• Journal of Embryo Transfer
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• v.31 no.3
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• pp.243-247
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• 2016

Growth traits, such as body weight, directly influence productivity and economic efficiency in the swine industry. In this study, we estimate heritability for body weight traits usinginformation from pedigree and genome-wide single nucleotide polymorphism (SNP) chip data. Four body weight phenotypes were measured in 1,105 $F_2$ progeny from an intercross between Landrace and Jeju native black pigs. All experimental animals were subjected to genotypic analysis using PorcineSNP60K BeadChip platform, and 39,992 autosomal SNP markers filtered by quality control criteria were used to construct genomic relationship matrix for heritability estimation. Restricted maximum likelihood estimates of heritability were obtained using both genomic- and pedigree- relationship matrix in a linear mixed model. The heritability estimates using SNP information were smaller (0.36-0.55) than those which were estimated using pedigree information (0.62-0.97). To investigate effect of common environment, such as maternal effect, on heritability estimation, we included maternal effect as an additional random effect term in the linear mixed model analysis. We detected substantial proportions of phenotypic variance components were explained by maternal effect. And the heritability estimates using both pedigree and SNP information were decreased. Therefore, heritability estimates must be interpreted cautiously when there are obvious common environmental variance components.

• Asian-Australasian Journal of Animal Sciences
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• v.29 no.8
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• pp.1083-1094
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• 2016

Carcass and price traits of 72,969 Hanwoo cows, bulls and steers aged 16 to 80 months at slaughter collected from 2002 to 2013 at 75 beef packing plants in Korea were analyzed to determine heritability, correlation and breeding value using the Multi-Trait restricted maximum likelihood (REML) animal model procedure. The traits included carcass measurements, scores and grades at 24 h postmortem and bid prices at auction. Relatively high heritability was found for maturity ($0.41{\pm}0.031$), while moderate heritability estimates were obtained for backfat thickness ($0.20{\pm}0.018$), longissimus muscle (LM) area ($0.23{\pm}0.020$), carcass weight ($0.28{\pm}0.019$), yield index ($0.20{\pm}0.018$), yield grade ($0.16{\pm}0.017$), marbling ($0.28{\pm}0.021$), texture ($0.14{\pm}0.016$), quality grade ($0.26{\pm}0.016$) and price/kg ($0.24{\pm}0.025$). Relatively low heritability estimates were observed for meat color ($0.06{\pm}0.013$) and fat color ($0.06{\pm}0.012$). Heritability estimates for most traits were lower than those in the literature. Genetic correlations of carcass measurements with characteristic scores or quality grade of carcass ranged from -0.27 to +0.21. Genetic correlations of yield grade with backfat thickness, LM area and carcass weight were 0.91, -0.43, and -0.09, respectively. Genetic correlations of quality grade with scores of marbling, meat color, fat color and texture were -0.99, 0.48, 0.47, and 0.98, respectively. Genetic correlations of price/kg with LM area, carcass weight, marbling, meat color, texture and maturity were 0.57, 0.64, 0.76, -0.41, -0.79, and -0.42, respectively. Genetic correlations of carcass price with LM area, carcass weight, marbling and texture were 0.61, 0.57, 0.64, and -0.73, respectively, with standard errors ranging from ${\pm}0.047$ to ${\pm}0.058$. The mean carcass weight breeding values increased by more than 8 kg, whereas the mean marbling scores decreased by approximately 0.2 from 2000 through 2009. Overall, the results suggest that genetic improvement of productivity and carcass quality could be obtained under the national scale breeding scheme of Korea for Hanwoo and that continuous efforts to improve the breeding scheme should be made to increase genetic progress.

• Journal of Embryo Transfer
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• v.22 no.3
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• pp.143-147
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• 2007

Records on 546 Korea native pigs for average daily gain (ADG), age at 70 kg (D70 kg) and backfat thickness (BF) made between 2001 and 2006 in herds on National Institutes of Animal Science in Korea were used to estimate genetic parameters. The data was analyzed by the DF-REML (Derivative-Free Restricted Maximum Likelihood) program of Boldman using a single-trait animal model. Heritabilities were 0.26, 0.09, and 0.29 for ADG, D70 kg and BF, respectively. The phenotypic correlations of ADG with D70 kg and BF were -0.71 and 0.30. The phenotypic correlation of D70 kg with BF was -0.15. The genetic correlations of ADG with D70 kg and BF were -0.11, 0.41, respectively. The genetic correlation of D70 kg with BF was -0.16. The data of weights and measurements on body length, body height and chest width after age at 11 months (days to 330) were shown scarcely less differences compare to data of age at 11 months.

