• Asian-Australasian Journal of Animal Sciences
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• v.11 no.2
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• pp.117-120
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• 1998

Relationships of breeding values of sires for first lactation milk yield with pedigree information or indices were examined to identify the optimal criteria of selecting young dairy bulls for future use in artificial insemination (AI). Records of performance data on 1087 crossbred daughters (Holstein - Friesian, Jersey and Brown Swiss with Hariana) of 147 sires, generated at Livestock Production Research (Cattle and Buffaloes) Farm, IVRI, Izatnagar, U.P., during 1972 - 1995 were used to obtain the estimates of sire's breeding values (EBV) using the Best Linear Unbiased Prediction Procedures. The correlations between young bull's EBV and the dam's first lactation milk yield was non-significantly different from zero. However, the young bull's EBV was negatively and significantly related (r = - 0.275 ; P < 0.05) to the dam's best lactation milk yield, suggesting that the selection of young dairy bulls from high yielding elite dams is not a suitable criteria for genetic improvement. The correlations of sire's and paternal grandsire's EBV's with young bull's EBV were high and positive (0.532, 0.844; P < 0.01). The maternal grandsire's EBV was positively but non-significantly related to grandson's EBV. The pedigree index incorporating dam's milk records and sire's EBV's showed a negative and non-significant correlation with young bull's EBV. However, the correlation of a pedigree index $(I_3)$ combining information on sire's and paternal grand-sire's EBV's with young bull's EBV's was considerably high and positive (0.797; P < 0.01). The regression coefficients of young bull's EBV on pedigree index $I_3$, was higher than those on other pedigree information. These results revealed that there was no advantage in basing selection on dam's performance or maternal grand-sire's EBV and that sire's and paternal grandsire's EBV's were reliable pedigree information for selection of young dairy bulls for future use in AI.

• Animal Bioscience
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• v.36 no.9
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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.

• Asian-Australasian Journal of Animal Sciences
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• v.31 no.5
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• pp.628-635
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• 2018

Objective: To determine the effects of genomic breeding values (GBV) and single nucleotide polymorphisms (SNP) on the total number of piglets born (TNB) in 3 pig breeds (Berkshire, Landrace, and Yorkshire). Methods: After collecting genomic information (Porcine SNP BeadChip) and phenotypic TNB records for each breed, the effects of GBV and SNP were estimated by using single step best linear unbiased prediction (ssBLUP) method. Results: The heritability estimates for TNB in Berkshire, Landrace, and Yorkshire breeds were 0.078, 0.107, and 0.121, respectively. The breeding value estimates for TNB in Berkshire, Landrace, and Yorkshire breeds were in the range of -1.34 to 1.47 heads, -1.79 to 1.87 heads, and -2.60 to 2.94 heads, respectively. Of sows having records for TNB, the reliability of breeding value for individuals with SNP information was higher than that for individuals without SNP information. Distributions of the SNP effects on TNB did not follow gamma distribution. Most SNP effects were near zero. Only a few SNPs had large effects. The numbers of SNPs with absolute value of more than 4 standard deviations in Berkshire, Landrace, and Yorkshire breeds were 11, 8, and 19, respectively. There was no SNP with absolute value of more than 5 standard deviations in Berkshire or Landrace. However, in Yorkshire, four SNPs (ASGA 0089457, ASGA0103374, ALGA0111816, and ALGA0098882) had absolute values of more than 5 standard deviations. Conclusion: There was no common SNP with large effect among breeds. This might be due to the large genetic composition differences and the small size of reference population. For the precise evaluation of genetic performance of individuals using a genomic selection method, it may be necessary to establish the appropriate size of reference population.

• Journal of the Korean Data and Information Science Society
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• v.11 no.1
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• pp.111-126
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• 2000

Small area estimation is becoming important in survey sampling due to a growing demand for reliable small area statistics. In estimating means, totals, and other parameters for small areas of a finite population, samplie sizes for small areas are typically small because the overall sample size is usually determined to provide specific accuracy at a much higher level of aggregation than that of small area. The usual direct estimators that use the only information which is gotten from the sample in a given small area provide unreliable estimates. However, indirect estimators utilize the information from the areas related with a given small area, that is, borrow strength from other related areas, and so give more accurate estimates than direct estimators. In this paper we investigate small area estimation methods such as synthetic, composite and empirical best linear unbiased prediction estimator, and apply them to real domestic data which is from the Survey of Hotels and Restaurants in In-Chon as of 1996 and then evaluate the performance of these methods by measuring average squared errors. This evaluation shows that indirect estimators, which are small area estimation methods, are more efficient than direct estimator.

