• 한국지능시스템학회:학술대회논문집
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• 한국퍼지및지능시스템학회 1998년도 The Third Asian Fuzzy Systems Symposium
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• pp.489-494
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• 1998

This paper describes a design of graphical user interface for a simulated breeding tool with multifield. The term field is used here as a population of visualized individuals that are candidates of selection. Multi-field interface enables the user to breed his/her favorite phenotypes by selection independently in each field, and he/she can copy arbitrary individual into another field. As known on genetic algorithms, a small population likely leads to premature convergence trapped by a local optimum, and migration among plural populations is useful to escape from local optimum. The multi-field user interface provides easy implementation of migration and wider diversity. We show the usefulness of multi-field user interface through an example of a breeding system of 2D CG images.

• Asian-Australasian Journal of Animal Sciences
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• 제24권11호
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• pp.1483-1503
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• 2011

To advance the effectiveness of the current Hanwoo improvement system, we developed a general simulation that compared a series of breeding schemes under realistic user circumstances. We call this system the Integrated General Model (IGM) and it allows users to control the breeding schemes and selection methods by manipulating the input parameters. The Current Hanwoo Performance and Progeny Test (CHPPT) scheme was simulated with a Modified Hanwoo Performance and Progeny Test (MHPPT) scheme using a Hanwoo Breeding Farm cow population of the Livestock Improvement Main Center (LOMC) of the National Agricultural Cooperatives Federation (NACF). To compare the two schemes, a new method, the Simple Hanwoo Performance Test (SHPT), which uses ultrasound technology for measuring the carcass traits of live animals, was developed. These three models, including the CHPPT, incorporated three types of selection criteria: phenotype (PH), true breeding value (TBV), and estimated breeding value (EBV). The simulation was scheduled to mimic an actual Hanwoo breeding program; thus, the simulation was run to include the years 1983-2020 for each breeding method and was replicated 10 times. The parameters for simulation were derived from the literature. Approximately 642,000 animals were simulated per replication for the CHPPT scheme; 129,000 animals were simulated for the MHPPT scheme and 112,000 animals for the SHPT scheme. Throughout the 38-year simulation, all estimated parameters of each simulated population, regardless of population size, showed results similar to the input parameters. The deviations between input and output values for the parameters in the large populations were statistically acceptable. In this study, we integrated three simulated models, including the CHPPT, in an attempt to achieve the greatest genetic gains within major economic traits including body weight at 12 months of age (BW12), body weight at 24 months of age (BW24), average daily gain from 6 to 12 months (ADG), carcass weight (CWT), carcass longissimus muscle area (CLMA), carcass marbling score (CMS), ultrasound scanned longissimus muscle area (ULMA), and ultrasound scanned marbling score (UMS).

• Asian-Australasian Journal of Animal Sciences
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• 제24권2호
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• pp.162-172
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• 2011

In this paper, simulation was used to determine accuracies of genomic breeding values for polygenic traits associated with many thousands of markers obtained from high density genome scans. The statistical approach was based upon stochastically simulating a pedigree with a specified base population and a specified set of population parameters including the effective and noneffective marker distances and generation time. For this population, marker and quantitative trait locus (QTL) genotypes were generated using either a single linkage group or multiple linkage group model. Single nucleotide polymorphism (SNP) was simulated for an entire bovine genome (except for the sex chromosome, n = 29) including linkage and recombination. Individuals drawn from the simulated population with specified marker and QTL genotypes were randomly mated to establish appropriate levels of linkage disequilibrium for ten generations. Phenotype and genomic SNP data sets were obtained from individuals starting after two generations. Genetic prediction was accomplished by statistically modeling the genomic relationship matrix and standard BLUP methods. The effect of the number of linkage groups was also investigated to determine its influence on the accuracy of breeding values for genomic selection. When using high density scan data (0.08 cM marker distance), accuracies of breeding values on juveniles were obtained of 0.60 and 0.82, for a low heritable trait (0.10) and high heritable trait (0.50), respectively, in the single linkage group model. Estimates of 0.38 and 0.60 were obtained for the same cases in the multiple linkage group models. Unexpectedly, use of BLUP regression methods across many chromosomes was found to give rise to reduced accuracy in breeding value determination. The reasons for this remain a target for further research, but the role of Mendelian sampling may play a fundamental role in producing this effect.

