Genetic Architecture and Population Structure of Hanwoo Cattle

Abstract

Characterization of genetic diversity and evolutionary history provides a low level handle on population structure which can be used to make decisions on how these populations will be managed. This has immediate implications for natural populations in conservation programs but is also highly relevant for Agricultural species. We used 29,844 SNPs to estimate genetic variability in 3 subpopulations of Hanwoo cattle (Jeju Black, Brindle and Brown) and their genetic distances to seven other breeds (Chinese Yeonbyun, Brahman and 5 European breeds). Jeju Black and Brindle, small isolated populations, are evidencing clear signs of island population effects with high FST=0.06 between them (FST between European and Eastern Asian breeds is Δ0.085) and Δ0.03 with the continental Brown. This may lead to negative consequences and even endanger these subpopulations in the future. Eastern Asian breeds show a relatively small genetic background originating from 'Bos indicus' which is identifiable in both Hanwoo and Yeonbyun (~5-10%). This suggests that at some point during radiation of 'Bos taurus' throughout Eastern Asia they crossed with zebu cattle radiating from India which contributed to the final genetic architecture of these breeds. Brown Hanwoo and Yeonbyun are genetically highly related with the latter showing higher levels of diversity which may be due to lack of intense artificial selection. This makes Yeonbyun cattle worthy of attention since they could potentially act as proxies to the ancestral Hanwoo prior to selection and assist in characterization of ancestral alleles in Hanwoo. This close relationship can reduce noise and lead to more robust identification of recent signatures of selection due to breeding for production traits, particularly marbling. Good genetic characterization of the Chinese breed can also be beneficial for genomic selection in Hanwoo which will benefit by being able to better distinguish genotypes between identity by descent and identity by state.