• Title, Summary, Keyword: Effective Population Size

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Linkage Disequilibrium and Effective Population Size in Hanwoo Korean Cattle

  • Lee, S.H.;Cho, Y.M.;Lim, D.;Kim, H.C.;Choi, B.H.;Park, H.S.;Kim, O.H.;Kim, S.;Kim, T.H.;Yoon, D.;Hong, S.K.
    • Asian-Australasian Journal of Animal Sciences
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    • v.24 no.12
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    • pp.1660-1665
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    • 2011
  • This study presents a linkage disequilibrium (LD) analysis and effective population size ($N_e$) for the entire Hanwoo Korean cattle genome, which is the first LD map and effective population size estimate ever calculated for this breed. A panel of 4,525 markers was used in the final LD analysis. The pairwise $r^2$ statistic of SNPs up to 50 Mb apart across the genome was estimated. A mean value of $r^2$ = 0.23 was observed in pairwise distances of <25 kb and dropped to 0.1 at 40 to 60 kb, which is similar to the average intermarker distance used in this study. The proportion of SNPs in useful LD ($r^2{\geq}0.25$) was 20% for the distance of 10 and 20 kb between SNPs. Analyses of past effective population size estimates based on direct estimates of recombination rates from SNP data demonstrated that a decline in effective population size to $N_e$ = 98.1 occurred up to three generations ago.

Estimation of effective population size using single-nucleotide polymorphism (SNP) data in Jeju horse

  • Do, Kyoung-Tag;Lee, Joon-Ho;Lee, Hak-Kyo;Kim, Jun;Park, Kyung-Do
    • Journal of Animal Science and Technology
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    • v.56 no.8
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    • pp.28.1-28.6
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    • 2014
  • This study was conducted to estimate the effective population size using SNPs data of 240 Jeju horses that had raced at the Jeju racing park. Of the total 61,746 genotyped autosomal SNPs, 17,320 (28.1%) SNPs (missing genotype rate of >10%, minor allele frequency of <0.05 and Hardy-Weinberg equilibrium test P-value of < $10^{-6}$) were excluded after quality control processes. SNPs on the X and Y chromosomes and genotyped individuals with missing genotype rate over 10% were also excluded, and finally, 44,426 (71.9%) SNPs were selected and used for the analysis. The measures of the LD, square of correlation coefficient ($r^2$) between SNP pairs, were calculated for each allele and the effective population size was determined based on $r^2$ measures. The polymorphism information contents (PIC) and expected heterozygosity (HE) were 0.27 and 0.34, respectively. In LD, the most rapid decline was observed over the first 1 Mb. But $r^2$ decreased more slowly with increasing distance and was constant after 2 Mb of distance and the decline was almost linear with log-transformed distance. The average $r^2$ between adjacent SNP pairs ranged from 0.20 to 0.31 in each chromosome and whole average was 0.26, while the whole average $r^2$ between all SNP pairs was 0.02. We observed an initial pattern of decreasing $N_e$ and estimated values were closer to 41 at 1 ~ 5 generations ago. The effective population size (41 heads) estimated in this study seems to be large considering Jeju horse's population size (about 2,000 heads), but it should be interpreted with caution because of the technical limitations of the methods and sample size.

Preventing Premature Convergence in Genetic Algorithms with Adaptive Population Size (유전자 집단의 크기 조절을 통한 Genetic Algorithm의 조기 포화 방지)

  • 박래정;박철훈
    • Journal of the Korean Institute of Telematics and Electronics B
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    • v.32B no.12
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    • pp.1680-1686
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    • 1995
  • GAs, effective stochastic search algorithms based on the model of natural evolution and genetics, have been successfully applied to various optimization problems. When population size is not large, GAs often suffer from the phenomenon of premature convergence in which all chromosomes in the population lose the diversity of genes before they find the optimal solution. In this paper, we propose that a new heuristic that maintains the diversity of genes by adding some chromosomes with random mutation and selective mutation into population during evolution. And population size changes dynamically with supplement of new chromosomes. Experimental results for several test functions show that when population size is rather small and the length of chromosome is not long, this method is effective.

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Demographic Trends in Korean Native Cattle Explained Using Bovine SNP50 Beadchip

  • Sharma, Aditi;Lim, Dajeong;Chai, Han-Ha;Choi, Bong-Hwan;Cho, Yongmin
    • 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.

Estimation of Linkage Disequilibrium and Effective Population Size using Whole Genome Single Nucleotide Polymorphisms in Hanwoo (한우에서 전장의 유전체 정보를 활용한 연관불평형 및 유효집단크기 추정에 관한 연구)

  • Cho, Chung-Il;Lee, Joon-Ho;Lee, Deuk-Hwan
    • Journal of Life Science
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    • v.22 no.3
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    • pp.366-372
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    • 2012
  • This study was conducted to estimate the extent of linkage disequilibrium (LD) and effective population size using whole genomic single nucleotide polymorphisms (SNP) genotyped by DNA chip in Hanwoo. Using the blood samples of 35 young bulls born from 2005 to 2008 and their progenies (N=253) in a Hanwoo nucleus population collected from Hanwoo Improvement Center, 51,582 SNPs were genotyped using Bovine SNP50 chips. A total of 40,851 SNPs were used in this study after elimination of SNPs with a missing genotyping rate of over 10 percent and monomorphic SNPs (10,730 SNPs). The total autosomal genome length, measured as the sum of the longest syntenic pairs of SNPs by chromosome, was 2,541.6 Mb (Mega base pairs). The average distances of all adjacent pairs by each BTA ranged from 0.55 to 0.74 cM. Decay of LD showed an exponential trend with physical distance. The means of LD ($r^2$) among syntenic SNP pairs were 0.136 at a range of 0-0.1 Mb in physical distance and 0.06 at a range of 0.1-0.2 Mb. When these results were used for Luo's formula, about 2,000 phenotypic records were found to be required to achieve power > 0.9 to detect 5% QTL in the population of Hanwoo. As a result of estimating effective population size by generation in Hanwoo, the estimated effective population size for the current status was 84 heads and the estimate of effective population size for 50 generations of ancestors was 1,150 heads. The average decreasing rates of effective population size by generation were 9.0% at about five generations and 17.3% at the current generation. The main cause of the rapid decrease in effective population size was considered to be the intensive use of a few prominent sires since the application of artificial insemination technology in Korea. To increase and/or sustain the effective population size, the selection of various proven bulls and mating systems that consider genetic diversity are needed.

