Yun Ho Choy

Proteins in longissimus muscle of Korean native cattle and their relationship to meat quality

Proteomic profiling by two-dimensional gel electrophoresis and mass spectrometry of longissimus dorsi muscle tissue from Korean native cattle identified seven proteins that are differentially expressed in animals producing low and high quality grade beef. The expression level of alpha actin is increased in high quality grade beef and the expression levels of T-complex protein 1 (TCP-1), heat shock protein beta-1 (HSP27), and inositol 1,4,5-triphosphate receptor type1 (IP3R1), a new protein to be associated with meat quality, are increased in low quality grade beef. In particular, the quantitation of HSP27 and IP3R1 by both silver staining and immunoblotting correlated well with intramuscular fat content, meat tenderness, and free calcium levels. The data suggest that HSP27 and IP3R1 are potential meat quality biomarkers and their identification provides new insight into the molecular mechanisms and pathways associated with overall beef quality.

Whole-genome resequencing of Hanwoo (Korean cattle) and insight into regions of homozygosity

BackgroundHanwoo (Korean cattle), which originated from natural crossbreeding between taurine and zebu cattle, migrated to the Korean peninsula through North China. Hanwoo were raised as draft animals until the 1970s without the introduction of foreign germplasm. Since 1979, Hanwoo has been bred as beef cattle. Genetic variation was analyzed by whole-genome deep resequencing of a Hanwoo bull. The Hanwoo genome was compared to that of two other breeds, Black Angus and Holstein, and genes within regions of homozygosity were investigated to elucidate the genetic and genomic characteristics of Hanwoo.ResultsThe Hanwoo bull genome was sequenced to 45.6-fold coverage using the ABI SOLiD system. In total, 4.7 million single-nucleotide polymorphisms and 0.4 million small indels were identified by comparison with the Btau4.0 reference assembly. Of the total number of SNPs and indels, 58% and 87%, respectively, were novel. The overall genotype concordance between the SNPs and BovineSNP50 BeadChip data was 96.4%. Of 1.6 million genetic differences in Hanwoo, approximately 25,000 non-synonymous SNPs, splice-site variants, and coding indels (NS/SS/Is) were detected in 8,360 genes. Among 1,045 genes containing reliable specific NS/SS/Is in Hanwoo, 109 genes contained more than one novel damaging NS/SS/I. Of the genes containing NS/SS/Is, 610 genes were assigned as trait-associated genes. Moreover, 16, 78, and 51 regions of homozygosity (ROHs) were detected in Hanwoo, Black Angus, and Holstein, respectively. ‘Regulation of actin filament length’ was revealed as a significant gene ontology term and 25 trait-associated genes for meat quality and disease resistance were found in 753 genes that resided in the ROHs of Hanwoo. In Hanwoo, 43 genes were located in common ROHs between whole-genome resequencing and SNP chips in BTA2, 10, and 13 coincided with quantitative trait loci for meat fat traits. In addition, the common ROHs in BTA2 and 16 were in agreement between Hanwoo and Black Angus.ConclusionsWe identified 4.7 million SNPs and 0.4 million small indels by whole-genome resequencing of a Hanwoo bull. Approximately 25,000 non-synonymous SNPs, splice-site variants, and coding indels (NS/SS/Is) were detected in 8,360 genes. Additionally, we found 25 trait-associated genes for meat quality and disease resistance among 753 genes that resided in the ROHs of Hanwoo. These findings will provide useful genomic information for identifying genes or casual mutations associated with economically important traits in cattle.