• Asian-Australasian Journal of Animal Sciences
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• v.15 no.5
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• pp.627-632
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• 2002

Genetic parameters for dairy performance traits were estimated, breeding values for the traits of all breeding sires and cows were predicted and the genetic trends were estimated using the breeding values in the Central Cattle Breeding Station (CCBS). A total of 3,801 records for Bangladeshi Local, 756 records for Red Sindhi and 959 records for Sahiwal covering the period from 1961 to 1997 were used in this analysis. Traits considered were total milk production per lactation (TLP), lactation length (LL) and daily milk yield (DMY). The genetic parameters were estimated by the REML using MTDFREML program. The breeding values were predicted by a best linear unbiased prediction (BLUP). In all sets of data, the genetic trends for the dairy performance traits were computed as averages of breeding values for cows born in the particular year. The estimates of heritability for TLP (0.26 and 0.27) and DMY (0.28 and 0.27) were moderate in Bangladeshi local and Red Sindhi breed, respectively. Furthermore, the heritability estimate for LL (0.24) was moderate in Red Sindhi. The estimates of heritabilities for all traits were low in Sahiwal. The repeatability estimate was high for TLP, moderate for LL and moderate to high for DMY. All variances estimated in Bangladeshi Local were low, comparing the respective values estimated in both Red Sindhi and Sahiwal. On the other hand, additive genetic variances for the three traits were estimated very low in Sahiwal. The genetic trends for the three dairy production traits have not been positive except for the recent trend in Bangladeshi Local.

• Asian-Australasian Journal of Animal Sciences
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• v.18 no.8
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• pp.1075-1079
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• 2005

The main objective of this study is to examine genetic changes in growth rate and carcass composition traits in group housed, ad libitum fed pigs, from lines of Large White divergently selected over four years for high and low post-weaning daily gain on a fixed but restricted ration. Genetic parameters for production and carcass traits were also estimated by using average information-restricted maximum likelihood applied to a multivariate individual animal model. All analyses were carried out on 1,728 records of group housed ad libitum fed pigs, and include a full pedigree of 5,324 animals. Estimates of heritability (standard errors in parentheses) were 0.11 (0.04) for lifetime daily liveweight gain (LDG), 0.13 (0.04) for daily carcass weight gain (CDG) and 0.28 (0.06) for carcass backfat (CFT). Genetic correlations between LDG and CDG were highly positive and between LDG and CFT negative, suggesting that selection for lifetime daily gain under commercial conditions of group housing with ad libitum feeding would result in favourable improvement in carcass traits. CFT showed negative genetic correlations with CDG. Correlated genetic responses evaluated as estimated breeding values (EBVs) were obtained from a multivariate animal model-best linear unbiased prediction analysis. After four years of divergent selection for 6 week post-weaning growth rate on restricted feeding, pigs performance tested on ad libitum feeding in groups exhibited changes in EBVs of 6.77 and -9.93 (g/d) for LDG, 4.25 and -7.08 (g/d) for CDG, and -1.42 and 1.55 (mm) for CFT, in the high and low lines, respectively. It is concluded that selection for growth rate on restricted feeding would significantly improve genetic performance and carcass composition of their descendants when group housed and ad libitum fed as is a common commercial practice.

• Proceedings of the Korean Association for Survey Research Conference
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• 2000.06a
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• pp.57-73
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• 2000

Small area estimation is becoming important in survey sampling due to a growing demand for reliable small area statistics. In estimating means, totals, and other parameters for small areas of a finite population, samplie sizes for small areas are typically small because the overall sample size is usually determined to provide specific accuracy at a much higher level of aggregation than that of small area. The usual direct estimators that use the only information which is gotten from the sample in a given small area provide unreliable estimates. However, indirect estimators utilize the information from the areas related with a given small area, that is borrow strength from other related areas, and so give more accurate estimates than direct estimators. In this paper we investigate small area estimation methods such as synthetic, composite and empirical best linear unbiased prediction estimator, and apply them to real domestic data which is from the Survey of Hotels and Restaurants in In-Chon as of 1996 and then evaluate the performance of these methods by measuring average squared errors. This evaluation shows that indirect estimators, which are small area estimation methods, are more efficient direct estimator.

