Cited by 25Genetic and phenotypic traits in livestockGenetic Mapping and Diversity in Plants and AnimalsLivestock Farming and Management

Long-Term Artificial Selection of Hanwoo (Korean) Cattle Left Genetic Signatures for the Breeding Traits and Has Altered the Genomic Structure

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Seo, Dongwon, Lee, Doo Ho, Jin, Shil, Won, Jung Il, Lim, Dajeong, Park, Mina, Kim, Tae Hun, Lee, Hak Kyo, Kim, Sidong, Choi, Inchul, Lee, Jun Heon, Gondro, Cedric, Lee, Seung Hwan·2022·Scientific Reports

Abstract

Indigenous Korean breeds such as Hanwoo (Korean) cattle have adapted to their local environment during the past 5000 years. In the 1980s, the National Genetic Improvement Program was established to develop a modern economic breed for beef production in Korea through artificial selection. This process is thought to have altered the genomic structure of breeding traits over time. The detection of genetic variants under selection could help to elucidate the genetic mechanism of artificial selection in modern cattle breeds. Indigenous Hanwoo cattle have adapted in response to local natural and artificial selection during a 40-year breeding program. We analyzed genomic changes in the selection signatures of an unselected population (USP; n = 362) and a selected population (KPN; n = 667) of Hanwoo cattle. Genomic changes due to long-term artificial selection were identified using a genome-wide integrated haplotype score (iHS) and a genome-wide association study (GWAS). Signatures of recent selection were detected as positive (piHS > 6) or negative (piHS < -6) iHS scores spanning more than 46 related genes in KPN cattle, but none in USP cattle. A region adjacent to the PLAG1 gene was found to be under strong selection for carcass weight. The GWAS results also showed a selection signature on BTA14, but none on BTA13. Pathway and quantitative trait locus analysis results identified candidate genes related to energy metabolism, feed efficiency, and reproductive traits in Hanwoo cattle. Strong selection significantly altered Hanwoo cattle genome structural properties such as linkage disequilibrium (LD) and haplotypes through causal mutation for target traits. Haplotype changes of genome structure which are changes of ancestral allele to derived alleles due to selection were clearly identified on BTA13 and BTA14; however, the structure of the LD block was not clearly observed except BTA14. Thus, selection based on EBVs would be working very well in Hanwoo cattle breeding program appears to have been highly successful.

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  • In Hanwoo, genomic regions under selection for carcass and growth traits are mainly located on chromosomes 6 and 14, including candidate genes LCORL, NCAPG, PPARGC1A, etc.

    “In Hanwoo, genomic regions under selection for carcass and growth traits are mainly located on chromosomes 6 and 14, including candidate genes LCORL, NCAPG, PPARGC1A, ABCG2, FAM110B, FABP4, DGAT1, PLAG1, and TOX [170,171].”

    From The Genomic Landscape of Cattle: Domestication, Dispersal, and Adaptive Evolution (2026) · cites this paper as [171]

    The Results and Discussion identify selection signals on BTA14 associated with carcass weight and eye muscle area, near PLAG1. They do not support the claim that the regions are mainly on chromosomes 6 and 14: the paper emphasizes BTA13 and BTA14, and the cited passages do not identify LCORL, NCAPG, or PPARGC1A as candidate genes from this study. Page numbers are unavailable in our copy. (LLM, conf=0.89)

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Authors
Seo, D., Lee, D. H., Jin, S., Won, J. I., Lim, D., Park, M., Kim, T. H., Lee, H. K., Kim, S., Choi, I., Lee, J. H., Gondro, C., & Lee, S. H.
Affiliations
  • Chungnam National University (KR)
  • Rural Development Administration (KR)
  • National Institute of Animal Science (KR)
  • Jeonbuk National University (KR)
  • Michigan State University (US)
Corresponding author
Lee, Seung Hwan
Venue
Scientific Reports
Published
2022-04-19
Volume
12
Issue
1
Pages
6438-6438
ISSN
2045-2322 (ISSN-L)
OpenAlex
W4224294535
Cited by
25
References
48
Citations by year
2026: 2 · 2025: 11 · 2024: 4 · 2023: 5 · 2022: 3
FWCI
3.47
Type
journal article
Language
en
Open access
Locations
  • Scientific Reports (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • Chungnam National University (2020-0-01441)
  • Ministry of Trade, Industry and Energy
  • Rural Development Administration
  • Ministry of Science and ICT, South Korea (2020-0-01441)
  • National Institute of Animal Science
  • Korea Evaluation Institute of Industrial Technology
  • Institute for Information and Communications Technology Promotion (2020-0-01441)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
  • Life Sciences › Agricultural and Biological Sciences › Agronomy and Crop Science › Livestock Farming and Management
Keywords
Hanwoo cattle, selective breeding, selection signatures, integrated haplotype score, PLAG1, carcass weight, BTA14, linkage disequilibrium, haplotype structure, beef cattle breeding, energy metabolism, feed efficiency, reproductive traits, indigenous cattle breeds
MeSH terms
Animals, Cattle, Selection, Genetic, Linkage Disequilibrium, Polymorphism, Single Nucleotide, Genomics, Quantitative Trait Loci, Genome-Wide Association Study

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