Yunho Choy

Genetic Parameter Estimation of Carcass Traits of Hanwoo Steers

The genetic parameters used in National Hanwoo Genetic Evaluation(NHGE) were needed to be monitored and updated periodically for accounting any possible changes in population parameters due to selection and environmental changes. Genetic parameters were estimated with single and two-trait models with MTDFREML package using 2,791 carcass records of steers collected from Hanwoo Progeny Test Program(HPTP). Single and two-trait models gave similar parameter estimates for all traits. The heritability estimates from single and two-trait models for carcass weight(CW), dressing percentage(DP), eye muscle area(EMA), back fat thickness(BFT) and marbling score(MS) were 0.30, 0.30, 0.37, 0.44 and 0.44, respectively. The heritability estimates for all the traits except BFT were slightly lower than those used in NHGE but seemed to be within the acceptable ranges. However, further monitoring is needed because the data might not have fully reflected the changes such as carcass grading standards in performance testing program. In order to shift statistical model of NHGE from single trait model to multiple-trait model, the genetic correlations between carcass traits were estimated with pairwise two-trait models. The genetic correlation coefficients between CW and DP, between CW and EMA, between CW and BFT and between CW and MS were 0.44, 0.63, 0.17 and 0.06, respectively. Those between DP and EMA, between DP and BFT and between DP and MS were 0.29, 0.40 and 0.20. Those between EMA and BFT and between EMA and MS were －0.24 and 0.15, respectively. The genetic correlation coefficient between BFT and MS was 0.03.

Development of International Genetic Evaluation Models for Dairy Cattle

This study was aimed to solve the problems of current national genetic evaluation systems in Korea and its development to pass the verification processes as required by International Bull Evaluation Service (Interbull). This will enable Korea to participate in international genetic evaluation program. A total of 1,416,589 test-day milk records with calving dates used in this study were collected by National Agricultural Cooperative Federation from 2001 to 2009. Parity was limited up to fifth calving and milk production records were adjusted to cumulative 305 day lactation. The pedigree consisted of 2,279,741 animals where 2,467 bulls had 535,409 parents. A newly developed multiple trait model was used in calculation of breeding values for milk yield, milk fat, and protein yield. Data were edited with SAS (version 9.2) and R programs, and genetic parameters were estimated using VCE 6.0. Results showed a continuous increase in genetic potentials, in general, and no remarkable differences were found between performances by parity. Except fat yield, potentials in milk yield and protein yield were well calculated. We found an increased number of daughters per each top ranked 1,000 bulls in recent years of calf births compared to the cases of previous evaluations. Of the bulls ranked top 100 by our new models (multiple-trait models) we found that increased numbers of bulls were included. Of twenty eight bulls born in 2006, twenty bulls born in 2007 and eight bulls born in 2008 that were listed by new models, only 23, 12, and 2 bulls born in respective years were represented on top 100 by old single-trait models. Re-ranking of the daughters or sires by multiple-trait models suggest that this new multiple trait approach should be used for dairy cattle genetic evaluation and seed-stock selection in the future to increase the accuracy of multiple trait selection. Breeding values for these traits should also be calculated by new method for international genetic evaluation. (Key words : Holestein, Genetic evaluation, Multiple trait models, Breeding values)

Estimation of Genetic Parameters for Economic Traits of Hanwoo Cows Using Ultrasound

This experiment was conducted to estimate the genetic parameters and breeding values of the economic traits measured from the cows (aged 15 months or older) using ultrasound and to use them as the information for the selection of stock animals at the farm level. The means and standard deviations of longissimus muscle area, backfat thickness and marbling score were 54.11 cm 2 ± 9.06, 3.57 mm ± 2.45 and 2.65 ± 2.88, respectively. While the linear regression coefficients of longissimus muscle area, backfat thickness and marbling score for age (in months) were all positive (0.3532, 0.0868 and 0.0833), the quadratic regression coefficients of them for age (in months) were all negative ( 0.0023, 0.0005 and 0.0006), and as the body condition score increased longissimus muscle area, backfat thickness and marbling score increased collectively. The heritability estimates for the longissimus muscle area, backfat thickness and marbling score were 0.39, 0.48 and 0.13, respectively and the estimated annual genetic gains for the longissimus muscle area, backfat thickness and marbling score were 0.00334 cm 2 , 0.0073 mm and 0.0043

