A study of the genomic estimated breeding value and accuracy using genotypes in Hanwoo steer (Korean cattle)

김은호,선두원,강호찬,김지영,명철현,이두호,이승환,임현태 충남대학교 농업과학연구소 2021 Korean Journal of Agricultural Science Vol.48 No.4

The estimated breeding value (EBV) and accuracy of Hanwoo steer (Korean cattle) is an indicator that can predict the slaughter time in the future and carcass performance outcomes. Recently, studies using pedigrees and genotypes are being actively conducted to improve the accuracy of the EBV. In this study, the pedigree and genotype of 46 steers obtained from livestock farm A in Gyeongnam were used for a pedigree best linear unbiased prediction (PBLUP) and a genomic best linear unbiased prediction (GBLUP) to estimate and analyze the breeding value and accuracy of the carcass weight (CWT), eye muscle area (EMA), backfat thickness (BFT), and marbling score (MS). PBLUP estimated the EBV and accuracy by constructing a numeric relationship matrix (NRM) from the 46 steers and reference population Ⅰ (545,483 heads) with the pedigree and phenotype. GBLUP estimated genomic EBV (GEBV) and accuracy by constructing a genomic relationship matrix (GRM) from the 46 steers and reference population Ⅱ (16,972 heads) with the genotype and phenotype. As a result, in the order of CWT, EMA, BFT, and MS, the accuracy levels of PBLUP were 0.531, 0.519, 0.524 and 0.530, while the accuracy outcomes of GBLUP were 0.799, 0.779, 0.768, and 0.810. The accuracy estimated by GBLUP was 50.1 - 53.1% higher than that estimated by PBLUP. GEBV estimated with the genotype is expected to show higher accuracy than the EBV calculated using only the pedigree and is thus expected to be used as basic data for genomic selection in the future.

한우 혈통 정확도 향상을 위한 SNP 정보 기반 친자 확인 평가

김지영,김은호,강호찬,명철현,임현태 경상국립대학교 농업생명과학연구원 2023 농업생명과학연구 Vol.57 No.5

본 연구는 국내의 한우 개량에 있어서 정확한 혈통 정보가 중요해짐에 따라 고밀도 Single Nucleotide Polymorphism (SNP) chip의 SNP정보들을 활용한 친자 확인으로 혈통 정보의 신뢰도 향상에 기여하고자 실시하였다. 이미 혈통 정보가 확인되고 Microsatellite (MS) 유전자형으로친자 여부가 확인된 14개의 가계, 318두로 친자 확인 분석을 하였다. Call rate 100%인 마커들을 활용한 친자 확인 분석 결과, 9두가 모 부정,19두가 완전 부정으로 총 28두가 부정으로 판정되었고, 이는 부모의 SNP 정보에서 나올 수 있는 조합과 다른 자식의 유전자형이 확인되었다. 이후, 친자 확인 정확도 향상을 위해 call rate와 minor allele frequency (MAF)를 기준으로 SNP 마커 수를 증가시켜 분석하였으나 부정으로판정되는 개체들이 추가적으로 발생하였고, 이는 SNP 정보의 결측치 증가 및 자식의 유전자형 변이로 인한 것으로 판단된다. 따라서 고밀도SNP chip을 활용한 친자 확인 분석에는 보다 신중한 접근이 필요하며, 본 연구 결과는 고밀도 SNP 정보를 이용한 친자 확인 연구에 있어서기초자료로 활용될 수 있을 것으로 사료된다. This study was conducted to contribute to improving the reliability of pedigree information by confirming paternity test using SingleNucleotide Polymorphism (SNP) information from high-density SNP chips. Accurate pedigree information is becoming increasinglyimportant in the efforts to improve Hanwoo. As a result of a paternity test using markers with a 100% call rate, 318 animals wereanalyzed. A paternity test was conducted using 318 animals from 14 families whose pedigree information had already been confirmed,and their paternity was confirmed by the Microsatellite (MS) genotype. As a result of the paternity test using markers that are callrate of 100%, confirmed that the offspring's genotype is different from the combination of SNP information from the parents. Sincethen, the number of SNP markers has increased and has been analyzed based on call rate and minor allele frequency (MAF). However,it was found that additional individuals tested incorrect, which is believed to be due to an increase in missing SNP genotype informationand changes in the genotype of the offspring. Therefore, a more careful approach is needed for paternity testing using high-densitySNP chips, and the results of this study are believed to be used as foundational data for research on paternity testing using high-densitySNP information

