PA-01
Identification of Stearoyl-CoA Desaturase(SCD) Gene Interactions in Korean Native Cattle based on the Multifactor-Dimensionality Reduction method 1 1 1 1 1 2 2 3 Dong-yep Oh , Jae-jung Ha , Jun-koo Yi , Dae Hyun Kim , Seung Min Oh , Seyoung Mun , Kyudong Han , Hee-Jong Roh , Chang- 3 4, 5 4, 5 Yeon Cho , Hong Sik Kong , Yoonseok Lee 1 2 Livestock Research institute, Gyeongsangbuk-Do Department of Nanobiomedical Science and BK21 PLUS NBM Global Research Center 3 for Regenerative Medicine, Dankook University, Cheonan 31116, Republic of Korea Senior Researcher/Researcher, Animal Genetic 4 Resources Center, National Institute of Animal Science, RDA, Namwon 55717, Republic of Korea Department of Biotechnology, Colleage 5 of Agriculture & Life Science, Hankyong National University, Center for Genetic information Hankyong National University
ABSTRACT Fat quality is determined by the composition of fatty acids. Genetic relationships between this composition and single nucleotide polymorphisms(SNPs) in the stearoyl-CoA desaturase1(SCD1) gene were examined using 513 Korean native cattle. Single and epistatic effects of 7 SNP genetic variations were investigated, and the multifactor dimensionality reduction(MDR) method was used to investigate gene interactions in terms of oleic acid(C18:1), mono- unsaturated fatty acids(MUFAs) and marbling score(MS). The g.6850+77 A>G and g.14047 C>T SNP interactions were identified as the statistically optimal combination(C18:1, MUFAs and MS permutation p-values were 0.000, 0.000 and 0.001 respectively) of two-way gene interactions. The interaction effects of g.6850+77 A>G, g.10213 T>C and g.14047 C>T reflected the highest training-balanced accuracy(63.76%, 64.70% and 61.85% respectively) and was better than the individual effects for C18:1, MUFAs and MS. In addition, the superior genotype groups were AATTCC, AGTTCC, GGTCCC, AGTCCT, GGCCCT and AGCCTT. These results suggest that the selected SNP combination of the SCD1 gene and superior genotype groups can provide useful inferences for the improvement of the fatty acid composition in Korean native cattle.
Key Words : Korean Native Cattle, Multifactor-Dimensionality Reduction(MDR), Single Nucleotide Polymorphism(SNP), Stearoyl-CoA Desaturase1(SCD1) Gene
PA-02
한우 계통 집단의 연관 불평형 및 유효집단 크기 분석
김현주¹, 이두호², 원정일¹, 이승환², 윤호백¹
¹농촌진흥청 국립축산과학원 한우연구소 ²충남대학교 동물자원과학부
ABSTRACT 본 연구는 국립축산과학원 한우연구소에서 조성중인 계통축군과 농가 및 보증 씨수소 집단의 집단 유지 가능성과 유전적 다양성의 정도를 비교 하기 위하여 수행 하였다. 본 연구에 사용한 자료는 계통축군 암소 287두, 수소 125두와 보증씨 수소 753두, 농가 암소 958두의 유전체 자료를 활 용하였다. 유전체 자료는 Illumina 50K beads chip을 이용하였으며, 네 집단의 자료를 합친 결과 총 2123두의 49,032개의 SNP로 분석을 진행하였 다. 먼저 LD 분석 결과 계통축 한우 집단이 KPN 및 농가 집단보다 그 값이 전반적으로 높게 추정 되었다. 또한 계통축 수소 및 KPN 집단과 비교 시에도 같은 결과를 얻었다. 이는 개량의 정도보다는 집단 및 데이터 크기가 계통축군이 작아서 상대적으로 그러한 결과를 나타낸 것으로 보인 다. 이를 바탕으로 유효집단의 크기를 분석한 결과 55.57세대 전 KPN 및 농가 집단은 1907.05, 계통축 전체 집단은 778.61, KPN 집단은 2243.85, 계통축 수소 집단은 615.78으로 LD의 결과와 마찬가지로 계통축 집단에서 더 낮게 나타났다. 하지만 위의 연구 결과들로 보아 현재 수준으로 두 집단이 유지되는데 큰 문제는 없는 것으로 사료된다.
