Genome-wide analysis of Hanwoo and Chikso populations using the BovineSNP50 genotyping array

• Published in: Genes & Genomics Vol. 40; no. 12; pp. 1373 - 1382
• Main Authors: Song, Jun-Seok, Seong, Ha-Seung, Choi, Bong-Hwan, Lee, Chang-Woo, Hwang, Nam-Hyun, Lim, Dajeong, Lee, Joon-Hee, Kim, Jin Soo, Kim, Jeong-Dae, Park, Yeon-Soo, Choi, Jung-Woo, Kim, Jong-Bok
• Format: Journal Article
• Language: English
• Published: Seoul Springer Science and Business Media LLC 01.12.2018; The Genetics Society of Korea; Springer Nature B.V; 한국유전학회
• Subjects: Animal Genetics and Genomics; Animals; Biomedical and Life Sciences; Bovidae; Cattle; Cattle - genetics; cattle breeds; Cell Differentiation; Cell Differentiation - genetics; data collection; genes; Genetic relationship; genetic relationships; genetic variation; Genome-Wide Association Study; Genomes; genomics; Genotype; Genotyping; Genotyping Techniques; Heterozygosity; Heterozygote; Human Genetics; Inbreeding; inbreeding coefficient; Life Sciences; Linkage disequilibrium; Livestock; Meat; Microbial Genetics and Genomics; Plant Genetics and Genomics; Polymorphism, Single Nucleotide; Polymorphism, Single Nucleotide - genetics; Population genetics; Principal Component Analysis; Principal components analysis; Quality control; Receptor, trkB; Receptor, trkB - genetics; Receptors, LDL; Receptors, LDL - genetics; reproductive traits; Research Article; Single-nucleotide polymorphism; 생물학; Bovine SNP50K BeadChip; Chikso; Hanwoo; Linkage disequilibrium
• ISSN: 1976-9571; 2092-9293; 2092-9293
• DOI: 10.1007/s13258-018-0733-x

Hanwoo and Chikso are classified as Korean native cattle breeds that are currently registered with the Food and Agriculture Organization. However, there is still a lack of genomic studies to compare Hanwoo to Chikso populations. The objective of this study was to perform genome-wide analysis of Hanwoo and Chikso populations, investigating the genetic relationships between these two populations. We genotyped a total of 319 cattle including 214 Hanwoo and 105 Chikso sampled from Gangwon Province Livestock Technology Research Institute, using the Illumina Bovine SNP50K Beadchip. After performing quality control on the initially generated datasets, we assessed linkage disequilibrium patterns for all the possible SNP pairs within 1 Mb apart. Overall, average r 2 values in Hanwoo (0.048) were lower than Chikso (0.074) population. The genetic relationship between the populations was further assured by the principal component analysis, exhibiting clear clusters in each of the Hanwoo and Chikso populations, respectively. Overall heterozygosity for Hanwoo (0.359) was slightly higher than Chikso (0.345) and inbreeding coefficient was also a bit higher in Hanwoo (− 0.015) than Chikso (− 0.035). The average F ST value was 0.036 between Hanwoo and Chikso, indicating little genetic differentiation between those two breeds. Furthermore, we found potential selection signatures including LRP1B and NTRK2 genes that might be implicated with meat and reproductive traits in cattle. In this study, the results showed that both Hanwoo and Chikso populations were not under severe level of inbreeding. Although the principal component analysis exhibited clear clusters in each of the populations, we did not see any clear evidence that those two populations are highly differentiated each other.