사슴의 개체 식별 및 친자 확인을 위한 microsatellite 마커 세트 구축

김지영,김은호,강호찬,명철현,김관우,임현태 한국동물유전육종학회 2022 한국동물유전육종학회지 Vol.6 No.4

Deer is mainly raised for the deer velvet antler used as herbal medicine in Korea, but the self-sufficiency rate of deer velvet antlers in Korea is low and there is no systematic system. Therefore, this study was conducted to establish a microsatellite (MS) marker set for individual identification and paternity test of elk (Cervus canadensis), red deer (Cervus elaphus), and sika deer (Cervus nippon), which are mainly raised in Korea. A total of 9 MS markers were selected and combined into one set based on the size of the marker, the heterozygosity, and the polymorphism information content (PIC). It is thought to be a suitable marker for sufficient use with an observation heterozygosity of 0.525, an expected heterozygosity of 0.643, and a PIC of 0.602. As a result of the probabilities of different individuals with the same genotype being found, the random mating population was 4.68 × 10-8 and the half-sib mating population was 3.23 × 10-6. And the non-exclusion probability was analyzed as 0.0516621 and 0.0045074 when there was no information about parents and only information about one parent. Therefore, if it is used as basic data for establishing a production traceability system or improvement of deer through individual identification and paternity test system, it is expected to revitalize the domestic deer industry.

전형매 가계 내 유전체정보량에 따른 유전체육종가 추정 및 정확도 분석

김은호,선두원,강호찬,명철현,김지영,이두호,이승환,임현태 경상국립대학교 농업생명과학연구원 2022 농업생명과학연구 Vol.56 No.6

The genomic estimated breeding value (GEBV) and accuracy of Korean beef (Hanwoo) are used as important indicators for selection, and recent studies using pedigree and genotype are being conducted to increase the reliability of the accuracy. Therefore, in this study, three families consisting of 10 Hanwoo with the same parents were collected to check the change in accuracy of individuals without genotypes according to the amount of genotypes in the family. GEBV and accuracy were estimated through single-step genomic best linear unbiased prediction (ssGBLUP) using 14,225 reference groups after assuming 5 test groups by selecting 10, 8, 6, 4, and 2 genotypes for each family. An H-matrix was constructed using pedigree and genotype of the groups, and the GEBV accuracy of carcass weight (CWT), eye muscle area (EMA), backfat thichness (BFT) and marbling score (MS) were estimated using the BLUPF90 program. Looking at the first family, the average GEBV accuracy of 10 heads with a genotype in the test group was estimated to be 0.734, 0.717, 0.712 and 0.745 in CWT, EMA, BFT and MS, respectively. Then, looking at the GEBV accuracy estimated by removing the genotype two by two, there was no change in accuracy in the case of individuals with a genotype, but the accuracy of the individuals without a genotype was estimated to be 0.114~0.168 lower on average. It was confirmed that the average GEBV accuracy of individuals without a genotype was 0.604~0.576, 0.6~0.573, 0.599~0.572 and 0.607~0.578 in CWT, EMA, BFT and MS, respectively. And it was confirmed that they decreased by 0.009 on average. Through this, although the amount of genotypes within a group did not have a significant effect on accuracy regardless of the presence of individual genotypes, the presence of individual genotypes had a greater effect on GEBV with high reliability. 한우 개량에 있어서 추정된 유전체육종가와 정확도는 선발에 중요한 지표로 사용되며, 최근 육종가 추정에 있어 정확도의 신뢰도를 높이기위해 혈통과 유전체정보를 이용한 연구가 활발히 진행되고 있다. 따라서, 본 연구는 가계 내 유전체정보량에 따라 유전체정보가 미포함된 개체의정확도 변화를 확인하고자 동일한 부모를 가진 한우 10두로 구성된 전형매 가계 3개를 수집하였으며, 각 가계 별로 유전체정보량을 10두, 8두, 6두, 4두, 2두씩 무작위로 선별하여 5가지의 검정집단으로 가정한 후 참조집단 14,225두를 이용하여 single step genomic best linear unbiased prediction (ssGBLUP)을 통해 genomic estimated breeding value (GEBV) 및 정확도를 추정하였다. 각 검정집단과 참조집단의 혈통 및 유전체정보를 이용하여 H-matrix를 구축하였고, BLUPF90 program을 사용하여 도체중, 등심단면적, 등지방두께, 근내지방도의 GEBV 및 정확도를 추정하였다. 첫 번째 가계를 대상으로 살펴보면, 검정집단에서 유전체정보를 보유하고 있는 10두의 GEBV 평균 정확도는 도체중 0.734, 등심단면적 0.717, 등지방두께 0.712, 근내지방도 0.745로 추정되었다. 이후 2두씩 무작위로 유전체정보를 제거하여 추정한 GEBV 정확도를 살펴보면, 유전체정보를보유한 개체의 경우 정확도의 변화가 나타나지 않았지만, 유전체정보가 미포함된 개체의 정확도가 평균 0.114 ~ 0.168 낮게 추정되었다. 가계내 유전체정보량에 따른 유전체정보가 미포함된 개체의 GEBV 평균 정확도는 도체중 0.604 ~ 0.576, 등심단면적 0.6 ~ 0.573, 등지방두께 0.599 ~ 0.572, 근내지방도 0.607 ~ 0.578로 평균 0.009씩 감소하는 것을 확인하였다. 이를 통해 가계 내 유전체정보량이 개체 별 유전체정보 유무와는상관없이 GEBV의 정확도 추정에 큰 영향이 없었으며, 신뢰도가 높은 GEBV 추정을 위해서는 개체 별 유전체정보의 유무가 더 큰 영향을 미친다는것을 확인하였다.