Key Words : 한우, 계통축, 연관불평형, 유효집단 크기
1 • 2019 International Symposium & Conference PA-03
Regulation of Interferon-tau Gene by a Trophoblast Transcription Factors during the peri- Implantation in Sheep † Min-Su Kim, Hyun-Joo Lim, Ji Hwan Lee, Seung Min Ha, Tae Young Heo and Jun Kyu Son
Dairy Science Division, National Institute of Animal Science, RDA
ABSTRACT Ovine interferon-tau (oIFNT) is a hormone like protein secreted by trophoblast cells of ruminant ungulates during early pregnancy.However, the molecular mechanisms by which ovine IFNT expression is restricted to the trophectoderm have not been fully elucidated. We and others have observed that OCT4 expression persists in the trophectoderm of ruminants; thus, both CDX2 and OCT4 coexist during the early stages of conceptus development. The aim of this study was to examine the effect of CDX2 and OCT4 on IFNT gene transcription when evaluated with other transcription factors. Accordingly, in transient transfection analyses using the upstream region (-654 to +51bp) of ovine IFNT gene (-654-oIFNT-Luc), over-expression of CDX2/OCT4 did affect the transcription of oIFNT-reporter construct in human choriocarcinoma JEG3 cells. Transfection of alone CDX2, and/or ETS2, AP1, CREBBP were had very effective in the up-regulation of the oIFNT construct transfected into JEG3 cells. However, down-regulated by OCT4 transcription factor, when cells were initially transfected with OCT4 followed by transfection with CDX2, and/or ETS2, AP1, CREBBP the expression of -654-oIFNT-Luc was reduced to levels. Also, OCT4 factor inhibited the stimulatory activity of CDX2 alone. In conclusion, it is suggested that prior to conceptus elongation, pre-existing OCT4 may inhibit IFNT expression, but as elongation proceeds, IFNT expression increases, resulting from incremental increases in CDX2 expression, diminished OCT4 expression, and possibly proper transcription factor complex formation.
Key Words : IFNT, Trophoblast, Jeg3, Transcription factor, transfection
PA-04
Genome-wide Association Study Dissects the Genetic Architecture of Personality Traits in Korean Jeju × Thoroughbred Horses † † M. S. A. Bhuiyan , Nam Young Kim*, Young Kuk Kim , Nam Geon Park, Byoung Chul Yang*, In Cheol Cho*, Sang Min Shin*, Jae † Hoon Woo*, Moon Cheol Shin*, Ji Hyun Yoo*, Jae Young Choi*, Seung Hwan Lee
† *Subtropical Livestock Research Institute, National Institute of Animal Science, RDA, Jeju 690-150, Korea Division of Animal & Dairy Science, Chung Nam National University, Daejeon 305-764, Korea
ABSTRACT Animal personality comprises behavioral attitudes that remains relatively stable across time and contexts, and is highly relevant for horse performance. We performed a genome-wide association study (GWAS) to identify single-nucleotide polymorphisms (SNPs) and candidate genes associated with personality traits in five Korean Jeju × Thoroughbred horses: docility, patience, aggression, sensitivity and friendship. A total of 160 yearling animals were assessed by three or four trained personnel for each trait, and all animals were genotyped using Illumina Equine SNP70 BeadChips. Association analysis revealed that 10 SNPs on ECA1, ECA7 and ECA20 were significantly associated with all traits except friendship. These SNPs were located in the USH1C, TFAP2, COPB and ABCC8 genes, or in close proximity to PRL and DQB2. Among these genes, USH1C, TFAP2 and PRL may be related to the sensory perception of sound and vision, inferior colliculus (auditory pathway) development and anti-dopaminergic effects. Moreover, a small proportion of SNPs (< 0.80%) with strong effects explained the majority (56.82–71.14%) of the total genetic variance. The remaining variance was explained by thousands of genes with weak effects, indicating that these personality traits are largely polygenic. Genomic heritability estimates based on SNP data ranged between 0.17 and 0.43. Our findings provide a basis for the genetic quantification of personality traits, and may facilitate further investigations of the genetic mechanisms and marker-assisted selection of these traits in horses.