• Journal of Animal Science and Technology
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• 제44권5호
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• pp.507-518
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• 2002

가축 육종 체계 또는 선발방법의 상호 비교를 할 수 있도록 다형질 컴퓨터 모의실험을 위한 확률모형을 개발하고, 기존 연구결과로부터 얻어진 평균과 상가적 유전효과 및 잔여오차의 분산 및 공분산 값을 실험 모수로 사용하여 모의실험 축군을 생성하였고, 선발방법은 임의교배, 표현형가, 참육종가 및 추정육종가에 의한 선발 중에서 선택할 수 있도록 하였다. 개체의 육종가는 MTDFREML package를 사용하여 추정하였다. 모의실험 프로그램의 정확성을 검증하기 위하여 크기가 다른 세 축군을 20년간 임의교배하여 모의실험한 결과, 평균값과 분산 및 공분산 값은 모의실험 모수로 주어진 값과 비슷하였고, 축군의 크기가 클수록 모의실험 모수로 주어진 값에 더욱 근접하였으며 표준오차가 작아졌다. 임의교배를 계속함에 따른 근교계수와 축군 평균 및 분산의 변화를 확인하기 위하여 종모우 1두, 종빈우 10두를 유지하는 소축군 10개를 500년간 모의실험 한 결과, 근교계수의 변화는 이론적 추정함수와 비슷하였으며, 평균값은 작은 축군에서 세대에 따라 임의부동현상을 보였지만 근교계수가 증가하여 1에 가까워지면 일정한 값으로 수렴하였다. 축군내 분산은 근교계수의 증가에 따라 감소하였다. 이상의 결과를 보면, 모의실험 모형에 의해 생성된 축군의 자료는 모의실험 모수와 같은 통계적 특성을 유지하는 것으로 사료된다.

• Asian-Australasian Journal of Animal Sciences
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• 제25권6호
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• pp.772-784
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• 2012

Marker-assisted gene pyramiding aims to produce individuals with superior economic traits according to the optimal breeding scheme which involves selecting a series of favorite target alleles after cross of base populations and pyramiding them into a single genotype. Inspired by the science of evolutionary computation, we used the metaphor of hill-climbing to model the dynamic behavior of gene pyramiding. In consideration of the traditional cross program of animals along with the features of animal segregating populations, four types of cross programs and two types of selection strategies for gene pyramiding are performed from a practical perspective. Two population cross for pyramiding two genes (denoted II), three population cascading cross for pyramiding three genes(denoted III), four population symmetry (denoted IIII-S) and cascading cross for pyramiding four genes (denoted IIII-C), and various schemes (denoted cross program-A-E) are designed for each cross program given different levels of initial favorite allele frequencies, base population sizes and trait heritabilities. The process of gene pyramiding breeding for various schemes are simulated and compared based on the population hamming distance, average superior genotype frequencies and average phenotypic values. By simulation, the results show that the larger base population size and the higher the initial favorite allele frequency the higher the efficiency of gene pyramiding. Parents cross order is shown to be the most important factor in a cascading cross, but has no significant influence on the symmetric cross. The results also show that genotypic selection strategy is superior to phenotypic selection in accelerating gene pyramiding. Moreover, the method and corresponding software was used to compare different cross schemes and selection strategies.

