Parameter estimation and assessment of bias in genetic evaluation of carcass traits in Hanwoo cattle using real and simulated data

Mohammed Bedhane,Julius van der Werf,Sara de las Heras-Saldana,Leland Ackerson IV,Dajeong Lim,박병호,박미나,Seung-Hee Roh,Samuel Clark 한국축산학회 2023 한국축산학회지 Vol.65 No.6

Most carcass and meat quality traits are moderate to highly heritable, indicating that they can be improved through selection. Genetic evaluation for these types of traits is performed using performance data obtained from commercial and progeny testing evaluation. The performance data from commercial farms are available in large volume, however, some drawbacks have been observed. The drawback of the commercial data is mainly due to sorting of animals based on live weight prior to slaughter, and this could lead to bias in the genetic evaluation of later measured traits such as carcass traits. The current study has two components to address the drawback of the commercial data. The first component of the study aimed to estimate genetic parameters for carcass and meat quality traits in Korean Hanwoo cattle using a large sample size of industry-based carcass performance records (n = 469,002). The second component of the study aimed to describe the impact of sorting animals into different contemporary groups based on an early measured trait and then examine the effect on the genetic evaluation of subsequently measured traits. To demonstrate our objectives, we used real performance data to estimate genetic parameters and simulated data was used to assess the bias in genetic evaluation. The results of our first study showed that commercial data obtained from slaughterhouses is a potential source of carcass performance data and useful for genetic evaluation of carcass traits to improve beef cattle performance. However, we observed some harvesting effect which leads to bias in genetic evaluation of carcass traits. This is mainly due to the selection of animal based on their body weight before arrival to slaughterhouse. Overall, the non-random allocation of animals into a contemporary group leads to a biased estimated breeding value in genetic evaluation, the severity of which increases when the evaluation traits are highly correlated.

Genetic parameters and correlations of related feed efficiency, growth, and carcass traits in Hanwoo beef cattle

Mehrban, Hossein,Naserkheil, Masoumeh,Lee, Deuk Hwan,Ibanez-Escriche, Noelia Asian Australasian Association of Animal Productio 2021 Animal Bioscience Vol.34 No.5

Objective: This study aimed to estimate the genetic parameters and genetic correlations for related feed efficiency, growth, and carcass traits in Hanwoo cattle. Methods: Phenotypic data from 15,279 animals born between 1989 and 2015 were considered. The related feed efficiency traits considered were Kleiber ratio (KR) and relative growth rate (RGR). Carcass traits analyzed were backfat thickness (BT), carcass weight, eye muscle area, and marbling score. Growth traits were assessed by the average daily gain (ADG), metabolic body weight (MBW) at mid-test age from 6 to 24 months, and yearling weight (YW). Variance and covariance components were estimated using restricted maximum likelihood using nine multi-trait animal models. Results: The heritability estimates for related feed efficiency (0.28±0.04 for KR and RGR) and growth traits (0.26±0.02 to 0.33±0.04) were moderate, but the carcass traits tended to be higher (0.38±0.04 to 0.61±0.06). The related feed efficiency traits were positively genetically correlated with all the carcass traits (0.37±0.09 to 0.47±0.07 for KR, and 0.14±0.09 to 0.37±0.09 for RGR), except for BT, which showed null to weak correlation. Conversely, the genetic correlations of RGR with MBW (-0.36±0.08) and YW (-0.30±0.08) were negative, and those of KR with MBW and YW were close to zero, whereas the genetic correlations of ADG with RGR (0.40±0.08) and KR (0.70±0.05) were positive and relatively moderate to high. The genetic (0.92±0.02) correlations between KR and RGR were very high. Conclusion: Sufficient genetic variability and heritability were observed for traits of interest. Moreover, the inclusion of KR and/or RGR in Hanwoo cattle breeding programs could improve the feed efficiency without producing any unfavorable effects on the carcass traits.