Key Words : Personality traits, GWAS, SNP, Jeju × Thoroughbred horse
Korean Society of Animal Breeding & Genetics • 2 PA-05
Functional transcriptome profiling for cytokine signaling mechanisms in response to dosage dependent interferon gamma treatment from the ex planted porcine endometrial tissue
Do-Young Kim¹, Hakhyun Ka² and Jun-Mo Kim¹*
¹Department of Animal Science and Technology, Chung-Ang University, Anseong-si, Gyeonggi-do, 17546, Republic of Korea ²Division of Biological Science and Technology, Yonsei University, Wonju, Republic of Korea
ABSTRACT In swine fertilization, the initial conception of implementation of embryos on the endometrium is important to be established of pregnancy. In the process of conception, the endometrial changes in the aspect of morphology have been well characterized through the action of cytokines and hormones. On the other hand, the molecular mechanisms and the key genes which were affected by cytokines were not well understood. The aim of this study was to analyze the response of interferon gamma (IFNG), a type of cytokine that embryos secrete to the endometrium cells of the porcine at the time of implantation, at the transcriptome level and to identify the signaling mechanism by interferon gamma treatment. The cultured endometrial cells were treated with serial dosages (0, 1, 10, 100 ng / ml) of IFNG. We analyzed transcriptome profiles and identified differentially expressed genes (DEGs) for each dosage based on IFNG 0. The all of DEGs in of IFNG 1 and IFNG 10 were included in the DEGs of IFNG 100, and their expression levels were proportional to the increase in IFNG dosage. We identified the functional DEGs by IFNG treatment indicated the immune response and cytokine interactions. An analysis of the gene set enrichment of the entire gene expressions between IFNG 0 and 100 showed that the term for interferon-gamma response was the most significant. In addition, the main functional annotation indicated the immune response and the chemokine signaling pathway. We suggest that IFNG contributes to the regulation of the immune function of the host during the implantation process. Further studies are required to validate the function of IFNG in vivo.
Key Words : Cytokine, IFNG, RNA-seq, Porcine, Implantation, Transcriptome
PA-06
The review on structure and function of selectin
Yunjeong Noh¹, Donghyun CHO¹, Haesu Ko¹, Dajeong LIM¹, Han-Ha CHAI²
¹National institute of animal science, RDA, Korea. ²National institute of animal science, RDA and College of Pharmacy, Chonnam national university, Korea.
ABSTRACT Selectin is a glycoprotein the sugar moieties is involved in cell adhesion. It is a vascular adhesion molecule that mediated responses such as chronic or acute inflammation, immunity, hemostasis, ischemic inflammation, skin inflammation and arteriosclerosis. Selectin is classified into L-selectin, E-selectin and P-selectin, it is lectin protein and transmembrane protein, form a tailed structure in the cytoplasm. L-selectin is involved in the rolling of leukocyte, E-selectin is expressed in activated endothelial cell and P-selectin is expressed on the surface of activated endothelial cell or platelets. Selectin has a ligand of glycan structure involved in leukocyte trafficking and inflammation, selectin and its ligands have the effect of cancer and various diseases. Without selectin and its ligand, causes serious result and disease to rat and human. Since selectin has a different structure and function depending on the type, additional studies using selectin are needed. In this review, we looked at the structure and function of each selectin, and show that selectin is involved in various diseases.