• Journal of Animal Science and Technology
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• 제53권1호
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• pp.1-6
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• 2011

연구는 유전체분석에 대해 모의실험한 연구로써 Reference Population (RP)이 구성되었을 때, 표현형 자료가 없고 유전체자료만 있는 Juven 1 또는 Juven 2 세대에 대해 유전평가의 정확도에 대해 알아보고자 연구를 실시하였다. 모의실험의 가정으로 염색체는 1개이며 염색체길이는 100cM로 가정하였다. 초기의 유효집단의 수는 100두의 다형성이 없는 초기집단에서 유전자 효과가 없는 표지인자(Marker)를 0.1cM 및 0.5cM 간격으로 균등하게 단일 염기 돌연변이에 의한 다형성을 발생시켰고 유전자 효과가 있는 QTL 좌위는 Marker와 동수의 비율로 임의위치를 지정하여 돌연변이에 의한 변이성을 생성하였으며 이때 유전자 효과는 Gamma 분포함수(scale=1.66, shape=0.4)에서 생성하였다. 배우자(gamete) 형성과정에서 Haldane의 가정하에 유전자 재조합을 생성하였으며 돌연변이 발생율은 Marker 및 QTL 좌위에서 $2.5{\times}10^{-3}$ 및 $2.5{\times}10^{-5}$의 확률로 발생시켜 1000세대까지 세대번식을 유지하였다. 이 후 1001세대부터 1004세대까지 세대당 2000두의 자손을 생성하였으며 이 때 유전력을 0.1 및 0.5의 가정하에 1001~1002 세대에서 표현형 자료를 생성하였고, 1003~1004세대는 오직 유전체자료만 생성하였다. Bayesian 방법을 이용하여 개체별 육종가를 추정하였으며 표지인자간 거리(0.1cM, 0.5cM), 유전력(0.1, 0.5) 및 반형매 집단크기(20두, 4두)에 따라 참육종가와 추정 육종가간의 상관으로 표현되는 육종가 정확도에 대해 비교한 결과 1003세 대에서 표지인자간 거리가 0.1cM 및 0.5cM일 때 육종가의 정확도는 각각 0.87, 0.81였고, 유전력이 0.1 및 0.5 일 때 각각 0.87, 0.94로 추정되었으며, 반형매 집단의 크기가 20두 일 때 0.87, 4두 일 때 0.84로 추정되었다. 위의 결과로 미루어 보아 다량의 SNP 표지정보 및 반형매 집단의 크기가 클수록 즉, 혈연계수가 높은 집단일 때 육종가의 정확도는 높게 나타났다. 유전체선발의 활용시 비교적 높은 정확도로써 조기선발이 가능하며 이로 인한 세대간격을 단축시킬 수 있어 개량의 효율을 높일 수 있을 것으로 사료된다. 반면에 유전체선발은 분석비용이 비싸며, 지속적인 유전체 선발시 특정유전자 선호로 인한 유전적 부동(Genetic Drift) 현상이 발생될 수 있기 때문에 지속적인 SNP 발굴에 대한 노력이 필요한(Meuwissen 2003) 단점이 있으나 한우 또는 젖소와 같은 대가축과 같이 세대간격이 긴 가축에서 유전체선발 할 경우 조기선발로 인한 세대간격 단축과 유전평가의 높은 정확도(0.8이상)로 인해 개량의 효율을 극대화 할 수 있을 것으로 사료된다.

• Asian-Australasian Journal of Animal Sciences
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• 제14권5호
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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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• 제25권3호
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• pp.299-303
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• 2012

