Division of Animal and Dairy Science, Chungnam National University, 99, Daehak-ro, Yuseong-gu, Daejeon, 34134, South Korea.
Hanwoo Research Institute, National Institute of Animal Science, RDA, Pyeongchang, South Korea.
Sci Rep. 2022 Apr 19;12(1):6438. doi: 10.1038/s41598-022-09425-0.
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.
韩国本土品种如韩牛（韩国）牛在过去 5000 年中适应了当地的环境。20 世纪 80 年代，韩国建立了国家遗传改良计划，通过人工选择为韩国的牛肉生产开发现代经济品种。这一过程被认为随着时间的推移改变了养殖性状的基因组结构。选择下遗传变异的检测有助于阐明现代牛品种人工选择的遗传机制。在 40 年的选育计划中，本土韩牛牛适应了当地的自然和人工选择。我们分析了未选育群体（USP；n=362）和韩牛选育群体（KPN；n=667）的选择特征的基因组变化。使用全基因组综合单倍型得分（iHS）和全基因组关联研究（GWAS）鉴定了由于长期人工选择而导致的基因组变化。在 KPN 牛中，发现了跨越 6 个以上相关基因的正（piHS>6）或负（piHS<-6）iHS 评分的近期选择特征，但在 USP 牛中没有发现。在 PLAG1 基因附近的一个区域被发现对胴体重量有强烈的选择。GWAS 结果还显示 BTA14 上存在选择特征，但 BTA13 上没有。途径和数量性状位点分析结果确定了与韩牛能量代谢、饲料效率和繁殖性状相关的候选基因。通过对目标性状的因果突变，强烈的选择显著改变了韩牛牛基因组结构特性，如连锁不平衡（LD）和单倍型。由于选择导致的祖先等位基因向衍生等位基因的基因组结构单倍型变化在 BTA13 和 BTA14 上被清楚地识别；然而，除了 BTA14 之外，LD 块的结构并没有被清楚地观察到。因此，基于 EBV 的选择在韩牛牛选育计划中似乎非常成功。
