Genetic characteristics and diversity of Korean Jeju Black cattle by whole genome SNP markers

Background Conservation and genetic improvement of cattle breeds requires to know the information about genetic diversity and population structure of animals. This study investigated the genetic diversity and population structure among the three breeds raised in Korean peninsula. Three popular breed found in Korea , i.e. Jeju Black, Hanwoo, Holstein with other six breeds such as Angus, Hereford, Brown Wagyu, Black Wagyu, Brahman and Nellore was examined in this study. Genetic diversity within the cattle breeds was analyzed using the popular measures of genetic diversity namely minor allele frequency (MAF), observed and expected heterozygosity (H O and H E ), inbreeding coefficient (F IS ) and past effective population size (N E ). Molecular variance and population structure were performed among the nine cattle breeds using model-based clustering (ADMIXTURE) analysis. Genetic distances between breed pairs were evaluated using Nei’s genetic distance (D A ) and with Weir and Cockerham’s F ST . Results This study revealed that Jeju Black cattle had lowest level of heterozygocity (HE = 0.21) among the studied taurine cattle breeds ranging from 0.25 to 0.30, and low MAF of 0.16, while other breeds have MAF ranging 0.11~0.21. The level of inbreeding was -0.076 in case of Jeju Black as compared to other breed (-0.018 ~ -0.118). PCA analysis and neighbor-joining (NJ) tree showed a clear separation of Jeju Black cattle from other local and exotic cattle breeds. Model-based clustering also revealed a distinct pattern of admixture of Jeju Black cattle having no clustering with other studied populations. The F ST value between Jeju Black cattle and Hanwoo was 0.106, which was lowest across the breeds ranging from 0.161 to 0.274, indicating some degree of genetic closeness of Jeju Black cattle with Hanwoo. The N E of Jeju Black cattle was 38, whereas Hanwoo was 209 in the most recent 13 generation ago. Conclusion This study indicates an alarming trend of reducing effective population size in Jeju Black cattle. Thus, a sustainable breeding policy should be implemented to increase the population of Jeju Black cattle for the genetic improvement and future conservation.

Identifying Loci Under Positive Selection in Yellow Korean Cattle (Hanwoo)

Jeju Black cattle is one of the aboriginal Korean cattle breeds that has been isolated in Jeju island for a long time, while Yellow Hanwoo cattle has been extensively selected for beef production traits for the last several decades. Aiming to investigate broader patterns of selection, we genotyped 352 Yellow Hanwoo and 169 Jeju Black cattle using a customized 150 K bovine chip. Our composite selection signals’ analysis to identify selection signatures (cross-population extended haplotype homozygosity [XP-EHH], ΔSAF, and FST) identified recent and strong signature of selection near many loci with mutations affecting the traits under strong selection as outlier in Yellow Hanwoo, including SCP2 ( P = 8.41 × 10−10) that may be involved in the meat quality. We found nine candidate regions with significant clusters of selection signals, and further bioinformatics analyses of the genes located within these regions revealed mainly genes involved in G-protein coupled receptor signaling pathway (GO:0007186) or olfactory transduction (bta04740), which may be due to adaptation to natural environments in Jeju island. Based on the stronger correlation of Ne10/Ne100 ratio between Yellow Hanwoo (0.61) and Jeju Black (0.66) cattle, our results suggest that the difference of chromosomal regions of selection signature between the 2 cattle breeds was due to a consequence of selection processes to adapt to environmental differences between Jeju island and the main inland, Korean peninsula.