Comparison of genomic predictions for carcass and reproduction traits in Berkshire, Duroc and Yorkshire populations in Korea

Asif Iqbal,최태정,김유삼,이윤미,M. Zahagir Alam,정종현,최호성,김종주 아세아·태평양축산학회 2019 Animal Bioscience Vol.32 No.11

Objective: A genome-based best linear unbiased prediction (GBLUP) method was applied to evaluate accuracies of genomic estimated breeding value (GEBV) of carcass and reproductive traits in Berkshire, Duroc and Yorkshire populations in Korean swine breeding farms. Methods: The data comprised a total of 1,870, 696, and 1,723 genotyped pigs belonging to Berkshire, Duroc and Yorkshire breeds, respectively. Reference populations for carcass traits consisted of 888 Berkshire, 466 Duroc, and 1,208 Yorkshire pigs, and those for reproductive traits comprised 210, 154, and 890 dams for the respective breeds. The carcass traits analyzed were backfat thickness (BFT) and carcass weight (CWT), and the reproductive traits were total number born (TNB) and number born alive (NBA). For each trait, GEBV accuracies were evaluated with a GEBV BLUP model and realized GEBVs. Results: The accuracies under the GBLUP model for BFT and CWT ranged from 0.33-0.72 and 0.33-0.63, respectively. For NBA and TNB, the model accuracies ranged 0.32 to 0.54 and 0.39 to 0.56, respectively. The realized accuracy estimates for BFT and CWT ranged 0.30 to 0.46 and 0.09 to 0.27, respectively, and 0.50 to 0.70 and 0.70 to 0.87 for NBA and TNB, respectively. For the carcass traits, the GEBV accuracies under the GBLUP model were higher than the realized GEBV accuracies across the breed populations, while for reproductive traits the realized accuracies were higher than the model based GEBV accuracies. Conclusion: The genomic prediction accuracy increased with reference population size and heritability of the trait. The GEBV accuracies were also influenced by GEBV estimation method, such that careful selection of animals based on the estimated GEBVs is needed. GEBV accuracy will increase with a larger sized reference population, which would be more beneficial for traits with low heritability such as reproductive traits.

한우 도체형질 관련 분자표지의 유전적 효과

신성철(Sung-Chul Shin),정의룡(Eui-Ryong Chung) 한국생명과학회 2020 생명과학회지 Vol.30 No.3

한우에서의 도체형질은 경제적으로 가장 중요한 형질이다. 최근 유전체학의 발달로 인해 DNA 표지인자 이용하여 소의 도체 및 육질형질을 규명하고 선발하는 방법이 주목 받고 있다. 본 연구는 한우의 도체형질 관련 분자표지의 현장 검증에 의한 유전적 효과를 평가하기 위해 수행하였다. TG g.371T>C, APM1 g.1454G>A, FABP4 g.2834C>G, FABP4 g.3533T>A, FABP4 g.3691G>A, SCD g.10153A>G, SCD g.10329T>C, CPE g.601T>C, EDG1 g.166A>G, NPY g.4271T>C, GPD1 g.2766C>T, PDE1B g.17122A>G, PDE1B g.17507A>C, TNNT1 g.6650C>T 및 RORC g.20152A>G 등 총 15개의 도체형질 관련 분자표지들에 대해 대규모 상업축 한우 집단(총 1,536두)을 대상으로 SNP 유전자형 분석을 수행하고, 분자표지와 도체형질과의 연관성을 조사하였다. PCR-RFLP 분석을 통해 SNP 유전자형과 도체형질과의 연관성을 분석한 결과 APM1 g.1454G>, FABP4 g.3691G>A, SCD g.10153A>G, CPE g.601T>C, PDE1B g.17122A>G, TNNT1 g.6650C>T 및 RORC g.20152A>G 등 총 7개의 SNP가 한우의 도체형질 가운데 근내지방도, 등지방두께, 배최장근단면적, 도체중, 육질등급, 육색 및 성숙도 등과 유의적으로 연관되어 있음을 확인하였다. 본 연구 결과는 이들 SNP가 육질이 우수한 한우 선발을 위한 분자표지로 활용될 수 있음을 시사한다. Carcass traits are the most economically important traits in Hanwoo (Korean cattle). Recently, the development of the field of genomics has made it possible to identify DNA markers for the genetic evaluation of carcass and meat quality traits in beef cattle. The objective of this study was to assess the genetic effects of single nucleotide polymorphism (SNP) markers related to carcass traits by field evaluations in a commercial Hanwoo population. We evaluated 15 SNP markers (TG g.371T>C, APM1 g.1454G>A, FABP4 g.2834C>G, FABP4 g.3533T>A, FABP4 g.3691G>A, SCD g.10153A>G, SCD g.10329T>C, CPE g.601T>C, EDG1 g.166A>G, NPY g.4271T>C, GPD1 g.2766C>T, PDE1B g.17122A>G, PDE1B g.17507A>C, TNNT1 g.6650C>T, and RORC g.20152A>G) related to carcass traits in Hanwoo. Genotyping of these SNP markers was performed using PCR-RFLP analysis in Hanwoo steers (n = 1,536) to evaluate their association with carcass traits. Seven SNPs, APM1 g.1454G>, FABP4 g.3691G>A, SCD g.10153A>G, CPE g.601T>C, PDE1B g.17122A>G, TNNT1 g.6650C>T, and RORC g.20152A>G, were significantly associated with carcass traits such as marbling score (MS), backfat thickness (BF), musculus longissimus dorsi area (LDA), carcass weight (CW), meat grade (MG), meat color (MC), and maturity score (MA). The results suggest that these SNPs may be used as DNA markers for the selection of Hanwoo with higher meat quality.

