• Genomics & Informatics
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• 제12권4호
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• pp.254-260
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• 2014

Best linear unbiased prediction (BLUP) has been used to estimate the fixed effects and random effects of complex traits. Traditionally, genomic relationship matrix-based (GRM) and random marker-based BLUP analyses are prevalent to estimate the genetic values of complex traits. We used three methods: GRM-based prediction (G-BLUP), random marker-based prediction using an identity matrix (so-called single-nucleotide polymorphism [SNP]-BLUP), and SNP-SNP variance-covariance matrix (so-called SNP-GBLUP). We used 35,675 SNPs and R package "rrBLUP" for the BLUP analysis. The SNP-SNP relationship matrix was calculated using the GRM and Sherman-Morrison-Woodbury lemma. The SNP-GBLUP result was very similar to G-BLUP in the prediction of genetic values. However, there were many discrepancies between SNP-BLUP and the other two BLUPs. SNP-GBLUP has the merit to be able to predict genetic values through SNP effects.

• Animal Bioscience
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• 제36권7호
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• pp.1003-1009
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• 2023

Objective: The objective was to compare (pedigree-based) best linear unbiased prediction (BLUP), genomic BLUP (GBLUP), and single-step GBLUP (ssGBLUP) methods for genomic evaluation of growth traits in a Mexican Braunvieh cattle population. Methods: Birth (BW), weaning (WW), and yearling weight (YW) data of a Mexican Braunvieh cattle population were analyzed with BLUP, GBLUP, and ssGBLUP methods. These methods are differentiated by the additive genetic relationship matrix included in the model and the animals under evaluation. The predictive ability of the model was evaluated using random partitions of the data in training and testing sets, consistently predicting about 20% of genotyped animals on all occasions. For each partition, the Pearson correlation coefficient between adjusted phenotypes for fixed effects and non-genetic random effects and the estimated breeding values (EBV) were computed. Results: The random contemporary group (CG) effect explained about 50%, 45%, and 35% of the phenotypic variance in BW, WW, and YW, respectively. For the three methods, the CG effect explained the highest proportion of the phenotypic variances (except for YW-GBLUP). The heritability estimate obtained with GBLUP was the lowest for BW, while the highest heritability was obtained with BLUP. For WW, the highest heritability estimate was obtained with BLUP, the estimates obtained with GBLUP and ssGBLUP were similar. For YW, the heritability estimates obtained with GBLUP and BLUP were similar, and the lowest heritability was obtained with ssGBLUP. Pearson correlation coefficients between adjusted phenotypes for non-genetic effects and EBVs were the highest for BLUP, followed by ssBLUP and GBLUP. Conclusion: The successful implementation of genetic evaluations that include genotyped and non-genotyped animals in our study indicate a promising method for use in genetic improvement programs of Braunvieh cattle. Our findings showed that simultaneous evaluation of genotyped and non-genotyped animals improved prediction accuracy for growth traits even with a limited number of genotyped animals.

• Asian-Australasian Journal of Animal Sciences
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• 제28권11호
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• pp.1551-1557
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• 2015

The missing heritability has been a major problem in the analysis of best linear unbiased prediction (BLUP). We introduced the traditional genome-wide association study (GWAS) into the BLUP to improve the heritability estimation. We analyzed eight pork quality traits of the Berkshire breeds using GWAS and BLUP. GWAS detects the putative quantitative trait loci regions given traits. The single nucleotide polymorphisms (SNPs) were obtained using GWAS results with p value <0.01. BLUP analyzed with significant SNPs was much more accurate than that with total genotyped SNPs in terms of narrow-sense heritability. It implies that genomic estimated breeding values (GEBVs) of pork quality traits can be calculated by BLUP via GWAS. The GWAS model was the linear regression using PLINK and BLUP model was the G-BLUP and SNP-GBLUP. The SNP-GBLUP uses SNP-SNP relationship matrix. The BLUP analysis using preprocessing of GWAS can be one of the possible alternatives of solving the missing heritability problem and it can provide alternative BLUP method which can find more accurate GEBVs.

