of homozygosity (ROH) analyses. Population structure analyses showed that crossbred populations were genetically influenced by the parental breeds according to their generation stage in the crossbreeding scheme. Moreover, principal component analysis showed the dispersed cluster of WRH, which might reflect introducing a new breeding group into the previous one. Expected heterozygosity values, which were used to assess genetic diversity, were .365, .349, .336, .330, and .211 for WRH, F2, F1, DUC, and KNP, respectively. The inbreeding coefficient based on ROH was the highest in KNP (.409), followed by WRH (.186), DUC (.178), F2 (.107), and F1 (.035). Moreover, the frequency of short ROH decreased according to the crossing stage (from F1 to WRH). Alternatively, the frequency of medium and long ROH increased, which indicated recent inbreeding in F2 and WRH. Furthermore, gene annotation of the ROH islands in WRH that might be inherited from their parental breeds revealed several interesting candidate genes that may be associated with adaptation, meat quality, production, and reproduction traits in pigs.

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Genetic Differentiation among Livestock Breeds—Values for Fst

Hall

2022

Animals

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(1) Background: The Fst statistic is widely used to characterize between-breed relationships. Fst = 0.1 has frequently been taken as indicating genetic distinctiveness between breeds. This study investigates whether this is justified. (2) Methods: A database was created of 35,080 breed pairs and their corresponding Fst values, deduced from microsatellite and SNP studies covering cattle, sheep, goats, pigs, horses, and chickens. Overall, 6560 (19%) of breed pairs were between breeds located in the same country, 7395 (21%) between breeds of different countries within the same region, 20,563 (59%) between breeds located far apart, and 562 (1%) between a breed and the supposed wild ancestor of the species. (3) Results: General values for between-breed Fst were as follows, cattle: microsatellite 0.06–0.12, SNP 0.08–0.15; sheep: microsatellite 0.06–0.10, SNP 0.06–0.17; horses: microsatellite 0.04–0.11, SNP 0.08–0.12; goats: microsatellite 0.04–0.14, SNP 0.08–0.16; pigs: microsatellite 0.06–0.27, SNP 0.15–0.22; chickens: microsatellite 0.05–0.28, SNP 0.08–0.26. (4) Conclusions: (1) Large amounts of Fst data are available for a substantial proportion of the world’s livestock breeds, (2) the value for between-breed Fst of 0.1 is not appropriate owing to its considerable variability, and (3) accumulated Fst data may have value for interdisciplinary research.

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Genome-wide investigation of a Korean synthetic breed, Woori-Heukdon using the Illumina PorcineSNP60K BeadChip

Cited by 3 publications

References 23 publications

Comprehensive analysis of mitogenome of native Henan pig breeds with 58 worldwide pig breeds

Comprehensive analysis of mitogenome of native Henan pig breeds with 58 worldwide pig breeds

Genome-Wide Assessment of a Korean Composite Pig Breed, Woori-Heukdon

Genetic Differentiation among Livestock Breeds—Values for Fst

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