• Asian-Australasian Journal of Animal Sciences
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• v.31 no.8
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• pp.1078-1087
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• 2018

Objective: The genetic diversity of the Landrace population, a representative maternal pig breed in Korea, is important for genetic improvement. Previously, the effective population size (Ne) has been used to infer the genetic diversity of a population of interest. In this study, we aimed to use single nucleotide polymorphism (SNP) data to characterize linkage disequilibrium (LD) and the Ne of the Korean Landrace population. Methods: We genotyped 1,128 Landrace individuals from three representative Korean major grand-grand-parent (GGP) farms using the Illumina PorcineSNP60 version2 BeadChip, which covers >61,565 SNPs located across all autosomes and mitochondrial and sex chromosomes. We estimated the expected LD and current Ne, as well as ancestral Ne. Results: In the Korean Landrace population, the mean LD ($r^2$) of 3.698 million SNP pairs was $0.135{\pm}0.204$. The mean $r^2$ decreased slowly with as the distance between SNPs increased, and remained constant beyond 3 Mb. According to the $r^2$ calculations, 8,085 of 3.698 million SNP pairs were in complete LD. The current Ne (${\pm}$standard deviation) of the Korean Landrace population is approximately 92.27 [79.46; 105.07] individuals. The ancestral Ne exhibited a slow and steady decline from 186.61 to 92.27 over the past 100 generations. Additionally, we observed more a rapid Ne decrease from the past 20 to 10 generations ago, compared with other intervals. Conclusion: We have presented an overview of LD and the current and ancestral Ne values in the Korean Landrace population. The mean LD and current Ne for the Korean Landrace population confirm the genetic diversity and reflect the history of this pig population in Korea.

• Genomics & Informatics
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• v.14 no.4
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• pp.230-233
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• 2016

Linkage disequilibrium (LD) is the non-random association between the loci and it could give us a preliminary insight into the genetic history of the population. In the present study LD patterns and effective population size (Ne) of three Korean cattle breeds along with Chinese, Japanese and Mongolian cattle were compared using the bovine Illumina SNP50 panel. The effective population size (Ne) is the number of breeding individuals in a population and is particularly important as it determines the rate at which genetic variation is lost. The genotype data in our study comprised a total of 129 samples, varying from 4 to 39 samples. After quality control there were ~29,000 single nucleotide polymorphisms (SNPs) for which $r^2$ value was calculated. Average distance between SNP pairs was 1.14 Mb across all breeds. Average $r^2$ between adjacent SNP pairs ranged between was 0.1 for Yanbian to 0.3 for Qinchuan. Effective population size of the breeds based on $r^2$ varied from 16 in Hainan to 226 in Yanbian. Amongst the Korean native breeds effective population size of Brindle Hanwoo was the least with Ne = 59 and Brown Hanwoo was the highest with Ne = 83. The effective population size of the Korean cattle breeds has been decreasing alarmingly over the past generations. We suggest appropriate measures to be taken to prevent these local breeds in their native tracts.

• Animal Bioscience
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• v.34 no.7
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• pp.1105-1115
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• 2021

Objective: To conserve and utilize the genetic resources of a traditional Chinese indigenous pig breed, Liangshan pig, we assessed the genetic diversity, genetic structure, and genetic distance in this study. Methods: We used 50K single nucleotide polymorphism (SNP) chip for SNP detection of 139 individuals in the Liangshan Pig Conservation Farm. Results: The genetically closed conserved population consisted of five overlapping generations, and the total effective content of the population (Ne) was 15. The whole population was divided into five boar families and one non-boar family. Among them, the effective size of each generation subpopulation continuously decreased. However, the proportion of polymorphic markers (P_N) first decreased and then increased. The average genetic distance of these 139 Liangshan pigs was 0.2823±0.0259, and the average genetic distance of the 14 boars was 0.2723±0.0384. Thus, it can be deduced that the genetic distance changed from generation to generation. In the conserved population, 983 runs of homozygosity (ROH) were detected, and the majority of ROH (80%) were within 100 Mb. The inbreeding coefficient calculated based on ROH showed an average value of 0.026 for the whole population. In addition, the inbreeding coefficient of each generation subpopulation initially increased and then decreased. In the pedigree of the whole conserved population, the error rate of paternal information was more than 11.35% while the maternal information was more than 2.13%. Conclusion: This molecular study of the population genetic structure of Liangshan pig showed loss of genetic diversity during the closed cross-generation reproduction process. It is necessary to improve the mating plan or introduce new outside blood to ensure long-term preservation of Liangshan pig.

• Korean Journal of Ichthyology
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• v.27 no.1
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• pp.10-15
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• 2015

Giant grouper (Epinephelus lanceolatus) is a endangered species considered as a vulnerable grade-organism in the International Union for Conservation of Nature (IUCN) red list. As a fundamental baseline study for establishing a giant grouper broodstock management system, the efficiency for parentage analysis was evaluated by using microsatellite makers previously available in this species. The eight microsatellites generated a total 52 alleles from 32 individuals, the mean expected heterozygosity was 0.663, and mean inbreeding coefficient was 0.011, consequently suggesting that the present broodstock has retained the high level of genetic diversity. However, our analysis also recommended the collection of more broodfish for more stable brood line, since the estimated value of the effective population size was proven to be 35. The average probability of identity was $6.85{\times}10^{-11}$. NE-2P and NE-PP of paternity non-exclusion probabilities were 0.00835 and 0.00027, respectively. As the result of principle coordinate analysis, the genotype of broodstock was not overlapped, suggesting that the management system of giant grouper based on eight selected microsatellite markers might be effective, although further validation with extended number of broodfish might also be needed in future. Data of present study could be a useful basis to avoid the unwanted selection of broodfish that possess close genetic relationship with current broodstock, and consequently to establish effective broodstock management system allowing the production of progeny with high genetic diversity.

• Journal of agriculture & life science
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• v.50 no.2
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• pp.107-116
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• 2016

The study was aimed to analyze pedigree structure and inbreeding coefficients for performance tested Holstein cows in Korea. A total of 400,029 Holstein cows data which born between 2002 and 2012 were obtained from Dairy Cattle Improvement Center of National Agricultural Cooperative Federation(NACF). Their related pedigrees, as obtained from Korean Animal Improvement Association(KAIA), consisted of 509,740 animals. Pedigree depth of the cows were traced back to 3 generations earlier. The percentage of cows with fully identified ancestors in various provinces of Korea were 55.18%(Gyeonggi-do), 23.49%(Gangwon-do), 47.83%(Chungcheongnam-do), 53.62%(Chungcheongbuk-do), 56.38%(Gyeongsangbuk-do), 51.35% (Gyeongsangnam-do), 26.58%(Jeollanam-do), 49.41%(Jeollabuk-do), and 56.90%(Jeju-do), whereas, it was about 63.20% as a whole in Korea. The average inbreeding coefficients showed increment across the consecutive years of birth such as, 0.43(2002), 0.44(2003), 0.58(2004), 0.64(2005), 0.78(2006), 0.93(2007), 1.08(2008), 1.23(2009), 1.46(2010), 1.77(2011), and 2.03 (2012). However, this coefficient was 0.93 in overall Korean population. An average generation interval for sire to daughter genetic path was 8.15 years; which was about 4.20 years considering dam to daughter genetic path. The estimated effective population sizes (Ne) were 56.5, 51.3, and 32.2 animals born in 2004, 2009, and 2012, respectively. These results indicated that an increased rate of inbreeding has led to a significant reduction in the Ne over the decade.