Genetic diversity and relationship analyses of the Korea native black goat line using microsatellite markers

강호찬,김관우,김은호,명철현,이정규,임현태 충남대학교 농업과학연구소 2021 Korean Journal of Agricultural Science Vol.48 No.4

The aim of this study was to analyze the genetic diversity and distance of the Korean native black goat line. Thus far, this Korean native black goat line has not been studied intensively, especially in genetic diversity and relationship studies in comparison with other breeds. In total, eleven microsatellite (MS) markers were used to evaluate alleles from 391 Korean native black goats and foreign hybrid animals. The genetic diversity index was evaluated based on the allele distributions. Four Korean native black goat lines showed expected ranges of observed heterozygosity, expected heterozygosity, and polymorphism information content (PIC) values for use in genetic diversity research (0.509 - 0.643, 0.434 - 0.623 and 0.356 - 0.567). Lines from the Korean native black goat and foreign hybrid were clearly separated according to principal coordinates analysis (PCoA), phylogenetic tree and tended to be clustered in each Korean native black goat line. Thus, this study can be used for analyzing the genetic relationships between Korean native black goats and foreign breeds for line preservation and for fundamental information to determine breed improvement strategies.

재래흑염소 개체식별과 친자확인을 위한 Microsatellite Marker Set 개발

이상훈(Sang-Hoon Lee),강호찬(Ho-Chan Kang),이성수(Sung-Soo Lee),이진욱(Jinwook Lee),김은호(Eun-Ho Kim),명철현(Hyun-Cheol Myung),김관우(Kwan-Woo Kim),임현태(Hyun-Tae Lim) 한국생명과학회 2020 생명과학회지 Vol.30 No.10

본 연구는 재래흑염소와 교잡종 염소 총 304두를 대상으로 Microsatellite (MS) marker의 대립유전자형 분석을 통해 염소의 개체식별과 친자확인을 목적으로 실시하였다. 각 MS marker 별 대립유전자형의 다형성을 토대로 11종의 MS marker를 선발하였다. 선발된 MS marker를 사용할 경우 동일한 유전자형을 가진 개체가 출현할 확률이 무작위, 반형매 교배집단에서 각각 5.58×10<SUP>-10</SUP>, 1.15×10<SUP>-7</SUP>으로 분석되었다. 또한 친자감정 확률은 부모의 정보가 있을 경우 0.999996, 부모의 정보가 없을 경우 0.999833으로 분석되어 국내에서 사육하고 있는 염소들의 개체식별 및 친자확인이 가능할 것으로 사료된다. 또한 국내 재래흑염소 4 계통과 교잡종 염소들 간의 혈연관계 분석을 통해 국내 재래흑염소의 유전적 특성을 확인하였다. 본 연구의 결과는 염소의 개량 기반 구축에 필요한 개체관리와 친자감별 및 향후 염소고기의 생산 이력 구축에 유용하게 활용 할 수 있을 것으로 판단된다. The Korean native black goat (Capra hircus coreanae) is the goat species to be officially registered in Korea under the Food and Agriculture Organization. The object of this study is to establish a set of microsatellite (MS) markers for the individual identification and parentage verification of goats. In this study, we analyzed alleles of MS markers in crosses between Korean native black goats and crossbred goats (n=304 animals), and, based on the diversity of alleles for each marker, we selected 11 MS markers for individual identification and parentage verification. Using these 11 MS markers, the probabilities of different individuals with the same genotype being found within random and half-sib mating populations were 5.58×10<SUP>-10</SUP> and 1.15×10<SUP>-7</SUP>, respectively. The parentage verification accuracy was 0.999996 when information about the parents was available and 0.999833 with no information. Thus, even given the total rearing population of 576,150 animals in South Korea, we concluded that these markers could be used for the individual identification and parentage verification of goats. Moreover, by analyzing the genetic relationships between the four lines of Korean native black goats and the crossbred goats, we verified the genetic characteristics of Korean native black goats, confirming their conservation value as a unique genetic resource.

