Seung Soo Lee

Research of Statistical Model for Genetic Evaluation of Hanwoo Carcass Traits

This study was conducted to study the environment effects on live weight, carcass weight, dressing percentage, eye muscle area, backfat thickness, and marbling score, which are the carcass traits of Hanwoo, based on the estimates and all the possible regression for the selection of variable and significance test for 231,382 heads that underwent the carcass measurements. The average and standard deviation for the live weight, carcass weight, dressing percentage, eye muscle area, backfat thickness, and marbling score were 654.79±91.61 kg, 362.30±67.15 kg, 59.52±0.03%, 81.79±12.21 cm

Inter- and intra-population genetic divergence of East Asian cattle populations: focusing on Korean cattle

In order to facilitate the on-going cattle conservation and improvement programs in Korea, we examined genetic relationships among East Asian cattle, focusing on Korean native cattle, using complete mitochondrial DNA control region sequences. In total, 67 haplotypes were discriminated by 97 variable sites in East Asian cattle. Of the variable sites, 35 represented singleton variable sites and 62 were parsimony informative sites. For Korean cattle, 30 haplotypes were discriminated by 40 variable sites. The variable sites identified in this study correspond to transition or transversion point mutations. Inter-populations genetic distance varied from 0.004 to 0.052 for East Asian cattle populations. The genetic divergence observed between Korean Brown and Jeju Black (0.004) was among the lowest. The Mongolian cattle were slightly divergent from other East Asian cattle populations studied. The network analysis uncovered that Jeju Black and Yunbian samples represented the possible ancestral Haplotype within T3 Bos taurus main lineage. Thus, we hypothesized that the Jeju and Yunbian cattle may represent one of the original native North East Asian cattle in the region.

Genetic Parameter Estimation in Seedstock Swine Population for Growth Performances

The objective of this study was to estimate genetic parameters that are to be used for across-herd genetic evaluations of seed stock pigs at GGP level. Performance data with pedigree information collected from swine breeder farms in Korea were provided by Korea Animal Improvement Association (AIAK). Performance data were composed of final body weights at test days and ultrasound measures of back fat thickness (BF), rib eye area (EMA) and retail cut percentage (RCP). Breeds of swine tested were Landrace, Yorkshire and Duroc. Days to 90 kg body weight (DAYS90) were estimated with linear function of age and ADG calculated from body weights at test days. Ultrasound measures were taken with A-mode ultrasound scanners by trained technicians. Number of performance records after censoring outliers and keeping records pigs only born from year 2000 were of 78,068 Duroc pigs, 101,821 Landrace pigs and 281,421 Yorkshire pigs. Models included contemporary groups defined by the same herd and the same seasons of births of the same year, which was regarded as fixed along with the effect of sex for all traits and body weight at test day as a linear covariate for ultrasound measures. REML estimation was processed with REMLF90 program. Heritability estimates were 0.40, 0.32, 0.21 0.39 for DAYS90, ADG, BF, EMA, RCP, respectively for Duroc population. Respective heritability estimates for Landrace population were 0.43, 0.41, 0.22, and 0.43 and for Yorkshire population were 0.36, 0.38, 0.22, and 0.42. Genetic correlation coefficients of DAYS90 with BF, EMA, or RCP were estimated to be 0.00 to 0.09, −0.15 to −0.25, 0.22 to 0.28, respectively for three breeds populations. Genetic correlation coefficients estimated between BF and EMA was −0.33 to −0.39. Genetic correlation coefficient estimated between BF and RCP was high and negative (−0.78 to −0.85) but the environmental correlation coefficients between these two traits was medium and negative (near −0.35), which describes a highly correlated genetic response to selection on one or the other of these traits. Genetic Trends of all three breeds tend to be towards bigger EMA or greater RCP and shorter DAYS90 especially from generations born after year 2000.