Effect of errors in pedigree on the accuracy of estimated breeding value for carcass traits in Korean Hanwoo cattle

Nwogwugwu Chiemela Peter,김영국,Chung Yun Ji,Jang Sung Bong,Roh Seung Hee,김시동,이준헌,최태정,이승환 아세아·태평양축산학회 2020 Animal Bioscience Vol.33 No.7

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 cm2, 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.

비거세 한우 집단에 있어 성장형질과 도체형질에 대한 유전모수의 추정

박철진,박영일 한국동물자원과학회 2003 한국축산학회지 Vol.45 No.1

본 연구는 농협중앙회 가축개량사업소와 한우개량단지에서 생산된 비거세 한우 숫소 3,415두의 자료를 이용하여 성장형질과 도체형질에 대한 유전모수를 추정하기 위하여 실시하였다. 본 연구에 이용된 한우 집단은 상반기와 하반기의 두 집단으로 구분하였는데 상반기 집단은 1986년부터 1990년까지 생산된 숫소 1,592두로서 6개월에 검정개시하여 18개월에 종료하였고, 단방식 우사에서 개체관리를 하였다. 하반기 집단은 1991년부터 1996년까지 출생한 1,823두로 10개월에 검정개시하여 22개월에 종료하였고, 군사식 우사에서 사양관리 하였다. 6∼12개월과 12∼18개월 일당증체량은 상반기 집단의 경우 1.01kg과 0.77kg이였고, 하반기 집단은 0.80kg과 0.95kg으로 하반기 집단에서 보상성장이 일어난 것으로 사료된다. 12개월 및 18개월 체중의 유전력은 상반기 집단의 경우 0.37 및 0.29이었고, 하반기 집단은 0.47 및 0.33이었으며, 6∼12개월 및 12∼18개월 일당증체량의 유전력은 상반기 집단에서 0.26 및 0.11이었고, 하반기 집단은 0.33 및 0.22으로 이들 형질의 유전력은 하반기에서 높았다. 상반기 집단위 12개월령 체고, 십자부고, 곤폭 및 흉위에 대한 유전력은 각각 0.30, 0.25, 0.11 및 0.13이었으며, 하반기의 경우 각각 0.53, 0.44, 0.36 및 0.56이었다. 상반기 집단의 18개월령 체고, 십자부고, 곤폭 및 흉위의 유전력은 각각 0.40, 0.22, 0.12 및 0.21이었고, 하반기의 경우 각각 0.45, 0.42, 0.42 및 0.35이었다. 상반기 집단의 냉도체중, 도체율, 배최장근단면적, 등지방두께 및 도체장에 대한 유전력은 각각 0.11, 0.24, 0.25, 0.18 및 0.21이었고, 하반기 집단의 경우 각각 0.32, 0.52, 0.33, 0.51 및 0.58이었으며, 근내지방도의 유전력은 0.31이었다. 상·하반기간 유전상관의 추정치는 12개월 흉위, 18개월 십자부고, 도체중 및 도체율의 경우 0.8 이상이었으나 다른 형질에서의 추정치는 이보다 낮았다. Genetic parameters for growth and carcass traits were estimated on the basis of the data from 3,415 heads of Hanwoo bulls tested at Livestock Improvement Main Center. The data were divided into two groups : the first period group consisted of 1,592 heads of bulls tested in individual pens from 1986 to 1990 and the second period group consisted of 1,823 heads of bulls tested in group pens from 1991 to 1996. The testing period was from 6 to 18 months of age in the first period group and 10 to 22 months of age in the second period group. The average daily gains during 6 to 12 months and 12 to 18 months were 1.01㎏and 0.77㎏, respectively, in the first period group and 0.80㎏ and 0.95㎏ in the second period group, and the compensated growth appeared to have occurred in the second period group. The heritability of body weight at 12 months estimated was 0.37 during the first period and 0.47 during the second period. The heritability of body weight at 18 months was 0.29 during the first period and 0.33 during the second period. The heritability of average daily gain during 6~12 months estimated was 0.26 for the first period and 0.33 for the second period. The heritability of average daily gain during 12~18 months estimated was 0.11 for the first period and 0.22 the second period. The