SHORT COMMUNICATION Genome-wide linkage disequilibrium and past effective population size in three Korean cattle breeds P. Sudrajad* † , D. W. Seo*, T. J. Choi ‡ , B. H. Park ‡ , S. H. Roh § , W. Y. Jung § , S. S. Lee § , J. H. Lee*, S. Kim ‡ and S. H. Lee* *Division of Animal and Dairy Science, Chungnam National University, Daejeon 305-764, Korea. † Indonesian Agency for Agricultural Research and Development, Ministry of Agriculture, Jakarta 12540, Indonesia. ‡ Animal Breeding and Genetics Division, National Institute of Animal Science, Seonghwan 31000, Korea. § Hanwoo Genetic Improvement Center, National Agricultural Cooperative Federation, Chungnam 356-831, Korea. Summary The routine collection and use of genomic data are useful for effectively managing breeding programs for endangered populations. Linkage disequilibrium (LD) using high-density DNA markers has been widely used to determine population structures and predict the genomic regions that are associated with economic traits in beef cattle. The extent of LD also provides information about historical events, including past effective population size (N e ), and it allows inferences on the genetic diversity of breeds. The objective of this study was to estimate the LD and N e in three Korean cattle breeds that are genetically similar but have different coat colors (Brown, Brindle and Jeju Black Hanwoo). Brindle and Jeju Black are endangered breeds with small populations, whereas Brown Hanwoo is the main breeding population in Korea. DNA samples from these cattle breeds were genotyped using the Illumina BovineSNP50 Bead Chip. We examined 13 cattle breeds, including European taurines, African taurines and indicines, and hybrids to compare their LD values. Brown Hanwoo consistently had the lowest mean LD compared to Jeju Black, Brindle and the other 13 cattle breeds (0.13, 0.19, 0.21 and 0.15–0.22 respectively). The high LD values of Brindle and Jeju Black contributed to small N e values (53 and 60 respectively), which were distinct from that of Brown Hanwoo (531) for 11 generations ago. The differences in LD and N e for each breed reflect the breeding strategy applied. The N e for these endangered cattle breeds remain low; thus, effort is needed to bring them back to a sustainable tract. Keywords genetic diversity, Hanwoo, population parameter The Food and Agricultural Organization of the United Nations (FAO) documents Korean cattle breeds on its Domestic Animal Diversity Information System. Korean cattle have been classified and named based on their body color and geographical distribution (Dadi et al. 2012; Suh et al. 2014). Brown Hanwoo is widely used for breeding in Korea, Brindle Hanwoo is from the Korean Peninsula and Jeju Black is from Jeju Island (Fig. S1). The Korean government has been trying to improve the genetic performance of these cattle breeds even though the condi- tions of the breeding populations are not the same. Brown Hanwoo has the largest population (3 million animals) with a well-established breeding program and progeny testing to select bulls (Park et al. 2013), whereas the others (Brindle and Jeju Black) are endangered (Suh et al. 2014), although these breeds have the potential to be developed as beef cattle with quality comparable to that of Brown Hanwoo (Lee et al. 2013c; Han et al. 2015). Current genetic improvement programs for Korean cattle rely on the framework of genomic selection, population structure, and genetic predictions – which have become routine genomic tools (Lee et al. 2014). Analysis of genomic data is becoming part of the beef cattle industry and useful for the improvement of the effectiveness of genetic programs for endangered breeds such as Brindle and Jeju Black. Linkage disequilibrium (LD) and effective population size (N e ) analyses are important, as these parameters are strongly influenced by historical events, including genetic Address for correspondence S. H. Lee, Division of Animal and Dairy Science, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 305-764, Korea. E-mail: slee46@cnu.ac.kr and S. Kim, Animal Breeding and Genetics Division, National Institute of Animal Science, Seonghwan 31000, Korea. E-mail: goldstar@korea.kr Accepted for publication 16 July 2016 doi: 10.1111/age.12488 1 © 2016 Stichting International Foundation for Animal Genetics