• Animal Bioscience
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• v.34 no.12
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• pp.1903-1911
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• 2021

Objective: The objective of this study was to estimate the genetic parameters and various litter trait trends of Danish pigs in South Vietnam, including the number born alive (NBA), number weaned (NW), and litter weight at the 21st day (LW21). Methods: Records of 936 Yorkshire sows with 3361 litters and 973 Landrace sows with 3161 litters were used to estimate the variance components, genetic parameters, and trends of NBA, NW, and LW21. The restricted maximum likelihood method was applied using VCE6 software to obtain the variance components and genetic parameters. Thereafter, the best linear unbiased prediction procedure with an animal model was applied using PEST software to estimate the breeding values of the studied traits. Results: The heritability estimates were low, ranging from 0.12 to 0.21 for NBA, 0.03 to 0.04 for NW, and from 0.11 to 0.13 for LW21. The genetic correlation between the NBA and NW was relatively strong in both breeds, at 0.77 and 0.60 for Yorkshire and Landrace, respectively. Similarly, the genetic correlation between the NW and LW21 was considerably stronger in Landrace pigs (0.71) than in Yorkshire pigs (0.48). The estimates of annual genetic progress were 0.0431, 0.0233, and 0.0461 for NBA, NW, and LW21 in Landrace pigs and 0434, 0.0202, and 0.0667 for NBA, NW, and LW21 in Yorkshire pigs, respectively. Conclusion: The positive genetic trends estimated for the additive genetic values of the selected traits indicated that the current breeding system has achieved favorable results.

• Journal of Animal Reproduction and Biotechnology
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• v.38 no.1
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• pp.32-37
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• 2023

This study has evaluated the genomic estimated breeding value (GEBV) of the commercial Hanwoo population using the genomic best linear unbiased prediction (GBLUP) method and genomic information. Furthermore, it analyzed the accuracy and realized accuracy of the GEBV. 1,740 heads of the Hanwoo population which were analyzed using a single nucleotide polymorphism (SNP) Chip has selected as the test population. For carcass weight (CWT), eye muscle area (EMA), back fat thickness (BFT), and marbling score (MS), the mean GEBVs estimated using the GBLUP method were 3.819, 0.740, -0.248, and 0.041, respectively and the accuracy of each trait was 0.743, 0.728, 0.737, and 0.765, respectively. The accuracy of the breeding value was affected by heritability. The accuracy was estimated to be low in EMA with low heritability and high in MS with high heritability. Realized accuracy values of 0.522, 0.404, 0.444, and 0.539 for CWT, EMA, BFT, and MS, respectively, showing the same pattern as the accuracy value. The results of this study suggest that the breeding value of each individual can be estimated with higher accuracy by estimating the GEBV using the genomic information of 18,499 reference populations. If this method is used and applied to individual selection in a commercial Hanwoo population, more precise and economical individual selection is possible. In addition, continuous verification of the GBLUP model and establishment of a reference population suitable for commercial Hanwoo populations in Korea will enable a more accurate evaluation of individuals.

• Animal Bioscience
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• v.37 no.3
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• pp.428-436
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• 2024

Objective: This study compared five distinct sets of biological pathways and associated genes related to semen volume (VOL), number of sperm (NS), and sperm motility (MOT) in the Thai multibreed dairy population. Methods: The phenotypic data included 13,533 VOL records, 12,773 NS records, and 12,660 MOT records from 131 bulls. The genotypic data consisted of 76,519 imputed and actual single nucleotide polymorphisms (SNPs) from 72 animals. The SNP additive genetic variances for VOL, NS, and MOT were estimated for SNP windows of one SNP (SW1), ten SNP (SW10), 30 SNP (SW30), 50 SNP (SW50), and 100 SNP (SW100) using a single-step genomic best linear unbiased prediction approach. The fixed effects in the model were contemporary group, ejaculate order, bull age, ambient temperature, and heterosis. The random effects accounted for animal additive genetic effects, permanent environment effects, and residual. The SNPs explaining at least 0.001% of the additive genetic variance in SW1, 0.01% in SW10, 0.03% in SW30, 0.05% in SW50, and 0.1% in SW100 were selected for gene identification through the NCBI database. The pathway analysis utilized genes associated with the identified SNP windows. Results: Comparison of overlapping and non-overlapping SNP windows revealed notable differences among the identified pathways and genes associated with the studied traits. Overlapping windows consistently yielded a larger number of shared biological pathways and genes than non-overlapping windows. In particular, overlapping SW30 and SW50 identified the largest number of shared pathways and genes in the Thai multibreed dairy population. Conclusion: This study yielded valuable insights into the genetic architecture of VOL, NS, and MOT. It also highlighted the importance of assessing overlapping and non-overlapping SNP windows of various sizes for their effectiveness to identify shared pathways and genes influencing multiple traits.