Inbreeding is the mating of relatives that produce progeny having more homozygous alleles than non-inbred animals. Inbreeding increases numbers of recessive alleles, which is often associated with decreased performance known as inbreeding depression. The magnitude of inbreeding depression depends on the level of inbreeding in the animal. Level of inbreeding is expressed by the inbreeding coefficient. One breeding goal in livestock is uniform productivity while maintaining acceptable inbreeding levels, especially keeping inbreeding less than 20%. However, in closed herds without the introduction of new genetic sources high levels of inbreeding over time are unavoidable. One method that increases selection response and minimizes inbreeding is selection of individuals by weighting estimated breeding values with average relationships among individuals. Optimum genetic contribution theory (OGC) uses relationships among individuals as weighting factors. The algorithm is as follows: i) Identify the individual having the best EBV; ii) Calculate average relationships ($\bar{r_j}$) between selected and candidates; iii) Select the individual having the best EBV adjusted for average relationships using the weighting factor k, $EBV^*=EBV_j(1-k\bar{{r}_j})$ Repeat process until the number of individuals selected equals number required. The objective of this study was to compare simulated results based on OGC selection under different conditions over 30 generations. Individuals (n = 110) were generated for the base population with pseudo random numbers of N~ (0, 3), ten were assumed male, and the remainder female. Each male was mated to ten females, and every female was assumed to have 5 progeny resulting in 500 individuals in the following generation. Results showed the OGC algorithm effectively controlled inbreeding and maintained consistent increases in selection response. Difference in breeding values between selection with OGC algorithm and by EBV only was 8%, however, rate of inbreeding was controlled by 47% after 20 generation. These results indicate that the OGC algorithm can be used effectively in long-term selection programs.

• Journal of Animal Science and Technology
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• 제64권1호
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• pp.183-186
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• 2022

Lactiplantibacillus plantarum (L. plantarum) ST was isolated from De'ang pickled tea in Yunnan Province, China. The genomes of strain ST were fully sequenced and analyzed using the PacBio RS II sequencing system. Our previous study has shown that L. plantarum ST is a potential probiotic strain. It had strong tolerance in the simulated artificial gastrointestinal tract, and in the antagonism tests, this strain showed strong antibacterial activity. Therefore, as a probiotic, it may be used in animal breeding. L. plantarum ST genome was composed of 1 circular chromosome and 7 plasmids. The length of the whole genome was 3320817 bp, and the annular chromosome size was 3058984 bp, guanine + cytosine (G ± C) content (%) was 44.76%, which contained 2945 protein-coding sequences (CDS). This study will contribute to a further comprehensive understanding of L. Plantarum ST at the genomic level and provide a theoretical basis for its future application in animal breeding.

• Journal of Animal Science and Technology
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• 제46권2호
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• pp.137-144
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• 2004

불연속 범주형 자료에 대한 잠재변수가 존재한다는 가정하에 임계값을 추정하고 잠재변수를 생성하며 생성된 잠재변수 및 기타 연속변량에 대한 관측치를 포함하는 다변량 임계개체모형을 설정하고 유전능력을 예측하기 위한 방법을 제시하였다. 각각의 범주형 조사 자료의 특성을 갖는 형질에 있어서 임계점의 추정은 추정 가능한 임계점에 대한 1차 미분값(gradient)과 2차 미분값(Hessian)을 이용한 Newton 방법을 이용하면 추정가능하며 지역모수인 육종가의 추정은 PCG 방법으로 구현 가능하다. 이러한 이론은 Quaas(2001)가 제시한 하나의 이산형 자료와 하나의 연속형 자료의 2변량 동시 분석방법을 확장하여 전개한 것이며 이때 잠재변수 및 임계점의 추정은 기타 형질의 잔차 회귀계수 및 상관을 고려해야 한다. 본 연구를 위한 모의실험은 2개의 연속변량으로 체중과 유량을 고려하였고 또 다른 2개의 불연속 변량인 분만난이도와 출생시 생존유무를 고려하여 4형질 동시 분석을 실시하였다. 임계모형에 의한 육종가 추정치의 정확도는 4개의 구간으로 분류되어 기록된 분만난이도의 경우에 91${\sim}$92%의 정확도를 보였고 이항분포인 분만시 생존유무에 대하여는 87~89%의 정확도를 보였다. 반면에 이들 범주형 자료를 선형으로 간주하고 분석한 선형 동물개체 혼합모형에서는 72${\sim}$84% 및 59${\sim}$70%으로 비교적 낮은 추정의 정확도를 보였다. 따라서 범주형 자료의 유전분석은 선형 혼합모형 보다 임계형 혼합모형이 크게 타당할 것으로 사료되었다.