Background: Recently, the single-step genomic best linear unbiased prediction (ssGBLUP) method, which incorporates not only genomic information but also phenotypic information of pedigree, is under study. In this study, we performed a ssGBLUP analysis on a commercial Hanwoo population using phenotypic, genotypic, and pedigree data. Methods: The test population comprised Hanwoo 1,740 heads raised in four regions of Korea, while the reference population used Hanwoo 18,499 heads raised across the country and two-generation pedigree data. Analysis was performed using genotype data generated by the Hanwoo 50 K SNP beadchip. Results: The mean Genome estimated breeding values (GEBVs) estimated using the ssGBLUP methods for carcass weight (CWT), eye muscle area (EMA), back fat thickness (BFT), and marbling score (MS) were 7.348, 1.515, -0.355, and 0.040, respectively, while the accuracy of each trait was 0.749, 0.733, 0.769, and 0.768, respectively. When the correlation analysis between the GEBVs as a result of this study and the actual slaughter performance was confirmed, CWT, EMA, BFT, and MS were reported to be 0.519, 0.435, 0.444, and 0.543, respectively. Conclusions: Our results suggest that the ssGBLUP method enables a more accurate evaluation because it conducts a genetic evaluation of an individual using not only genotype information but also phenotypic information of the pedigree. Individual evaluation using the ssGBLUP method is considered effective for enhancing the genetic ability of farms and enabling accurate and rapid improvements. It is considered that if more pedigree information of reference population is collected for analysis, genetic ability can be evaluated more accurately.

This study has evaluated the genomic estimated breeding value (GEBV) of the commercial Hanwoo population using the genomic best linear unbiased prediction (GBLUP) method and genomic information. Furthermore, it analyzed the accuracy and realized accuracy of the GEBV. 1,740 heads of the Hanwoo population which were analyzed using a single nucleotide polymorphism (SNP) Chip has selected as the test population. For carcass weight (CWT), eye muscle area (EMA), back fat thickness (BFT), and marbling score (MS), the mean GEBVs estimated using the GBLUP method were 3.819, 0.740, -0.248, and 0.041, respectively and the accuracy of each trait was 0.743, 0.728, 0.737, and 0.765, respectively. The accuracy of the breeding value was affected by heritability. The accuracy was estimated to be low in EMA with low heritability and high in MS with high heritability. Realized accuracy values of 0.522, 0.404, 0.444, and 0.539 for CWT, EMA, BFT, and MS, respectively, showing the same pattern as the accuracy value. The results of this study suggest that the breeding value of each individual can be estimated with higher accuracy by estimating the GEBV using the genomic information of 18,499 reference populations. If this method is used and applied to individual selection in a commercial Hanwoo population, more precise and economical individual selection is possible. In addition, continuous verification of the GBLUP model and establishment of a reference population suitable for commercial Hanwoo populations in Korea will enable a more accurate evaluation of individuals.

본 연구는 한우 보증씨수소 844두를 출생년도를 기준으로 8개 집단으로 분류하고, 각 개체들의 친자확인용 유전자 마커정보를 농협경제지주 한우개량사업소 홈페이지에서 제공 받아 유전적 다양성 및 구조 변화 분석에 활용하였다. 한우 보증씨수소 전체 집단의 대립유전자수(number of alleles)의 평균은 10.54개, 기대 및 관측 이형접합율(Hex, Hob)의 평균은 각각 0.764, 0.773, 다형성 정보량 지수(PIC)의 평균은 0.727 그리고 Fis의 평균은 –0.014로 확인되었다. 한우 보증씨수소 집단을 출생년도 별로 구분한 8개 집단의 유전적 다양성 및 구조 분석 결과, D집단(2005-2004년)의 기대이형접합율(0.777), 관측이형접합율(0.792) 그리고 다형성정보지수(0.740)가 가장 높은 것으로 확인되었다. C집단(2003-2004년)과 E집단(2007-2008년)에서는 기대이형접합율이 관측이형접합율 보다 큰 것으로 확인되었고, 나머지 그룹 모두에서는 관측이형접합율이 기대이형접합율 보다 큰 것으로 확인되었다. 대립유전자 출현빈도를 기반으로 유전적 조성과 구조를 추론하기 위해 STRUCTURE software를 이용하여 분석한 결과 세대가 지남에 따라 특정 유전적 성분의 변화 또는 비중의 증감을 확인 할 수 있었다. 이는 개량 목표를 설정하고 지속적으로 추진되고 있는 개량 사업이 한우 씨수소 집단의 유전적 구조 변화에 영향을 미치고 있음을 확인 할 수 있는 중요한 자료로, 한우 개량 사업의 효율적인 추진을 위해 유용하게 활용 될것으로 사료된다.