• Asian-Australasian Journal of Animal Sciences
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• v.28 no.9
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• pp.1259-1265
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• 2015

The present study was performed to study the genetic relationship of productive life with production and type traits of Korean Holsteins at first three lactations. The data for the analysis from 56,054, 28,997, and 11,816 animals of first, second and third parity cows which were born from 2006 to 2011 were collected by Dairy Cattle Improvement Center, National Agricultural Co-operative Federation. Milk, protein and fat yields adjusted for 305 days and average somatic cell score considered as production traits and analyzed type traits were stature, strength, body depth, dairy form, rump angle, rump width, rear leg side view, foot angle, front attachment placement, rear attachment height, rear attachment width, udder cleft, udder depth, front teat placement and front teat length. A multi trait genetic analysis was performed using Wombat program with restricted maximum likelihood animal model composed of fixed effect of birth year, farm and the random effect of animal and random residual effect according to the traits. Heritability estimates of productive life were between 0.06 and 0.13. Genetic and phenotypic correlations between production and productive life traits ranged from 0.35 to 0.04 for milk, 0.16 to 0.05 for protein and 0.18 to 0.02 f 15-0034 (2nd) 150520 or fat. Somatic cells score showed a negative genetic and phenotypic correlation with productive life and also udder type traits, indicating that the selection for higher udder traits will likely to improve resistance to mastitis and persistence in the herd. Among all dairy form type traits, udder characters such as udder cleft showed a significant relationship with productive life. However, a specific change of heritabilities or correlations were not observed with the change of parity. Moreover, further studies are needed to further confirm the significance of the above traits and the effect of parity on above relationships in order to minimize both voluntary and involuntary culling rates while improving herd health and maintaining high yielding dairy cows.

• Asian-Australasian Journal of Animal Sciences
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• v.33 no.7
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• pp.1057-1067
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• 2020

Objective: This study evaluated the effect of pedigree errors (PEs) on the accuracy of estimated breeding value (EBV) and genetic gain for carcass traits in Korean Hanwoo cattle. Methods: The raw data set was based on the pedigree records of Korean Hanwoo cattle. The animals' information was obtained using Hanwoo registration records from Korean animal improvement association database. The record comprised of 46,704 animals, where the number of the sires used was 1,298 and the dams were 38,366 animals. The traits considered were carcass weight (CWT), eye muscle area (EMA), back fat thickness (BFT), and marbling score (MS). Errors were introduced in the pedigree dataset through randomly assigning sires to all progenies. The error rates substituted were 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, and 80%, respectively. A simulation was performed to produce a population of 1,650 animals from the pedigree data. A restricted maximum likelihood based animal model was applied to estimate the EBV, accuracy of the EBV, expected genetic gain, variance components, and heritability (h²) estimates for carcass traits. Correlation of the simulated data under PEs was also estimated using Pearson's method. Results: The results showed that the carcass traits per slaughter year were not consistent. The average CWT, EMA, BFT, and MS were 342.60 kg, 78.76 ㎠, 8.63 mm, and 3.31, respectively. When errors were introduced in the pedigree, the accuracy of EBV, genetic gain and h² of carcass traits was reduced in this study. In addition, the correlation of the simulation was slightly affected under PEs. Conclusion: This study reveals the effect of PEs on the accuracy of EBV and genetic parameters for carcass traits, which provides valuable information for further study in Korean Hanwoo cattle.

• Korean Journal of Agricultural Science
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• v.40 no.4
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• pp.339-345
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• 2013

The objective of this study was to establish genetic evaluation systems with carcass data collected by 68 individual farms from 2007 to 2011 in Pyeongchang area of Kangwon province. All the possible of environment effects were corrected by analysis of variance (ANOVA) to estimate more accurate genetic parameters. Heritabilities and genetic correlations were estimated from carcass data collected from Hanwoo steers(n=10,441) born in Pyeongchang region from 2005 to 2008. Traits evaluated included carcass weight (CWT), eye muscle area (EMA), back fat thickness (BF) and marbling score (MS). As for the mean value and standard deviation for carcass traits, CWT, EMA, BF and MS were 424.5, 92, 13.7 and 5.7. Parameters were estimated using a multiple trait animal model and derivative-free restricted maximum likelihood procedures. Estimated heritabilities for CWT, EMA, BF and MS were 0.30, 0.21, 0.42 and 0.42, respectively. Genetic correlation of CWT with EMA, BF and MS were estimated to 0.24, 0.36 and 0.07, respectively. Genetic correlation of EMA with BF and MS was -0.27 and 0.61, respectively.