Estimation of Relative Economic Weights of Hanwoo Carcass Traits Based on Carcass Market Price

The objective of this study was to estimate economic weights of Hanwoo carcass traits that can be used to build economic selection indexes for selection of seedstocks. Data from carcass measures for determining beef yield and quality grades were collected and provided by the Korean Institute for Animal Products Quality Evaluation (KAPE). Out of 1,556,971 records, 476,430 records collected from 13 abattoirs from 2008 to 2010 after deletion of outlying observations were used to estimate relative economic weights of bid price per kg carcass weight on cold carcass weight (CW), eye muscle area (EMA), backfat thickness (BF) and marbling score (MS) and the phenotypic relationships among component traits. Price of carcass tended to increase linearly as yield grades or quality grades, in marginal or in combination, increased. Partial regression coefficients for MS, EMA, BF, and for CW in original scales were +948.5 won/score, +27.3 won/cm2, −95.2 won/mm and +7.3 won/kg when all three sex categories were taken into account. Among four grade determining traits, relative economic weight of MS was the greatest. Variations in partial regression coefficients by sex categories were great but the trends in relative weights for each carcass measures were similar. Relative economic weights of four traits in integer values when standardized measures were fit into covariance model were +4:+1:−1:+1 for MS:EMA:BF:CW. Further research is required to account for the cost of production per unit carcass weight or per unit production under different economic situations.

Comparison of Hanwoo Proven and Young Bulls for Major Economic Traits

2004년부터 2006년까지 상 하반기에 후대검정에 공시한 후보씨수소와 동일 시점에 판매한 보증씨수소의 표현형 및 유전 능력을 비교하였다. 12개월령 체중, 도체중 및 등심단면적의 표현형 능력의 경우 대부분 후보씨수소가 유의하게 우수하였으며, 등지방두께 표현형 능력의 경우 후보씨수소가 유의하게 두꺼웠다. 12개월령 체중, 도체중, 등심단면적, 등지방두께 및 근내지방도의 유전능력과 선발지수를 비교한 결과 후보씨수소와 보증씨수소 사이에 대부분 유의한 차이가 없었다. 후보씨수소와 1등급 보증씨수소의 유전능력을 비교한 결과 등심단면적을 제외하고는 유의한 차이가 없었다. 【This study was conducted to compare the phenotypic performance and genetic merits in terms of weight at 12 months, carcass weight, eye muscle area, backfat thickness, marbling score and selection index of Hanwoo young bulls and proven bulls from the year 2004 to 2006. The data of 208 bulls used in this study were taken from the Nnational Hanwoo genetic evaluation coordinated by National Institute of Animal Science. Hanwoo young bulls were superior in the phenotypic performance of weight at 12 months, carcass weight, and eye muscle area showing significant differences from Hanwoo proven bulls in most comparisons. The backfat thickness of Hanwoo young bulls was significantly thicker higher than Hanwoo proven bulls in all comparisons (p】

Genome-wide linkage disequilibrium and past effective population size in three Korean cattle breeds.

The routine collection and use of genomic data are useful for effectively managing breeding programs for endangered populations. Linkage disequilibrium (LD) using high-density DNA markers has been widely used to determine population structures and predict the genomic regions that are associated with economic traits in beef cattle. The extent of LD also provides information about historical events, including past effective population size (Ne ), and it allows inferences on the genetic diversity of breeds. The objective of this study was to estimate the LD and Ne in three Korean cattle breeds that are genetically similar but have different coat colors (Brown, Brindle and Jeju Black Hanwoo). Brindle and Jeju Black are endangered breeds with small populations, whereas Brown Hanwoo is the main breeding population in Korea. DNA samples from these cattle breeds were genotyped using the Illumina BovineSNP50 Bead Chip. We examined 13 cattle breeds, including European taurines, African taurines and indicines, and hybrids to compare their LD values. Brown Hanwoo consistently had the lowest mean LD compared to Jeju Black, Brindle and the other 13 cattle breeds (0.13, 0.19, 0.21 and 0.15-0.22 respectively). The high LD values of Brindle and Jeju Black contributed to small Ne values (53 and 60 respectively), which were distinct from that of Brown Hanwoo (531) for 11 generations ago. The differences in LD and Ne for each breed reflect the breeding strategy applied. The Ne for these endangered cattle breeds remain low; thus, effort is needed to bring them back to a sustainable tract.

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.