• 응용통계연구
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• 제16권2호
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• pp.239-246
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• 2003

소지역에서 직접(direct) 시계열추정을 할 수 있다면, 소지역들 추정에서 최적선형 불편 예측량(BLUP)을 일반화 시킬 수 있다. 특히 조사에서 얻어지는 관측 값의 오차가 시간상으로 상관관계가 있다면 Kalman Filter(KF)기법이 사용 될 수 있다. 이 연구는 예측 값을 활용한 소지역의 실업자 수 추정에서 표본으로 추출되지 않은, 즉 관측되지 않은 값의 예측모형에 KF기법을 적용하였다. 이는 경제활동인구수를 이용하여 현 시점의 소지역 실업자 수를 예측함수(BLUP)를 통해 추정하게 된다. 그리고 이를 단순 회귀분석 추정치와 비교하였다.

• 한국통계학회:학술대회논문집
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• 한국통계학회 2002년도 추계 학술발표회 논문집
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• pp.305-309
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• 2002

소지역에서 직접(direct) 시계열추정을 할 수 있다면, 소지역들 추정에서 최적선형 불편예측량(BLUP)을 일반화 시킬 수 있다. 특히 조사에서 얻어지는 관측 값의 오차가 시간상으로 상관관계가 있다면 Kalman-Filter(K-F)기법이 사용 될 수 있다. 이 연구는 소지역의 실업자 수 추정에서 K-F기법으로 경제활동인구수를 이용하여 현 시점의 소지역 실업자 수를 예측함수(BLUP)를 통해 추정하였다. 그리고 단순 회귀분석 추정치와 비교하였다.

• 종축개량
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• 제17권2호
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• pp.57-60
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• 1995

카나다의 돼지개량에 대한 국가적 유전능력 평가는 산육능력(100kg의 등지방과 일령)과 모돈의 번식능력(총산자수)을 BLUP animal model(최선형 불변예상치 가축모형 : Best Linear Unbiased Predictor Animal Model)을 이용하여 정규적으로 평가하고 있다. 새로운 검정자료가 수집되어 질때마다 매번 BLUP평가가 이루어져 농장으로 제공된다. 현재의 유전능력 변화에 대한 추정가는 연간 등지방 두께 0.35mm와 100kg도달일령 1.5일이 향상되었다. 이것은 1985년 BLUP이 소개된 이전보다 등지방 $50\%$, 일령 20배 이상의 개량효과이다. 그 외에 모돈의 번식형질에 대한 개량은 계속적으로 연구가 진행되고 있으며 국가적 육종계획에는 도체와 육질에 대한 유전적 개량사업이 추진되고 있다.

• Asian-Australasian Journal of Animal Sciences
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• 제19권9호
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• pp.1225-1228
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• 2006

A total of 1,367 first lactation records of daughters of 81 sires, having 5 or more progeny were used to evaluate sires by 3 different methods viz., least squares (LS), best linear unbiased prediction (BLUP) and derivative free restricted maximum likelihood (DFREML) method. The highest and lowest overall average breeding value of sires for first lactation 305 days or less milk yield was obtained by BLUP (1,520.72 kg) and LS method (1,502.22 kg), respectively. The accuracy, efficiency and stability of different sire evaluation methods were compared to judge their effectiveness. The error variance of DFREML method was lowest ($191,112kg^2$) and its coefficient of determination of fitting the model was highest (33.39%) revealing that this method of sire evaluation was most efficient and accurate as compared to other methods. However, the BLUP method was most stable amongst all the methods having coefficient of variation (%) very near to unadjusted data (18.72% versus 19.89%). The higher rank correlations (0.7979 to 0.9568) between different sire evaluation methods indicated that there was higher degree of similarity of ranking sires by different methods ranging from about 80 to 96 percent. However, the DFREML method seemed to be the most effective sire evaluation method as compared to other methods for the present set of data.