Estimation of Genetic Parameters for Somatic Cell Scores of Holsteins Using Multi-trait Lactation Models in Korea

The study was conducted to analyze the genetic parameters of somatic cell score (SCS) of Holstein cows, which is an important indicator to udder health. Test-day records of somatic cell counts (SCC) of 305-day lactation design from first to fifth lactations were collected on Holsteins in Korea during 2000 to 2012. Records of animals within 18 to 42 months, 30 to 54 months, 42 to 66 months, 54 to 78 months, and 66 to 90 months of age at the first, second, third, fourth and fifth parities were analyzed, respectively. Somatic cell scores were calculated, and adjusted for lactation production stages by Wilmink’s function. Lactation averages of SCS (LSCS1 through LSCS5) were derived by further adjustments of each test-day SCS for five age groups in particular lactations. Two datasets were prepared through restrictions on number of sires/herd and dams/herd, progenies/sire, and number of parities/cow to reduce data size and attain better relationships among animals. All LSCS traits were treated as individual trait and, analyzed through multiple-trait sire models and single trait animal models via VCE 6.0 software package. Herd-year was fitted as a random effect. Age at calving was regressed as a fixed covariate. The mean LSCS of five lactations were between 3.507 and 4.322 that corresponded to a SCC range between 71,000 and 125,000 cells/mL; with coefficient of variation from 28.2% to 29.9%. Heritability estimates from sire models were within the range of 0.10 to 0.16 for all LSCS. Heritability was the highest at lactation 2 from both datasets (0.14/0.16) and lowest at lactation 5 (0.11/0.10) using sire model. Heritabilities from single trait animal model analyses were slightly higher than sire models. Genetic correlations between LSCS traits were strong (0.62 to 0.99). Very strong associations (0.96 to 0.99) were present between successive records of later lactations. Phenotypic correlations were relatively weaker (<0.55). All correlations became weaker at distant lactations. The estimated breeding values (EBVs) of LSCS traits were somewhat similar over the years for a particular lactation, but increased with lactation number increment. The lowest EBV in first lactation indicated that selection for SCS (mastitis resistance) might be better with later lactation records. It is expected that results obtained from these multi-trait lactation model analyses, being the first large scale SCS data analysis in Korea, would create a good starting step for application of advanced statistical tools for future genomic studies focusing on selection for mastitis resistance in Holsteins of Korea.

Estimation of Genetic Parameters for Milk Production Traits in Holstein Dairy Cattle

The purpose of this study was to estimate (co) variance components of three milk production traits for genetic evaluation using a multiple lactation model. Each of the first five lactations was treated as different traits. For the parameter estimation study, a data set was set up including lactations from cows calved from 2001 to 2009. The total number of raw lactation records in first to fifth parities reached 1,416,589. At least 10 cows were required for each contemporary group, herd-year-season effect. Sires with fewer than 10 daughters were discarded. Lactations with 305d milk yield exceeding 15,000 kg were removed. In total, 1,456 sires of cows were remained after all the selection steps. A complete pedigree consisting of 292,382 records was used for the study. A sire model containing herd-year-season, caving age, and sire additive genetic effects was applied to the selected lactation data and pedigree for estimating (co) variance components via VCE. Heritabilities and genetic or residual correlations were then derived from the (co) variance estimates using R package. Genetic correlations between lactations ranged from 0.76 to 0.98 for milk yield, 0.79~1.00 for fat yield, 0.75~1.00 for protein yield. On individual lactation basis, relatively low heritability values were obtained 0.14~0.23, 0.13~0.20 and 0.14~0.19 for milk, fat, and protein yields, respectively. For the combined lactation heritability values were 0.29, 0.28, and 0.26 for milk, fat, and protein yields. The estimated parameters will be used in national genetic evaluations for production traits. (Key words : Holestein, Genetic parameters, Milk production traits, Heritability )