Polymorphisms of the Exons 13, 15 and 16 of Transferrin Gene in Cheju Horses

This study was conducted to determine the polymorphism of transferrin exons 13, 15 and 16 by Single-Strand Conformation Polymorphism(SSCP) analysis and to compare their genotypes of Cheju horse Group I (Cheju Institute), Cheju horse Group II (farms), and Thoroughbred (KRA). SSCP of transferrin exon 13, 15, and 16 showed two (A, B), three (A, B, C) and three (A, B, C) codominant alleles, respectively. The Group I and Thoroughbred showed the similar frequencies of allele A and B in transferrin exon 13, but only allele A was observed in Group Ⅱ. In transferrin exons 15 and 16, the frequencies of each allele were different in each Groups. The multiple allele frequencies in exons 15 and 16 suggested that the genotyping of this locus could be used to identify an individual and to test the parentage of offspring. The probability for parentage exclusion were 0.46 and 0.374 for exons 15 and 16 for Cheju horse Group I. Among the 13 combined genotypes of exons 13, 15 and 16, the genotype AA-AB-AB (0.372) is the most common in Cheju horse Group I, but genotype AA-AA-AA is common in the Cheju horse Group II (0.366) and Thoroughbred (0.767). The present study showed two new SNP, which was at the cDNA position 1626 (A/G) in B allele of the exon 13 and 2075 (C/T) in C allele of the exon 16 resulting in amino acid change (Threonine Methionine). Result showed that polymorphism of exons 13, 15 and 16 in Cheju horses was as high as in Thoroughbred and there was a differences of transferrin allele frequencies in Cheju horses.

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.

Studies on Genetic Diversity and Phylogenetic relationships of Chikso (Korea Native Brindle Cattle) Using the Microsatellite Marker

This study examined the genetic distance among Chikso (Korea native brindle cattle) in nine regional areas using allele frequencies and a genetic diversity analysis with microsatellite markers. The analysis of the genetic diversity and genetic relationships of 2068 Chikso (383 KW, 180 GG, 52 KN, 129 KB, 332 UL, 24 JN, 198 JB, 148 CN, 622 CB) was carried out using 11 microsatellite markers. The number of alleles, observed heterozygostiy (Hobs), expected heterozygosity (Hexp), and polymorphism information content (PIC) of the 11 microsatellite markers were 8–24, 0.672–0.834, 0.687–0.886, and 0.638–0.876, respectively. The expected probability of identity values in random individuals (PI), random half-sib (PIhalf-sibs), and random sibs (PIsibs) were estimated to be 5.24×10 , 2.63×10, and 2.63× 10, respectively, indicating that these markers can be used for traceability systems in Chikso cattle. The results of a phylogenetic tree (neighbor-joining tree), principle component analysis (PCA), and factorial component analysis (FCA) revealed genetic distance among nine Chikso populations. In conclusion, this study provides useful basic data that can be utilized in Chikso breeding and development. In addition, we will have to manage and conserve as a valuable genetic resource, without losing diversity of Chikso.This study examined the genetic distance among Chikso (Korea native brindle cattle) in nine regional areas using allele frequencies and a genetic diversity analysis with microsatellite markers. The analysis of the genetic diversity and genetic relationships of 2068 Chikso (383 KW, 180 GG, 52 KN, 129 KB, 332 UL, 24 JN, 198 JB, 148 CN, 622 CB) was carried out using 11 microsatellite markers. The number of alleles, observed heterozygostiy (Hobs), expected heterozygosity (H exp ), and polymorphism information content (PIC) of the 11 microsatellite markers were 8?24, 0.672?0.834, 0.687?0.886, and 0.638?0.876, respectively. The expected probability of identity values in random individuals (PI), random half-sib (PI half-sibs ), and random sibs (PI sibs ) were estimated to be 5.24×10 -19 , 2.63×10 -06 , and 2.63× 10 -06 , respectively, indicating that these markers can be used for traceability systems in Chikso cattle. The results of a phylogenetic tree (neighbor-joining tree), principle component analysis (PCA), and factorial component analysis (FCA) revealed genetic distance among nine Chikso populations. In conclusion, this study provides useful basic data that can be utilized in Chikso breeding and development. In addition, we will have to manage and conserve as a valuable genetic resource, without losing diversity of Chikso.