• Genomics & Informatics
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• v.6 no.1
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• pp.14-17
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• 2008

GENDISCAN study (Gene Discovery for Complex traits in Asian population of Northeast area) was designed to incorporate methodologies which enhance the power to identify genetic variations underlying complex disorders. Use of population isolates as the target population is a unique feather of this study. However, population isolates may have hidden inbreeding structures which can affect the validity of the study. To understand how this issue may affect results of GENDISCAN, we estimated inbreeding coefficients in two study populations in Mongolia. We analyzed the status of Hardy-Weinberg Equilibrium (HWE), polymorphism information contents (PIC), heterozygosity, allelic diversity, and inbreeding coefficients, using 317 and 1,044 STR (short tandem repeat) markers in Orkhontuul and Dashbalbar populations. HWE assumptions were generally met in most markers (88.6% and 94.2% respectively), and single marker PIC ranged between 0.2 and 0.9. Inbreeding coefficients were estimated to be 0.0023 and 0.0021, which are small enough to assure that conventional genetic analysis would work without any specific modification. We concluded that the population isolates used in GENDISCAN study would not present significant inflation of type I errors from inbreeding effects in its gene discovery analysis.

• Journal of the Korea Academia-Industrial cooperation Society
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• v.20 no.6
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• pp.514-520
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• 2019

The reduction in performance due to inbreeding (i.e. inbreeding depression) has long been documented in plant and animal populations. The population of Korean native pigs are small and this breed is valuable in Korea.. This study was aimed to investigate effects of inbreeding depression on total number of piglets born (TNB) and number of piglets born alive (NBA) in Korean native pigs. We used 2,806 pedigree and 303 sows's data with 483 phenotypic records. After estimating genetic parameters for each traits, inbreeding depression was estimated using a mixed model in which the inbreeding coefficient was included as a covariate. Korean native pigs had high heritability for each traits. Inbreeding coefficient constantly increased from 1998 to 2017~2018 but there is no reduction for each traits in 2017~2018 in compared with those in 1998. Significant inbreeding depression was detected for TNB (p=0.03) but not for NBA (p=0.41). In addition there are significantly positive interactions between inbreeding coefficient and breeding value for both traits (p<0.05). These results suggest that Korean native pigs are still having genetic variation for TNB and NBA, which could overcome reproductive risks from inbreeding coefficient increase.

• The Korean Journal of Malacology
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• v.30 no.4
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• pp.415-419
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• 2014

Inbreeding depression may be an avoidable phenomenon for abalone culture. However, only a few studies were carried out on inbreeding depression. In the present study, to demonstrate inbreeding depression in growth trait of Pacific abalone, H. discus hannai, inbreeding and outbreeding families were produced in 2010. Inbred and outbred families from each experiment were reared in same tank until 10 month for the same breed environment. The individual of inbred and outbred were distinguished by paternity test using microsatellite DNA. The shell length between inbred and outbred families was compared. At the results, significantly higher shell length was observed in the outbred families at 10 mon (P < 0.05). These results indicate that inbreeding depression is obviously observed in growth traits in the first generation of full-sib family of the H. discus hannai.

• Asian-Australasian Journal of Animal Sciences
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• v.28 no.9
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• pp.1244-1251
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• 2015

A herd of Berkshire pigs was established in 2003 and subjected to selection without introduction of any genetic resources until 2007. The complete pedigree, including 410 boars and 916 sows, as well as the records from 5,845 pigs and 822 litters were used to investigate the results obtained from the selections. The index of selection for breeding values included days to 90 kg (D90kg), backfat thickness (BF) and number of piglets born alive (NBA). The average inbreeding coefficients of pigs were found to be 0.023, 0.008, 0.013, 0.025, 0.026, and 0.005 from 2003 to 2007, respectively. The genetic gains per year were 12.1 g, -0.04 mm, -3.13 days, and 0.181 head for average daily gain (ADG), BF, D90kg, and NBA, respectively. Breeding values of ADG, BF and D90kg were not significantly correlated with inbreeding coefficients of individuals, except for NBA (-0.21). The response per additional 1% of inbreeding was 0.0278 head reduction in NBA. The annual increase of inbreeding was 0.23% and the annual decrease in NBA due to inbreeding was 0.0064 head. This magnitude could be disregarded when compared with the annual gain in NBA (0.181 head). These results suggest that inbreeding and inbreeding depression on ordinary farms can be controlled with a proper breeding scheme and that breeding programs are economical and safe relative to the risks associated with importation of pigs.