heritabilities of body weights and average daily gains estimated tended to be higher in the second period than in the first period. The heritability of body measurements at 12 months during the first period estimated was 0.30 for withers height, 0.25 for rump height, 0.11 for thurls width and 0.13 for chest girth. The heritability of body measurments at 12 months during the second period was 0.53 for withers height, 0.44 for rump height, 0.36 for thruls width and 0.56 chest girth. The heritabilities of withers height, rump height, thurls width and chest girth at 18 months of age were 0.40, 0.22, 0.12 and 0.21 during the first period and 0.45, 0.42, 0.42 and 0.35 during the second period, respectively. The heritability of carcass traits estimated during the first period was 0.11 for carcass weight, 0.24 for dressing percent, 0.25 for eye muscle area, 0.18 for backfat thickness and 0.21 for carcass length. The heritabilities of carcass weight, dressing percent, eye muscle area, backfat thickness, carcass length and marbling score during the second period estimated were 0.32, 0.52, 0.33, 0.51, 0.58 and 0.31, respectively. The genetic correlations between the first and second periods estimated were higher than 0.8 for chest girth at 12 months, rump height at 18 months, carcass weight and dressing percent, but were lower for other traits.

지속가능한 친환경 한우 사양 전략 수립을 위한 일당증체량과 도체 특성에 관한 상관성

박명선 ( Park Myungsun ),전은정 ( Jeon Eunjeong ),한재규 ( Han Jaekyu ),김정용 ( Kim Joung-yong ),원미영 ( Won Mi-young ) 한국유기농업학회 2021 韓國有機農業學會誌 Vol.29 No.1

The present study investigated the effect of average daily gain (ADG) on carcass traits of Hanwoo steers. A total of 233 heads of Hanwoo steer slaughtered from 2017 to 2020 were employed in the analysis. Their body weight profiles during feedlot and carcass traits were used. The entire feedlot period is split into two periods. ADG during the first period (ADG1) was then defined as an independent variable in statistical analysis. In the meantime, it was examined that how the cutoff month for the period split altered the significance of the effect of ADG1 on carcass traits. Subsequently, steers were assigned to two groups (High vs. Low) based on the median of total ADG1, and we compared the carcass traits of each group using a linear mixed model. ADG1 during 10 to 23 months showed a significant effect on all carcass traits except the marbling score. ADG1 significantly influenced carcass weight and eye muscle area of Hanwoo steers. And it was found that greater ADG1 could get greater carcass weight and eye muscle area (p<0.001). The result of this study provides preliminary information for the target month in the calculation of ADG1 mostly influencing carcass performance, and feeding strategy of Hanwoo steer in terms of sustainability.

