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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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Details
1 Chungnam National University, Division of Animal and Dairy Science, Daejeon, South Korea (GRID:grid.254230.2) (ISNI:0000 0001 0722 6377)
2 National Institute of Animal Science, RDA, Hanwoo Research Institute, Pyeongchang, South Korea (GRID:grid.484502.f) (ISNI:0000 0004 5935 1171)
3 National Institute of Animal Science, RDA, Animal Genomics and Bioinformatics Division, Jeonju, Korea (GRID:grid.420186.9) (ISNI:0000 0004 0636 2782)
4 National Institute of Animal Science, RDA, Animal Breeding and Genetics Division, Seonghwan, South Korea (GRID:grid.484502.f) (ISNI:0000 0004 5935 1171)
5 Jeonbuk National University, Department of Animal Biotechnology, Jeonju, South Korea (GRID:grid.411545.0) (ISNI:0000 0004 0470 4320)
6 National Institute of Animal Science, RDA, Poultry Institute, Pyeongchang, South Korea (GRID:grid.484502.f) (ISNI:0000 0004 5935 1171)
7 Michigan State University, Beacon Center for the Study of Evolution in Action and Department of Animal Science, East Lansing, USA (GRID:grid.17088.36) (ISNI:0000 0001 2150 1785)