• Animal Bioscience
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• v.35 no.6
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• pp.804-813
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• 2022

Objective: A formula is needed that is practical for current livestock breeding methods and that predicts the approximate rate of inbreeding (ΔF) in populations where selection is performed according to four-path programs (sires to breed sons, sires to breed daughters, dams to breed sons, and dams to breed daughters). The formula widely used to predict inbreeding neglects selection, we need to develop a new formula that can be applied with or without selection. Methods: The core of the prediction is to incorporate the long-tern genetic influence of the selected parents in four-selection paths executed as sires to breed sons, sires to breed daughters, dams to breed sons, and dams to breed daughters. The rate of inbreeding was computed as the magnitude that is proportional to the sum of squared long-term genetic contributions of the parents of four-selection paths to the selected offspring. Results: We developed a formula to predict the rate of inbreeding in populations undergoing four-path selection on genomically enhanced breeding values and with discrete generations. The new formula can be applied with or without selection. Neglecting the effects of selection led to underestimation of the rate of inbreeding by 40% to 45%. Conclusion: The formula we developed here would be highly useful as a practical method for predicting the approximate rate of inbreeding (ΔF) in populations where selection is performed according to four-path programs.

• Asian-Australasian Journal of Animal Sciences
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• v.10 no.5
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• pp.510-513
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• 1997

This study examined the effects of ignoring inbreeding depression on (co)variance components for weaning weight through the use of Monte Carlo simulation. Weaning weight is of particular interest as a trait for which additive direct and maternal genetic components exist and there then is the potential for a direct-maternal genetic covariance. Ignoring inbreeding depression in the analytical model (.8 kg reduction of phenotypic value per 1% inbreeding) led to biased estimates of all genetic (co) variance components, all estimates being larger than the true values of the parameters. In particular, a negative bias in the direct-maternal genetic covariance was observed in analyses that ignored inbreeding depression. A small spurious sire-by-year interaction variance was also observed.

• Asian-Australasian Journal of Animal Sciences
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• v.14 no.5
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• pp.597-602
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• 2001

This study was conducted to examine the relationships between the methods used to determine the number of transferable embryos collected per flush and the estimated cumulative genetic improvements in the Japanese Holstein MOET breeding population. Cumulative genetic improvements were predicted by Monte Carlo simulation using three different determination methods (MODEL 1, MODEL 2, and MODEL 3), for calculating the number of embryos collected per flush. Moreover EBVs were estimated including or ignoring coefficients of inbreeding in MME. Inbreeding coefficients were also predicted. The number of transferable embryos was determined using normal, gamma, and Poisson distributions in MODEL 1, gamma and Poisson distributions in MODEL 2, and only the Poisson distribution in MODEL 3. The fitness of MODEL 2 in relation to field data from Hokkaido Japan was the best, and the results for MODEL3 indicated that this model is unsuitable for determining the number of transferable embryos. The largest cumulative genetic improvement (3.11) in the 10th generation was predicted by MODEL 3 and the smallest (2.83) by MODEL 2. Mean coefficients of correlation between the true and estimated breeding values were 0.738, 0.729, and 0.773 in MODELS 1, 2, and 3, respectively. It is suggested that the smallest genetic improvement in MODEL 2 resulted from the smallest correlation coefficient between the true and estimated breeding values. The differences in milk, fat, and protein yields between MODELS 2 and 3 were 182.0, 7.0, and 5.6 kg, respectively, in real units when each trait was independently selected. The inbreeding coefficient was the highest (0.374) in MODEL 2 and the lowest (0.357) in MODEL 3. The effects of different methods for determining the number of transferable embryos per flush on genetic improvements and inbreeding coefficients of the simulated populations were remarkable. The effects of including coefficients of inbreeding in MME, however, were unclear.