KIIE 2019 영광의 수상자 소개

변재현,정명철,이동호,박훈석,박동현,백민우,엄주명,정재윤,신천세,정남용,오세영,이경식,전승호,송의찬,박새롬,한은진,이지윤 대한산업공학회 2019 ie 매거진 Vol.26 No.4

압전 세라믹의 제작 방법에 따른 압전성능 변화 연구

강명철(MyeongCheol Kang),한대현(Dea-Hyun Han),강래형(Lae-Hyong Kang) 항공우주시스템공학회 2015 항공우주시스템공학회 학술대회 발표집 Vol.2015 No.5

구조 손상 검사를 위한 비접촉 초음파 발생 장치 제작

강명철(MyeongCheol Kang),황문영(Mun-Young Hwang),한대현(Dae-Hyun Han),강래형(Lae-Hyong Kang) 항공우주시스템공학회 2016 항공우주시스템공학회 학술대회 발표집 Vol.2016 No.11

이방성재료에 대한 코스틱스법의 적용

백명철,최선호,황재석,김원현 대한기계학회 1992 대한기계학회논문집 Vol.16 No.12

본 연구에서는 이방성체에 대한 구체적인 코스틱스 실험법을 확립하기 위하여 다음과 같은 연구를 수행 하였다. 첫째, 이방성체에 대한 코스틱스상 및 초기곡선의 사상방정식을 기하광학 및 Sih의 응력장을 이용하여 구하고, 이 식에 의한 이론상을 여러가지 경계조건하에서 컴퓨터 그래픽 하여 유도한 사상방정식의 타당성을 검토 하 였다.둘째, 본 논문에서 개발한 두 가지 종류의 직교이방성체를 사용하여 실험을 수행하고 실험에 의한 코스틱스상을 이론상과 비교, 검토 하였다.셋째, 이방성체의 코스틱스상으로부터 응력확대계수를 구하는 방법을 제시하고 이 방법을 실제 시편에 적용하여 신뢰 할수 있는 결과를 얻는 초기곡선의 범위를 결정 하였다. 그리고 이 범위에서 구한 응력확대 계수 값을 경계요소법을 이용한 변위외삽법에 의한 결과와 비 교함으로써 본 논문에서 제시하는 방법이 이방성체의 응력확대계수를 구하는 한 방법 으로 유효하게 사용될 수 있음을 밝혔다. This paper studies the applicability of the method of caustics into anisotropic materials under mode I and mixed static loading conditions and introduces the procedure to obtain stress intensity factors(S.I.F.) in anisotropic materials by the method of caustics. The mapping equations for initial and caustic curves in anisotropic materials were introduced and their computer graphical images were compared to the experimental ones to check the validity of the mapping equations proposed in this paper. The agreement between them was found to satisfactory. Two kinds of method to determine S.I.F. in anisotropic materials by the method of caustics were proposed in this paper and applied into the orthotropic materials under various loading conditions. In the case of mode I loading condition, the S.I.F.'s obtained by this paper's methods were found to be quite similar to the results by other method, boundary element method(B.E.M) and in the case of mixed loading condtion, the S.I.F's by this paper and B.E.M. showed a little differences(2.2-24.4%) with respect to the slanted angle of crack.