• Asian-Australasian Journal of Animal Sciences
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• v.29 no.9
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• pp.1222-1228
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• 2016

The objective of this research was to estimate genetic parameters and trends for length of productive life (LPL), lifetime number of piglets born alive (LBA), lifetime number of piglets weaned (LPW), lifetime litter birth weight (LBW), and lifetime litter weaning weight (LWW) in a commercial swine farm in Northern Thailand. Data were gathered during a 24-year period from July 1989 to August 2013. A total of 3,109 phenotypic records from 2,271 Landrace (L) and 838 Yorkshire sows (Y) were analyzed. Variance and covariance components, heritabilities and correlations were estimated using an Average Information Restricted Maximum Likelihood (AIREML) procedure. The 5-trait animal model contained the fixed effects of first farrowing year-season, breed group, and age at first farrowing. Random effects were sow and residual. Estimates of heritabilities were medium for all five traits ($0.17{\pm}0.04$ for LPL and LBA to $0.20{\pm}0.04$ for LPW). Genetic correlations among these traits were high, positive, and favorable (p<0.05), ranging from $0.93{\pm}0.02$ (LPL-LWW) to $0.99{\pm}0.02$ (LPL-LPW). Sow genetic trends were non-significant for LPL and all lifetime production traits. Sire genetic trends were negative and significant for LPL ($-2.54{\pm}0.65d/yr$; p = 0.0007), LBA ($-0.12{\pm}0.04piglets/yr$; p = 0.0073), LPW ($-0.14{\pm}0.04piglets/yr$; p = 0.0037), LBW ($-0.13{\pm}0.06kg/yr$; p = 0.0487), and LWW ($-0.69{\pm}0.31kg/yr$; p = 0.0365). Dam genetic trends were positive, small and significant for all traits ($1.04{\pm}0.42d/yr$ for LPL, p = 0.0217; $0.16{\pm}0.03piglets/yr$ for LBA, p<0.0001; $0.12{\pm}0.03piglets/yr$ for LPW, p = 0.0002; $0.29{\pm}0.04kg/yr$ for LBW, p<0.0001 and $1.23{\pm}0.19kg/yr$ for LWW, p<0.0001). Thus, the selection program in this commercial herd managed to improve both LPL and lifetime productive traits in sires and dams. It was ineffective to improve LPL and lifetime productive traits in sows.

• Asian-Australasian Journal of Animal Sciences
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• v.22 no.4
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• pp.459-464
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• 2009

Data and pedigree information for Lori-Bakhtiari sheep used in this study were 6,239 records of lamb mortality from 246 sires and 1,721 dams, collected from 1989 through 2007 from a Lori-Bakhtiari flock at Shooli station in Shahrekord. The traits investigated were cumulative lamb mortality from birth up to 7 days, up to 14 days, up to 21 days, and up to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 and 12 months of age. The models included fixed factors that had significant effects and random direct genetic, maternal genetic and maternal permanent environmental effects. Variance components were estimated using the restricted maximum likelihood procedure applying three animal models with and without maternal and common environmental effects. The overall mean of cumulative lamb mortality rate was 22.95% from birth to 1 year of age, while the overall mortality rate up to 3 and from 3 to 6 months of age was 6.14% and 12.76%, respectively. The mortality rate after 6 months of age declined as the lambs grew older. The age of dam had no important effect on lamb mortality. The type of birth was more important during the preweaning period than at later ages, and lamb mortality rate was higher in twins. The year of birth, month of birth and sex of lamb significantly (p${\leq}$0.01) affected the cumulative lamb mortality rate at all ages. The least square mean of mortality during the final one-third of the lambing period was higher than the first and middle onethird of the lambing period. Male lambs were found to be at a higher risk of mortality than females. Birth weight of the lamb had a highly significant (p${\leq}$0.01) effect on lamb mortality at all ages as a quadratic regression. Direct and maternal heritability estimates of lamb mortality ranged from 0.01 to 0.13 and 0.01 to 0.05, respectively. Direct heritability increased with age of lamb, while maternal effects (genetic and common environmental) were important in the preweaning period. These results indicate that lamb mortality can be reduced first through farm management practices and secondly by genetic selection. Both animal and maternal effects should be considered in breeding programmes for reducing lamb mortality at preweaning.