• Asian-Australasian Journal of Animal Sciences
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• v.33 no.9
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• pp.1369-1377
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• 2020

Objective: The main objectives of the present study were to assess the genetic diversity, population structure and to appraise the efficiency of ongoing selective breeding program in the closed nucleus herd of Nellore sheep through pedigree analysis. Methods: Information utilized in the study was collected from the pedigree records of Livestock Research Station, Palamaner during the period from 1989 to 2016. Genealogical parameters like generation interval, pedigree completeness, inbreeding level, average relatedness among the animals and genetic conservation index were estimated based on gene origin probabilities. Lambs born during 2012 and 2016 were considered as reference population. Two animal models either with the use of F_i or ΔF_i as linear co-variables were evaluated to know the effects of inbreeding on the growth traits of Nellore sheep. Results: Average generation interval and realized effective population size for the reference cohort were estimated as 3.38±0.10 and 91.56±1.58, respectively and the average inbreeding coefficient for reference population was 3.32%. Similarly, the effective number of founders, ancestors and founder genome equivalent of the reference population were observed as 47, 37, and 22.48, respectively. Fifty per cent of the genetic variability was explained by 14 influential ancestors in the reference cohort. The ratio f_e/f_a obtained in the study was 1.21, which is an indicator of bottlenecks in the population. The number of equivalent generations obtained in the study was 4.23 and this estimate suggested the fair depth of the pedigree. Conclusion: Study suggested that the population had decent levels of genetic diversity and a non-significant influence of inbreeding coefficient on growth traits of Nellore lambs. However, small portion of genetic diversity was lost due to a disproportionate contribution of founders and bottlenecks. Hence, breeding strategies which improve the genetic gain, widens the selection process and with optimum levels of inbreeding are recommended for the herd.

• Asian-Australasian Journal of Animal Sciences
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• v.21 no.11
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• pp.1559-1571
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• 2008

A rule was developed to constrain the annual rate of inbreeding to a predefined value in a population with different lifetimes between sires and dams, and to maximize the selection response over generations. This rule considers that the animals in a population should be divided into sex-age classes based on the theory of gene flow, and restricts the increase of average inbreeding coefficient for new offspring by limiting the increase of the mean additive genetic relationship for parents selected. The optimization problem of this rule was formulated as a quadratic programming problem. Inputs for the rule were the BLUP estimated breeding values, the additive genetic relationship matrix of all animals, and the long-term contributions of sex-age classes. Outputs were optimal number and contributions of selected animals. In addition, this rule was combined with the optimization of emphasis given to QTL, and further increased the genetic gain over the planning horizon. Stochastic simulations of closed nucleus schemes for pigs were used to investigate the potential advantages obtained from this rule by combining the standard QTL selection, optimal QTL selection and conventional BLUP selection. Results showed that the predefined rates of inbreeding were actually achieved by this rule in three selection strategies. The rule obtained up to 9.23% extra genetic gain over truncation selection at the same rates of inbreeding. The combination of the extended rule and the optimization of emphasis given to QTL allowed substantial increases in selection response at a fixed annual rate of inbreeding, and solved substantially the conflict between short-term and long-term selection response in QTL-assisted selection schemes.

• Korean Journal of Agricultural Science
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• v.41 no.1
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• pp.41-46
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• 2014

The pedigree data of 86,639 heads from six major swine breeding farms were investigated to check levels of inbreeding and effective population size of breeding stocks. The average rate of inbreeding was 1.04%, 0.87%, 3.17%, 1.05%, 3.23% and 3.33% for farms A, B, C, D, E and F, respectively. The average inbreeding rate was highest for F farm and lowest for B farm. In farms D and E, there were quite large numbers of immigrant animals per generation compared to other farms. The effective population sizes calculated from the average rate of inbreeding were distributed between 83.0 and 814.8. Specific values were 282.3, 225.5, 83.0, 814.8, 302.9 and 175.7 for farms A, B, C, D, E and F, respectively. The results showed that there was no cause for concern over the current inbreeding level of major swine breeding farm populations and the inbreeding level was within an acceptable range. In addition, internal sharing rather than importing pig is necessary to strengthen seed sovereignty.