Effective Population Size of Korean Populations

  • Park, Leeyoung
    • Genomics & Informatics
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    • v.12 no.4
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    • pp.208-215
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    • 2014
  • Recently, new methods have been developed for estimating the current and recent changes in effective population sizes. Based on the methods, the effective population sizes of Korean populations were estimated using data from the Korean Association Resource (KARE) project. The overall changes in the population sizes of the total populations were similar to CHB (Han Chinese in Beijing, China) and JPT (Japanese in Tokyo, Japan) of the HapMap project. There were no differences in past changes in population sizes with a comparison between an urban area and a rural area. Age-dependent current and recent effective population sizes represent the modern history of Korean populations, including the effects of World War II, the Korean War, and urbanization. The oldest age group showed that the population growth of Koreans had already been substantial at least since the end of the 19th century.

Extent of linkage disequilibrium and effective population size of the Landrace population in Korea

  • Shin, Donghyun;Kim, Sung-Hoon;Park, Joowan;Lee, Hak-Kyo;Song, Ki-Duk
    • 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.

Extent of linkage disequilibrium and effective population size of Korean Yorkshire swine

  • Shin, Donghyun;Won, Kyeong-Hye;Kim, Sung-Hoon;Kim, Yong-Min
    • Asian-Australasian Journal of Animal Sciences
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    • v.31 no.12
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    • pp.1843-1851
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    • 2018
  • Objective: We aimed to characterize linkage disequilibrium (LD) and effective population size ($N_e$) in a Korean Yorkshire population using genomic data from thousands of individuals. Methods: We genotyped 2,470 Yorkshire individuals from four major Grand-Grand-Parent farms in Korea using the Illumina PorcineSNP60 version2 BeadChip, which covers >61,565 single nucleotide polymorphisms (SNPs) located across all chromosomes and mitochondria. We estimated the expected LD and inferred current $N_e$ as well as ancestral $N_e$. Results: We identified 61,565 SNP from autosomes, mitochondria, and sex chromosomes and characterized the LD of the Yorkshire population, which was relatively high between closely linked markers (>0.55 at 50 kb) and declined with increasing genetic distance. The current $N_e$ of this Korean Yorkshire population was 122.87 (106.90; 138.84), while the historical $N_e$ of Yorkshire pigs suggests that the ancestor $N_e$ has decreased by 99.6% over the last 10,000 generations. Conclusion: To maintain genetic diversity of a domesticated animal population, we must carefully consider appropriate breed management methods to avoid inbreeding. Although attenuated selection can affect short-term genetic gain, it is essential for maintaining the long-term genetic variability of the Korean Yorkshire population. Continuous and long-term monitoring would also be needed to maintain the pig population to avoid an unintended reduction of $N_e$. The best way to preserve a sustainable population is to maintain a sufficient $N_e$.

Design of Adaptive Population-size on Bias in Genetic Algorithms (유전자 알고리즘에서 bias에 의한 adaptive한 개체군 크기의 설정)

  • 김용범;오충환
    • Journal of the Society of Korea Industrial and Systems Engineering
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    • v.18 no.36
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    • pp.133-141
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    • 1995
  • One of the problems brought up in the effective execution of genetic algorithms is that if they come under any influences according as the population size is large or small. In the case of small population size the opportunities of premature convergence are increased when the greatly powerful or no good individual is generated during search of the solution space. And searching the solution space in the case of large population size, the difficulties under the execution cause to searching all for one by one individual in every generation applied is limited, this gives the many interruptions to the convergence of final solution. Now this paper gives a suggestion to set up the adaptive population size which could compute the more correct solution and simplify the development of computation performance.

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Estimation of Inbreeding Coefficients and Effective Population Size in Breeding Bulls of Hanwoo (Korean Cattle) (한우 씨수소의 근교계수와 유효집단크기의 추정)

  • Dang, Chang-Gwon;Lee, Jung-Jae;Kim, Nae-Soo
    • Journal of Animal Science and Technology
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    • v.53 no.4
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    • pp.297-302
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    • 2011
  • This study was carried out to estimate average inbreeding coefficients, relatedness and effective population size of breeding bulls and to suggest optimal alternatives on problems of current Hanwoo improvement system. Data on proven and young bulls were obtained from 1,128 heads of Livestock Improvement Main Center from 1983 to 2008. Pedigree information on proven and young bulls was obtained from 3,760 heads of Korea Animal Improvement Association. Average inbreeding coefficients and average relatedness of proven and young bulls were estimated at the range of 0.04-0.07%, 0.10-6.82%, respectively. Effective population size was estimated for 220 heads from the average rate of inbreeding of last 26 years. Average inbreeding coefficient is rising rapidly for the last two years as well as average relatedness. Effective population size was estimated for 47 heads for the last five years. These results suggest that selection criteria of proven bulls should include not only genetic evaluation of carcass performance from progeny-test, but also inbreeding and relationship coefficients, in order to maintain genetic variability of Hanwoo. In addition, effective population size should be increased by increasing the number of proven bulls.