title: Genome-wide linkage disequilibrium and past effective population size in three Korean cattle breeds.
abstract: 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 (Ne), and it allows inferences on the genetic diversity of breeds. The objective of this study was to estimate the LD and Nein 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 Nevalues (53 and 60 respectively), which were distinct from that of Brown Hanwoo (531) for 11 generations ago. The differences in LD and Nefor each breed reflect the breeding strategy applied. The Nefor these endangered cattle breeds remain low; thus, effort is needed to bring them back to a sustainable tract.
authors.affiliation: 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.
authors.forename: P
authors.initials: P
authors.lastname: Sudrajad
authors.affiliation: Division of Animal and Dairy Science, Chungnam National University, Daejeon, 305-764, Korea.
authors.forename: D W
authors.initials: DW
authors.lastname: Seo
authors.affiliation: Animal Breeding and Genetics Division, National Institute of Animal Science, Seonghwan, 31000, Korea.
authors.forename: T J
authors.initials: TJ
authors.lastname: Choi
authors.affiliation: Animal Breeding and Genetics Division, National Institute of Animal Science, Seonghwan, 31000, Korea.
authors.forename: B H
authors.initials: BH
authors.lastname: Park
authors.affiliation: Hanwoo Genetic Improvement Center, National Agricultural Cooperative Federation, Chungnam, 356-831, Korea.
authors.forename: S H
authors.initials: SH
authors.lastname: Roh
authors.affiliation: Hanwoo Genetic Improvement Center, National Agricultural Cooperative Federation, Chungnam, 356-831, Korea.
authors.forename: W Y
authors.initials: WY
authors.lastname: Jung
authors.affiliation: Hanwoo Genetic Improvement Center, National Agricultural Cooperative Federation, Chungnam, 356-831, Korea.
authors.forename: S S
authors.initials: SS
authors.lastname: Lee
authors.affiliation: Division of Animal and Dairy Science, Chungnam National University, Daejeon, 305-764, Korea.
authors.forename: J H
authors.initials: JH
authors.lastname: Lee
authors.affiliation: Animal Breeding and Genetics Division, National Institute of Animal Science, Seonghwan, 31000, Korea.
authors.forename: S
authors.initials: S
authors.lastname: Kim
authors.affiliation: Division of Animal and Dairy Science, Chungnam National University, Daejeon, 305-764, Korea.
authors.forename: S H
authors.initials: SH
authors.lastname: Lee
mesh_terms: D000818:Animals; D001947:Breeding; D002417:Cattle / Q000235:genetics*; D019143:Evolution, Molecular; D005260:Female; D005819:Genetic Markers; D014644:Genetic Variation; D023281:Genomics; D005838:Genotype; D015810:Linkage Disequilibrium; D008297:Male; D020641:Polymorphism, Single Nucleotide; D011156:Population Density; D056910:Republic of Korea
chemical_list: D005819:Genetic Markers
keywords: Hanwoo; genetic diversity; population parameter