Effect of Carcass Traits on Carcass Prices of Holstein Steers in Korea

The present study investigated the contribution of carcass traits on carcass prices of Holstein steers in Korea. Phenotypic data consisted of 76,814 slaughtered Holsteins (1 to 6 yrs) from all over Korea. The means for live body weight at slaughter (BWT), chilled carcass weight (CWT), dressing percentage (DP), quantity grade index (QGI), eye muscle area (EMA), backfat thickness (BF) and marbling score (MS), carcass unit price (CUP), and carcass sell prices (CSP) were 729.0 kg, 414.2 kg, 56.79%, 64.42, 75.26 cm2, 5.77 mm, 1.98, 8,952.80 Korean won/kg and 3,722.80 Thousand Korean won/head. Least squares means were significantly different by various age groups, season of slaughter, marbling scores and yield grades. Pearson’s correlation coefficients of CUP with carcass traits ranged from 0.12 to 0.62. Besides, the relationships of carcass traits with CSP were relatively stronger than those with CUP. The multiple regression models for CUP and CSP with carcass traits accounted 39 to 63% of the total variation, respectively. Marbling score had maximum economic effects (partial coefficients) on both prices. In addition, the highest standardized partial coefficients (relative economic weights) for CUP and CSP were calculated to be on MS and CWT by 0.608 and 0.520, respectively. Path analyses showed that MS (0.376) and CWT (0.336) had maximum total effects on CUP and CSP, respectively; whereas BF contributed negatively. Further sub-group (age and season of slaughter) analyses also confirmed the overall outcomes. However, the relative economic weights and total path contributions also varied among the animal sub-groups. This study suggested the significant influences of carcass traits on carcass prices; especially MS and CWT were found to govern the carcass prices of Holstein steers in Korea.

Estimation of the genetic milk yield parameters of Holstein cattle under heat stress in South Korea

Objective The objective of this study was to investigate the genetic components of daily milk yield and to re-rank bulls in South Korea by estimated breeding value (EBV) under heat stress using the temperature-humidity index (THI). Methods This study was conducted using 125,312 monthly test-day records, collected from January 2000 to February 2017 for 19,889 Holstein cows from 647 farms in South Korea. Milk production data were collected from two agencies, the Dairy Cattle Genetic Improvement Center and the Korea Animal Improvement Association, and meteorological data were obtained from 41 regional weather stations using the Automated Surface Observing System (ASOS) installed throughout South Korea. A random regression model using the THI was applied to estimate genetic parameters of heat tolerance based on the test-day records. The model included herd-year-season, calving age, and days-in-milk as fixed effects, as well as heat tolerance as an additive genetic effect, permanent environmental effect, and direct additive and permanent environmental effect. Results Below the THI threshold (≤72; no heat stress), the variance in heat tolerance was zero. However, the heat tolerance variance began to increase as THI exceeded the threshold. The covariance between the genetic additive effect and the heat tolerance effect was −0.33. Heritability estimates of milk yield ranged from 0.111 to 0.176 (average: 0.128). Heritability decreased slightly as THI increased, and began to increase at a THI of 79. The predicted bull EBV ranking varied with THI. Conclusion We conclude that genetic evaluation using the THI function could be useful for selecting bulls for heat tolerance in South Korea.

Models for Estimating Genetic Parameters of Milk Production Traits Using Random Regression Models in Korean Holstein Cattle.

The objectives of the study were to estimate genetic parameters for milk production traits of Holstein cattle using random regression models (RRMs), and to compare the goodness of fit of various RRMs with homogeneous and heterogeneous residual variances. A total of 126,980 test-day milk production records of the first parity Holstein cows between 2007 and 2014 from the Dairy Cattle Improvement Center of National Agricultural Cooperative Federation in South Korea were used. These records included milk yield (MILK), fat yield (FAT), protein yield (PROT), and solids-not-fat yield (SNF). The statistical models included random effects of genetic and permanent environments using Legendre polynomials (LP) of the third to fifth order (L3–L5), fixed effects of herd-test day, year-season at calving, and a fixed regression for the test-day record (third to fifth order). The residual variances in the models were either homogeneous (HOM) or heterogeneous (15 classes, HET15; 60 classes, HET60). A total of nine models (3 orders of polynomials×3 types of residual variance) including L3-HOM, L3-HET15, L3-HET60, L4-HOM, L4-HET15, L4-HET60, L5-HOM, L5-HET15, and L5-HET60 were compared using Akaike information criteria (AIC) and/or Schwarz Bayesian information criteria (BIC) statistics to identify the model(s) of best fit for their respective traits. The lowest BIC value was observed for the models L5-HET15 (MILK; PROT; SNF) and L4-HET15 (FAT), which fit the best. In general, the BIC values of HET15 models for a particular polynomial order was lower than that of the HET60 model in most cases. This implies that the orders of LP and types of residual variances affect the goodness of models. Also, the heterogeneity of residual variances should be considered for the test-day analysis. The heritability estimates of from the best fitted models ranged from 0.08 to 0.15 for MILK, 0.06 to 0.14 for FAT, 0.08 to 0.12 for PROT, and 0.07 to 0.13 for SNF according to days in milk of first lactation. Genetic variances for studied traits tended to decrease during the earlier stages of lactation, which were followed by increases in the middle and decreases further at the end of lactation. With regards to the fitness of the models and the differential genetic parameters across the lactation stages, we could estimate genetic parameters more accurately from RRMs than from lactation models. Therefore, we suggest using RRMs in place of lactation models to make national dairy cattle genetic evaluations for milk production traits in Korea.

