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 (N ), and it allows inferences on the genetic diversity of breeds. The objective of this study was to estimate the LD and N 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 values (53 and 60 respectively), which were distinct from that of Brown Hanwoo (531) for 11 generations ago. The differences in LD and N for each breed reflect the breeding strategy applied. The N for these endangered cattle breeds remain low; thus, effort is needed to bring them back to a sustainable tract.

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

“…Differences in the various reports might be caused by many factors such as sample size, SNP quality control measures and model used to study LD and N E [6]. However, in our study the sample size of JJBC was 78 which was highest among all previous reports [2,6,12].…”

“…Differences in the various reports might be caused by many factors such as sample size, SNP quality control measures and model used to study LD and N E [6]. However, in our study the sample size of JJBC was 78 which was highest among all previous reports [2,6,12]. The N e value of JJBC seems to be sufficient for maintaining genetic diversity for the short term as suggested by Frankham [33] but not enough for long term species management.…”

“…whereas other studies performed by Sharma [12] showed their number to be 67. Sudrajad [6] calculated N E in JJBC to be 60 until 11 generation ago and Eva [2] reported their number seems to be 11 at nearest generation. Other Korean cattle Hanwoo had a large N E value of 209 among studied cattle breeds but till the differences is higher those reported by Li and Kim [9] who estimated N E of Hanwoo was 630 at most recent 11 generation ago and Sudrajad [6] estimated N E is about 531.…”

“…Measuring LD might be useful in rare breeds like Jeju Black cattle where it can be used to calculate population genetic parameters in the absence of pedigree data. It is reported that registered Jeju Black cattle have a population size approximately 619 (Korea Seed stock Database), other sources mentioned their number might be 400 ~500 [6,7]. Due to the small size of the remaining population of Jeju Black cattle only in the Jeju Island, it is essential to estimate the level of inbreeding as it is an important parameter to assess the genetic diversity of a given species.…”

“…Development of sustainable breed improvement strategies is dependent on the precise characterization of animal genetic diversity [11]. Although several studies have investigated the diversity pattern of Korean cattle along with Jeju Black Cattle [2,6,12] but it is still controversial whether Jeju Black formed as a separate breed or as a varieties of Hanwoo. Accurate refinement to decipher the origin of Jeju Black cattle is necessary for their future conservation and improvement program.…”