• Asian-Australasian Journal of Animal Sciences
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• v.33 no.10
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• pp.1558-1565
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• 2020

Objective: The objective of this study was to characterize the number of loci affecting growth traits and the distribution of single nucleotide polymorphism (SNP) effects on growth traits, and to understand the genetic architecture for growth traits in Hanwoo (Korean cattle) using genome-wide association study (GWAS), genomic partitioning, and hierarchical Bayesian mixture models. Methods: GWAS: A single-marker regression-based mixed model was used to test the association between SNPs and causal variants. A genotype relationship matrix was fitted as a random effect in this linear mixed model to correct the genetic structure of a sire family. Genomic restricted maximum likelihood and BayesR: A priori information included setting the fixed additive genetic variance to a pre-specified value; the first mixture component was set to zero, the second to 0.0001×σ²_g, the third 0.001×σ²_g, and the fourth to 0.01×σ²_g. BayesR fixed a priori information was not more than 1% of the genetic variance for each of the SNPs affecting the mixed distribution. Results: The GWAS revealed common genomic regions of 2 Mb on bovine chromosome 14 (BTA14) and 3 had a moderate effect that may contain causal variants for body weight at 6, 12, 18, and 24 months. This genomic region explained approximately 10% of the variance against total additive genetic variance and body weight heritability at 12, 18, and 24 months. BayesR identified the exact genomic region containing causal SNPs on BTA14, 3, and 22. However, the genetic variance explained by each chromosome or SNP was estimated to be very small compared to the total additive genetic variance. Causal SNPs for growth trait on BTA14 explained only 0.04% to 0.5% of the genetic variance Conclusion: Segregating mutations have a moderate effect on BTA14, 3, and 19; many other loci with small effects on growth traits at different ages were also identified.

• Asian-Australasian Journal of Animal Sciences
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• v.26 no.9
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• pp.1237-1246
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• 2013

The objective of this study was to estimate variance components and genetic parameters for lactation milk yield (LY), lactation length (LL), average milk yield per day (YD), initial milk yield (IY), peak milk yield (PY), days to peak (DP) and parameters (ln(a) and c) of the modified incomplete gamma function (MIG) in an Ethiopian multibreed dairy cattle population. The dataset was composed of 5,507 lactation records collected from 1,639 cows in three locations (Bako, Debre Zeit and Holetta) in Ethiopia from 1977 to 2010. Parameters for MIG were obtained from regression analysis of monthly test-day milk data on days in milk. The cows were purebred (Bos indicus) Boran (B) and Horro (H) and their crosses with different fractions of Friesian (F), Jersey (J) and Simmental (S). There were 23 breed groups (B, H, and their crossbreds with F, J, and S) in the population. Fixed and mixed models were used to analyse the data. The fixed model considered herd-year-season, parity and breed group as fixed effects, and residual as random. The single and two-traits mixed animal repeatability models, considered the fixed effects of herd-year-season and parity subclasses, breed as a function of cow H, F, J, and S breed fractions and general heterosis as a function of heterozygosity, and the random additive animal, permanent environment, and residual effects. For the analysis of LY, LL was added as a fixed covariate to all models. Variance components and genetic parameters were estimated using average information restricted maximum likelihood procedures. The results indicated that all traits were affected (p<0.001) by the considered fixed effects. High grade $B{\times}F$ cows (3/16B 13/16F) had the highest least squares means (LSM) for LY ($2,490{\pm}178.9kg$), IY ($10.5{\pm}0.8kg$), PY ($12.7{\pm}0.9kg$), YD ($7.6{\pm}0.55kg$) and LL ($361.4{\pm}31.2d$), while B cows had the lowest LSM values for these traits. The LSM of LY, IY, YD, and PY tended to increase from the first to the fifth parity. Single-trait analyses yielded low heritability ($0.03{\pm}0.03$ and $0.08{\pm}0.02$) and repeatability ($0.14{\pm}0.01$ to $0.24{\pm}0.02$) estimates for LL, DP and parameter c. Medium heritability ($0.21{\pm}0.03$ to $0.33{\pm}0.04$) and repeatability ($0.27{\pm}0.02$ to $0.53{\pm}0.01$) estimates were obtained for LY, IY, PY, YD and ln(a). Genetic correlations between LY, IY, PY, YD, ln(a), and LL ranged from 0.59 to 0.99. Spearman's rank correlations between sire estimated breeding values for LY, LL, IY, PY, YD, ln(a) and c were positive (0.67 to 0.99, p<0.001). These results suggested that selection for IY, PY, YD, or LY would genetically improve lactation milk yield in this Ethiopian dairy cattle population.