Effect of Single Nucleotide Polymorphisms of Acetyl-CoA Carboxylase α(ACACA) Gene on Carcass Traits in Hanwoo (Korean Cattle)

Shin, Sung-Chul,Heo, Jae-Pil,Chung, Eui-Ryong Asian Australasian Association of Animal Productio 2011 Animal Bioscience Vol.24 No.6

Meat production and quality traits in beef cattle are largely affected by genetic factors. Acetyl-Coenzyme A carboxylase-${\alpha}$ (ACACA) plays a key role in the regulation and metabolism of fatty acid biosynthesis in mammalian animals. The gene encoding ACACA enzyme was chosen as a candidate gene for carcass and meat traits. In this study, we investigated effects of single nucleotide polymorphisms (SNPs) in the ACACA gene on beef carcass and meat traits in Hanwoo (Korean cattle) populations. We have sequenced a fragment of intron I region of the Hanwoo ACACA gene and identified two SNPs. Genotyping of the two SNP markers (g.2344T>C and g.2447C>A) was carried out using PCR-SSCP analysis in 309 Hanwoo steers to evaluate their association with carcass and meat production traits. The g.2344C SNP marker showed a significant increasing effect on LW (p = 0.009) and CW (p = 0.017). Animals with the CC genotype had higher CW and LW compared with TT and TC genotypes (p<0.05). The g.2447A SNP marker was associated with higher MC (p = 0.019). Animals with the AA genotype had higher MC than animals with CC and CA genotypes (p<0.05). Although the degree of linkage disequilibrium (LD) was not strong between g.2344T>C and g.2447C>A in the LD analysis, four major haplotype classes were formed with two SNP information within the ACACA gene. We constructed haplotypes using the HaploView software package program and analyzed association between haplotypes and carcass traits. The haplotype of ACACA gene significantly affected the LW (p = 0.027), CW (p = 0.041) and MC (p = 0.036). The effect of h1 haplotype on LW and CW was larger than that of h3 haplotype. Animals with the h1 haplotype also had greater MC than did animals with h2 haplotype. Consequently, the ACACA gene could be useful as a DNA marker for meat production traits such as carcass yield and meat contents in Hanwoo.

유전 및 육종 : 한우 도체형질의 유전능력평가를 위한 통계모형 탐색

구양모 ( Yang Mo Koo ),김시동 ( Si Dong Kim ),김정일 ( Jung Il Kim ),송치은 ( Chi Eun Song ),이기환 ( Ki Hwam Lee ),정용호 ( Yeoung Ho Jeoung ),이재윤 ( Jae Youn Lee ),장현기 ( Hyun Gi Jang ),박병호 ( Byoung Ho Park ),최태정 ( Te 한국동물자원과학회(구 한국축산학회) 2011 한국축산학회지 Vol.53 No.4