Genetic Analysis of Carcass Traits in Hanwoo with Different Slaughter End-points

Y.H.Choy*,H.B.Yoon*,S.B.Choi*andH.W.Chung**HanwooExperimentStationofNationalLivestockResearchInstitute,Pyongchang*DepartmentofAnimalHusbandry,ChonanYonamCollegeofAgriculture,Chonan**적 요한우의성장과도체형질에대한유전능력평가모형을개발하기위해 가지공분산모형을적용하4여후대검정에공시된수소와거세수소의자료에대한표현형및유전자형에대한분산 공분산을－추정하였다 가지모형은검정소와검정차수로구분한동기그룹의고정효과와임의효과인종모우효. 4과로구성된부계반형매모형을적용하였다 도체형질에대해서는 가지공변량을추가하였는데모. 4형 에는도축일령의 차식효과를 모형 에는도축연령의 차와 차식효과를사용하였고 모형 에1 1 , 2 1 2 , 3는절식체중을모형 에는등지방두께를각기 차식공변량으로사용하였다 도축일령의 차식효과4 1 . 2는유의적이지않았으나도축일령에대한회귀로인하여 개도체형질에대한유전분산 공분산성4 －분에큰차이를보였다 도축일령을공변량으로하였을때등지방두께 등심단면적 도체중 근내지. , , ,방도와도체율에대한유전력은각기 로추정되었다 도체중과다른도체형0.34, 0.22, 0.24, 0.42, 0.18 .질간에는정 의유전상관을보였으나등지방두께와등심단면적그리고근내지방도와도체율간에(+) , ,는낮은부 의유전상관을보였다 절식체중에대한회귀는도체중에대한유전분산과타도체형( ) .－질과의유전공분산을감소시켰으며등지방두께에대한회귀는등심단면적에대한유전분산과등심,단면적과도체중간의유전공분산을증가시켰다 절식체중이나등지방두께를공변량으로한모형으.로부터추정된분산 공분산성분은도축일령을공변량으로했을때와상이한구조를보였는데 이－ ,들두가지공변량은골격 근육 지방조직으로구성되는신체부분적발달정도와관련이있는것－ －으로판단된다.(Keywords :Hanwoo,Heritability,Correlation,Carcasstraits,Differentialgrowth)

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.

Genetic Relationship Between Weaning Weight and Carcass Traits in Hanwoo

ABSTRACT The objective of this study was to evaluate the genetic relationship between weaning weight (WW) and carcass traits. Carcass traits were eye muscle area (EMA), back fat thickness (BFT), marbling score 1 (MS1) in 21 grade scales, marbling score 2 (MS2) in 7 grade scales and meat color scores (Mcolor). Parameters were estimated by REML procedure with MTDFREML package. Models included contemporary group as defined by the same year-season-sex at birth, linear covariates of age (days) at weaning, age of dam (days) and age at slaughter (days) as fixed effects and animal random effects for all the traits. Heritability estimates of WW, EMA, BFT, MS1, MS2 and Mcolor were 0.25, 0.20, 0.20, 0.32, 0.32 and 0.22, respectively. Genetic(phenotypic) correlation coefficients of WW with EMA, BFT, MS1, MS2 and Mcolor were 0.75(0.16), 0.18 (0.05), 0.41 ( 0.09), 0.40 (0.11) and 0.07 (0.05), respectively. Results from this study suggest that single trait selection for weaning weight would lead to progeny population having carcass with large EMA, thick BFT and decreased MS.(

Genetic Parameters of Pre-adjusted Body Weight Growth and Ultrasound Measures of Body Tissue Development in Three Seedstock Pig Breed Populations in Korea

The objective of this study was to compare the effects of body weight growth adjustment methods on genetic parameters of body growth and tissue among three pig breeds. Data collected on 101,820 Landrace, 281,411 Yorkshire, and 78,068 Duroc pigs, born in Korean swine breeder farms since 2000, were analyzed. Records included body weights on test day and amplitude (A)-mode ultrasound carcass measures of backfat thickness (BF), eye muscle area (EMA), and retail cut percentage (RCP). Days to 90 kg body weight (DAYS90), through an adjustment of the age based on the body weight at the test day, were obtained. Ultrasound measures were also pre-adjusted (ABF, EMA, AEMA, ARCP) based on their test day measures. The (co)variance components were obtained with 3 multi-trait animal models using the REMLF90 software package. Model I included DAYS90 and ultrasound traits, whereas model II and III accounted DAYS90 and pre-adjusted ultrasound traits. Fixed factors were sex (sex) and contemporary groups (herd-year-month of birth) for all traits among the models. Additionally, model I and II considered a linear covariate of final weight on the ultrasound measure traits. Heritability (h2) estimates for DAYS90, BF, EMA, and RCP ranged from 0.36 to 0.42, 0.34 to 0.43, 0.20 to 0.22, and 0.39 to 0.45, respectively, among the models. The h2 estimates of DAYS90 from model II and III were also somewhat similar. The h2 for ABF, AEMA, and ARCP were 0.35 to 0.44, 0.20 to 0.25, and 0.41 to 0.46, respectively. Our heritability estimates varied mostly among the breeds. The genetic correlations (rG) were moderately negative between DAYS90 and BF (−0.29 to −0.38), and between DAYS90 and EMA (−0.16 to −0.26). BF had strong rG with RCP (−0.87 to −0.93). Moderately positive rG existed between DAYS90 and RCP (0.20 to 0.28) and between EMA and RCP (0.35 to 0.44) among the breeds. For DAYS90, model II and III, its correlations with ABF, AEMA, and ARCP were mostly low or negligible except the rG between DAYS90 and AEMA from model III (0.27 to 0.30). The rG between AEMA and ABF and between AEMA and ARCP were moderate but with negative and positive signs, respectively; also reflected influence of pre-adjustments. However, the rG between BF and RCP remained non-influential to trait pre-adjustments or covariable fits. Therefore, we conclude that ultrasound measures taken at a body weight of about 90 kg as the test final should be adjusted for body weight growth. Our adjustment formulas, particularly those for BF and EMA, should be revised further to accommodate the added variation due to different performance testing endpoints with regard to differential growth in body composition.