Genotyping-by-sequencing (GBS) is a cost-efficient method which can be useful for SNP marker discovery in a population of interest. GBS is genome reduction sequencing method using restriction enzyme. The quality of DNA is a key factor which could have an influence in downstream analysis. However, there have not been many studies which investigated the impact of DNA degradation and the quality of the data on marker discovery. In this study, GBS data of 6 Hanwoo samples (H1~6) showing differing level of DNA degradation were compared. Re-sequencing pipeline was followed to investigate the impact of DNA degradation on marker discovery. As a result, we found that the quantity and quality of SNPs were not affected in the sample H5 and H6 with moderately degraded DNA. On the other hand, marker discovery was greatly affected in samples with severe DNA degradation (H3 and H4). The findings in this study support that GBS is a robust genotyping method towards moderate DNA degradation.

본 연구는 한우의 경제형질 관련 유전적 표지인자(DNA marker) 개발을 목적으로 한우 도체형질과의 기능적 후보유전자로부터 검출된 10개의 유전마커(Single Nucleotide Polymorphism; SNP)에 대해서, 환경효과가 다양하게 포함되어 있는 상용축을 대상으로 마커효과를 검정하였다. 그 결과, 한우 후대 검정우에서 통계적 유의성이 인정되었던 다수의 SNP 좌위중 IP3R1 유전자에서 검출된 DNA 마커만 상용축의 근내지방도와 통계적 유의차를 보였으며, 이는 각 좌위마다의 환경 효과와의 보다 더 통계분석이 요구되는 것이며, 향후 근내지방도와 연관된 다수의 마커와 함께 혼합모델을 통하여 개체의 표현형 예측등에 활용이 가능할 것으로 사료된다.

The objective of this study was to compare the effects of the levels of inbreeding on body weight traits between two breed populations, Hanwoo and Korea Brindle cattle. Birth weight (BW), weaning weight (WW), body weight at 6 months of age (W6) and yearling weight (YW). Records of 1,745 calves (1,513 from Hanwoo, and 232 from Korea Brindle calves) were collected from Livestock Research Institutes in Kangwon, Gyeongbuk and Chungbuk provinces. The least squares means (LSM) and their standard errors for BW, WW, W6 and YW were 25.4±0.1 kg, 81.0±1.8 kg, 146.1±3.7 kg and 291.5±2.4 kg, respectively in Hanwoo calves and 22.6±0.3 kg, 79.9±2.3 kg, 137.6±4.6 kg and 249.3±6.6 kg, respectively in Korea Brindle calves. Pedigree data showed that 14.8% (316 out of 2131) of Hanwoo was inbred and the average inbreeding coefficient was 0.0209 (2.09%). Inbreeding coefficients of ten calves out of 316 total inbred Hanwoo calves were 12.5% or higher, whereas those of the other 306 calves were less than 12.5%. In both breeds, calves were divided into three groups of inbreeding classes - highly inbred group(F≥ 0.125), lowly to medially inbred group(0<F<0.125) and no inbred group(F=0). In Korea Brindle calf populations, 12.2% of the calves observed (57 out of 467 calves) were inbred and the average inbreeding coefficient was 0.1367(13.67%). Forty four calves out of 57 inbred Korea Brindle calves had inbreeding coefficients of 12.5% or higher and the other 13 calves had less than 12.5% of inbreeding coefficients. Average inbreeding coefficient and the number of calves with greater than 12.5% inbreeding coefficient were higher in Korea Brindle calf groups than in Hanwoo calf groups. On the average, body weight growth of Korea Brindle calves was slower than that of Hanwoo calves. This would be due to very small breeding population structure of Korea Brindle cattle as compared to Hanwoo cattle, which would lead to rapid increase in inbreeding coefficients in the population. In conclusion, our study suggests that planned mating system is needed to control inbreeding in Korea Brindle population.