Effect of Number of Lactation Records on the Selection Rates in Holstein Dairy Cattle

This experiment was conducted to investigate the effects of lactation records in Holstein dairy cattle on the selection rates using a total of 341,436 test records from 113, 812 heads of cattle from first to third lactation. Heritabilities for milk, fat, and protein yields were highest at first lactation (0.28, 0.24, and 0.27, respectively), and decreased to 0.14, 0.15, and 0.13 at third lactation. For the milk yields, phenotypic correlations between first and second lactation, first and third lactation, and second and third lactation were low (0.49, 0.39, and 0.47, respectively), while genetic correlations among consecutive lactations and between second and third were above 0.8 and 0.9. In Model I, of the 1,138 heads the top 1% were selected based on first lactation records, only 32.4% (396 heads) were re-selected when the second lactation records were included and the 67.6% (769 heads) were newly selected animals. While in Model II, 85.1% (1,138 heads) of the animals which were selected as the top 1% on the basis of first and second lactation records were included. A multiple trait evaluation method using multiple lactation records is more desirable than a single trait evaluation method using first lactation records only.

Development of Algorithm in Analysis of Single Trait Animal Model for Genetic Evaluation of Hanwoo

Estimate breeding value can be used as single trait animal model was developed directly using the Fortran language program. The program is based on data computed by using the indirect method repeatedly. The program develops a common algorithm and imprves efficiency. Algorithm efficiency was compared between the two programs. Estimated using the solution is easy to farm and brand the service, pedigree data base was associated with the development of an improved system. The existing program that uses the single trait animal model and the comparative analysis of efficiency is weak because the estimation of the solution and the conventional algorithm programmed through regular formulation involve many repetition; therefore, the newly developed algorithm was conducted to improve speed by reducing the repetition. Single trait animal model was used to analyze Gauss-Seidel iteration method, and the aforesaid two algorithms were compared thorough the mixed model equation which is used the most commonly in estimating the current breeding value by applying the procedures such as the preparation of information necessary for modelling, removal of duplicative data, verifying the parent information of based population in the pedigree data, and assigning sequential numbers, etc. The existing conventional algorithm is the method for reading and recording the data by utilizing the successive repetitive sentences, while new algorithm is the method for directly generating the left hand side for estimation based on effect. Two programs were developed to ensure the accurate evaluation. BLUPF90 and MTDFREML were compared using the estimated solution. In relation to the pearson and spearman correlation, the estimated breeding value correlation coefficients were highest among all traits over 99.5%. Depending on the breeding value of the high correlation in Model I and Model II, accurate evaluation can be found. The number of iteration to convergence was 2,568 in Model I and 1,038 in Model II. The speed of solving was 256.008 seconds in Model I and 235.729 seconds in Model II. Model II had a speed of approximately 10% more than Model I. Therefore, it is considered to be much more effective to analyze large data through the improved algorithm than the existing method. If the corresponding program is systemized and utilized for the consulting of farm and industrial services, it would make contribution to the early selection of individual, shorten the generation, and cultivation of superior groups, and help develop the Hanwoo industry further through the improvement of breeding value based enhancement, ultimately paving the way for the country to evolve into an advanced livestock country.