Genetic correlation between live body measurements and beef cutability traits in Hanwoo steers

Objective The growth, carcass and retail cut yield records on 1,428 Hanwoo steers obtained through progeny testing were analyzed in this study, and their heritability and genetic relationships among the traits were estimated using animal models. Methods Two different models were compared in this study. Each model was fitted for different fixed class effects, date of slaughter for carcass traits and batch of progeny test live measurement traits, and a choice of covariates (carcass weight in Model 1 or backfat thickness in Model 2) for carcass traits. Results The differences in body composition among individuals were deemed being unaffected by their age at slaughter, except for carcass weight and backfat thickness. Heritability estimates of body size measurements were 0.21 to 0.36. Heritability estimates of retail cut percentage were high (0.56 from Model 1 and 0.47 from Model 2). And the heritability estimates for loin muscle percentage were 0.36 from Model 1 and 0.42 from Model 2, which were high enough to consider direct selection on carcass cutability traits as effective. The genetic correlations between body size measurements and retail cut ratio (RCR) were close to zero. But, some negative genetic correlations were found with chest girths measured at yearling (Model 1) or at 24 months of age or with chest widths. Loin muscle ratio (LMR) was genetically negatively correlated with body weights or body size measurements, in general in Model 1. These relationships were low close to zero but positive in Model 2. Phenotypic correlation between cutability traits (RCR, LMR) and live body size measurements were moderate and negative in Model 1 while those in Model 2 were all close to zero. Conclusion Therefore, the body weights or linear body measurements at an earlier age may not be the most desirable selection traits for exploitation of correlated responses to improve loin muscle or lean meat yield.

Genetic Parameters of Calving Ease using Sire-Maternal Grandsire Model in Korean Holsteins

Objective Calving ease (CE) is a complex reproductive trait of economic importance in dairy cattle. This study was aimed to investigate the genetic merits of CE for Holsteins in Korea. Methods A total of 297,614 field records of CE, from 2000 to 2015, from first parity Holstein heifers were recorded initially. After necessary data pruning such as age at first calving (18 to 42 mo), gestation length, and presence of sire information, final datasets for CE consisted of 147,526 and 132,080 records for service sire calving ease (SCE) and daughter calving ease (DCE) evaluations, respectively. The CE categories were ordered and scores ranged from CE1 to CE5 (CE1, easy; CE2, slight assistance; CE3, moderate assistance; CE4, difficult calving; CE5, extreme difficulty calving). A linear transformation of CE score was obtained on each category using Snell procedure, and a scaling factor was applied to attain the spread between 0 (CE5) and 100% (CE1). A sire-maternal grandsire model analysis was performed using ASREML 3.0 software package. Results The estimated direct heritability (h2) from SCE and DCE evaluations were 0.11±0.01 and 0.08±0.01, respectively. Maternal h2 estimates were 0.05±0.02 and 0.04±0.01 from SCE and DCE approaches, respectively. Estimates of genetic correlations between direct and maternal genetic components were −0.68±0.09 (SCE) and −0.71±0.09 (DCE). The average direct genetic effect increased over time, whereas average maternal effect was low and consistent. The estimated direct predicted transmitting ability (PTA) was desirable and increasing over time, but the maternal PTA was undesirable and decreasing. Conclusion The evidence on sufficient genetic variances in this study could reflect a possible selection improvement over time regarding ease of calving. It is expected that the estimated genetic parameters could be a valuable resource to formulate sire selection and breeding plans which would be directed towards the reduction of calving difficulty in Korean Holsteins.

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.