2006년부터 2009년까지 축산물품질평가원에서 등급 판정된 도체성적이 있는 개체와 한국종축개량협회에 등록이 확인된 231,382두의 자료를 이용하여 각 도체형질의 자료구조 분석 등을 살펴보고, 각 요인별로 도체형질에 어떠한 영향을 주는 지에 대한 환경효과 등을 분석하고, 변수선택법 등을 이용하여 향후 유전능력평가에서 사용 가능한 통계모형 찾아내고자 실시하였다. 한우 암, 수, 거세를 포함한 전체집단에서 출하체중, 도체율, 등지방두께, 근내지방도에서 정규분포를 보이고 있었고, 다른 형질은 정규분포에 근접함을 확인할 수 있었다. 각 요인에 대한 분산분석에서는 한우 도체형질에 대하여 성별, 출생년도-계절, 도축년도-계절, 출생지역, 도축일령의 모두 고도의 유의성(p<0.01)이 인정되었다. 변수선택법을 이용한 모형적합도 검정에서는 출하체중, 도체중, 도체율, 배최장근단면적은 다섯 가지 환경효과를 선택하는 것이 최적이었고, 등지방두께와 근내지방도는 네 가지 환경효과를 고려하는 것이 최적이었지만, 다형질 분석으로 한 번에 분석을 하기 위해서는 다섯 가지 환경효과를 함께 고려하는 것이 적합하다고 사료된다. 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±91.61kg, 362.30±67.15kg, 59.52±0.03%, 81.79±12.21cm², 11.39±5.40mm, 4.38±2.29, respectively. The live weight, carcass weight, dressing percentage, eye muscle area, backfat thickness, and marbling score for cow were 532.79±78.38kg, 313.40±44.90kg, 56.50±0.03%, 75.24±10.69cm², 11.82±5.10mm, 4.30±2.06, respectively, while for bull were 619.74±93.27kg, 376.89±48.62kg, 58.61±0.02%, 85.61±10.46cm², 5.64±2.71mm, 1.41±0.83, respectively, and for steer were 681.78±70.72kg, 415.23±49.43kg, 60.19±0.02%, 88.29±10.27cm², 12.71±5.23mm, 5.42±1.99, respectively. In the environmental variables selection based on the variables selection method, the examination by carcass traits suggested that the most appropriate model could be determined when five variables were selected for the live weight, carcass weight, dressing percentage, eye muscle area, and four variables for backfat thickness, and marbling score. When they were considered at a time altogether based on multiple traits, it was deemed to be desirable to insert all five variables into the variables for analysis. In addition, high significance was found by carcass traits.

Validation of Single Nucleotide Polymorphisms Associated with Carcass Traits in a Commercial Hanwoo Population

Sudrajad, Pita,Sharma, Aditi,Dang, Chang Gwon,Kim, Jong Joo,Kim, Kwan Suk,Lee, Jun Heon,Kim, Sidong,Lee, Seung Hwan Asian Australasian Association of Animal Productio 2016 Animal Bioscience Vol.29 No.11

Four carcass traits, namely carcass weight (CW), eye muscle area (EMA), back fat thickness (BF), and marbling score (MS), are the main price decision parameters used for purchasing Hanwoo beef. The development of DNA markers for these carcass traits for use in a beef management system could result in substantial profit for beef producers in Korea. The objective of this study was to validate the association of highly significant single nucleotide polymorphisms (SNPs) identified in a previous genome-wide association study (GWAS) with the four carcass traits in a commercial Hanwoo population. We genotyped 83 SNPs distributed across all 29 autosomes in 867 steers from a Korean Hanwoo feedlot. Six SNPs, namely ARS-BFGL-NGS-22774 (Chr4, Pos:4889229), ARS-BFGL-NGS-100046 (Chr6, Pos:61917424), ARS-BFGL-NGS-39006 (Chr27, Pos:38059196), ARS-BFGL-NGS-18790 (Chr10, Pos:26489109), ARS-BFGL-NGS-43879 (Chr9, Pos:39964297), and BTB-00775794 (Chr20, Pos:20476265), were found to be associated with CW, EMA, BF, and MS. The ARS-BFGL-NGS-22774, BTB-00775794, and ARS-BFGL-NGS-39006 markers accounted for 1.80%, 1.72%, and 1.35% (p<0.01), respectively, of the phenotypic variance in the commercial Hanwoo population. Many genes located in close proximity to the significant SNPs identified in this study were previously reported to have roles in carcass traits. The results of this study could be useful for marker-assisted selection programs.