• Asian-Australasian Journal of Animal Sciences
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• 제30권2호
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• pp.149-153
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• 2017

Objective: This study was to determine the relationship between estimated breeding value and phenotype information after farrowing when juvenile selection was made in candidate pigs without phenotype information. Methods: After collecting phenotypic and genomic information for the total number of piglets born by Landrace pigs, selection accuracy between genomic breeding value estimates using genomic information and breeding value estimates of best linear unbiased prediction (BLUP) using conventional pedigree information were compared. Results: Genetic standard deviation (${\sigma}_a$) for the total number of piglets born was 0.91. Since the total number of piglets born for candidate pigs was unknown, the accuracy of the breeding value estimated from pedigree information was 0.080. When genomic information was used, the accuracy of the breeding value was 0.216. Assuming that the replacement rate of sows per year is 100% and generation interval is 1 year, genetic gain per year is 0.346 head when genomic information is used. It is 0.128 when BLUP is used. Conclusion: Genetic gain estimated from single step best linear unbiased prediction (ssBLUP) method is by 2.7 times higher than that the one estimated from BLUP method, i.e., 270% more improvement in efficiency.

• 한국조사연구학회지:조사연구
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• 제11권1호
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• pp.19-41
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• 2010

순환표본조사를 시행할 경우 매 순환주기별로 적절한 통계적 신뢰도를 가진 전체 모집단 특성이 추정될 수 있는 반면에, 작은 표본크기로 인하여 통계적 신뢰도가 높은 소지역 추정량의 산출은 어렵다. 따라서 소지역 추정량은 일반적으로 일정 주기 후 혹은 전체조사가 마무리된 후 독립적인 순환표본들을 결합하여 얻어진 최종표본을 통해 산출된다. 본 연구에서 는 순환표본을 결합하여 추정량을 만들 때 필요한 가중치 산출의 문제를 고려하였다. 기존의 연구들이 각 조사에 따른 경험을 바탕으로 조사별로 가능한 순환표본 결합 가중치를 정의하였으나, 본 연구에서는 모든 가능한 관심변수에 적용 가능하도록 표본설계변수에만 의존하는 모형을 설정하고 주어진 모형하에서의 최량선형불편예측치(Best Linear Unbiased Predictor: BLUP)를 고려하였다. 모의실험을 통하여 각 모형 하에서 정의되는 여러 BLUP을 비교하여 모형변화에 강건한 추정량을 제안하고 그 결과를 제4기 국민건강영양조사에 적용하였다.

• Animal Bioscience
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• 제36권9호
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• pp.1327-1335
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• 2023

Objective: When evaluating individuals with the same parent and no phenotype by pedigree best linear unbiased prediction (BLUP), it is difficult to explain carcass grade difference and select individuals because they have the same value in pedigree BLUP (PBLUP). However, single step GBLUP (ssGBLUP), which can estimate the breeding value suitable for the individual by adding genotype, is more accurate than the existing method. Methods: The breeding value and accuracy were estimated with pedigree BLUP and ssGBLUP using pedigree and genotype of 408 Hanwoo cattle from 16 families with the same parent among siblings produced by fertilized egg transplantation. A total of 14,225 Hanwoo cattle with pedigree, genotype and phenotype were used as the reference population. PBLUP obtained estimated breeding value (EBV) using the pedigree of the test and reference populations, and ssGBLUP obtained genomic EBV (GEBV) after constructing and H-matrix by integrating the pedigree and genotype of the test and reference populations. Results: For all traits, the accuracy of GEBV using ssGBLUP is 0.18 to 0.20 higher than the accuracy of EBV obtained with PBLUP. Comparison of EBV and GEBV of individuals without phenotype, since the value of EBV is estimated based on expected values of alleles passed down from common ancestors. It does not take Mendelian sampling into consideration, so the EBV of all individuals within the same family is estimated to be the same value. However, GEBV makes estimating true kinship coefficient based on different genotypes of individuals possible, so GEBV that corresponds to each individual is estimated rather than a uniform GEBV for each individual. Conclusion: Since Hanwoo cows bred through embryo transfer have a high possibility of having the same parent, if ssGBLUP after adding genotype is used, estimating true kinship coefficient corresponding to each individual becomes possible, allowing for more accurate estimation of breeding value.