Key Words : Selectin, L-selectin, E-selectin, P-selectin.
3 • 2019 International Symposium & Conference PA-07
국내 홀스타인 품종의 신규형질 개발을 위한 연구
Jae gu Lee, Changgwon Dang and Yeon Ho Choy
National Institute of Animal Science, RDA, Cheonan, Korea
ABSTRACT 북미나 유럽의 낙농선진국들은 젖소의 개량을 위하여 번식, 사료효율 및 건강과 관련된 형질들을 이용하고 있다. 그러나 국내에서는 이러한 효 율성 관련 형질에 대한 평가가 부재되어 있다. 따라서 본 연구에서는 젖소의 번식형질 중 하나인 딸소 수태율을 유전평가 형질로 새롭게 추가하 기 위 한 첫 단계로 기초통계분석을 실시하였다. 연구에 이용된 수태율의 자료 수는 모든 산차를 포함하여 1997년부터 2017년까지 농협 젖소개 량사업소 에서 수집된 1,881,607건의 자료를 이용하였다. 산차별 딸소 수태율의 평 균은 1산 36.85%, 2산 35.74%, 3산 35.37%로 산차가 진행될 수록 낮아지는 추세였다. 또한 분만간격, 공태일수 및 누적착유량이 증가할수록 딸소 수 태율은 감소하는 경향을 나타냈다(r: -0.11 ~ -0.74). 현 재까지 국가단위 젖 소개량은 유생산 및 체형위주의 개량을 진행하였다. 따라서 본 연구를 시작으로 씨수소 선발을 위한 유전평가 항목에 딸소 수태율과 같은 번식형질을 추가하여 낙농선진국과 동일 수준의 유전평가항목을 갖추는 것이 필요할 것으로 사료된다.
Key Words : Korea Dairy Cattle, Daughter Pregnancy Rate
PA-08
국내 홀스타인 젖소정액 사용현황 조사
Jae gu Lee, Changgwon Dang and Yeon Ho Choy
National Institute of Animal Science, RDA, Cheonan, Korea
ABSTRACT 국내 홀스타인 품종의 경우 미국 및 캐나다에서 젖소정액을 수입하여 인공수정에 이용하고 있으며 국내에서도 국내 젖소 AI센터에서 한국형 및 도입우를 활용하여 정액을 생산·보급하고 있다. 본 연구의 목적은 국내에서 유통 중인 젖소정액의 연도·지역별 수입산 및 국내산 정액의 비율을 조사하여 국내산 정액의 경쟁력 제고를 위한 기초자료로서 활용하고자 진행하였다. 분석을 위하여 1991~2019년도까지 유우군 능력검정사업을 통해 수집된 수정기록 5,528,467건을 활용하였다. 수정연도별 정액사용 빈도는 꾸준히 증가하는 추세였으며 원산지별 비율은 한국형 12%, 도입 34%, 수입 54%이었다. 광역시·도 단위에서는 대전(46%), 대구(25%), 울산(18%), 경남(17%) 그리고 제주(16%) 순으로 한국형 정액의 이용률이 높았으며 세종(65%), 경기(62%) 및 강원(62%) 순으로 수입산 정액의 비율이 높은 것으로 나타났다. 특히 전체 정액사용 비율의 절반 이상(53%) 을 차지하는 경기 지역의 수입산 정액의 이용률이 높은 것이 국내산 정액의 점유율 열위의 가장 큰 원인이라 사료된다.
Key Words : Holstein, Proven Bull, Semen
Korean Society of Animal Breeding & Genetics • 4 PA-09
국가단위 염소 개량방향 설정을 위한 현장실태 조사
최유림, 장혁기, 당창권, 최연호, 이승수, 이재구, 최재관, 박병호, 박미나, 김시동
농촌진흥청 국립축산과학원
ABSTRACT 국내 염소산업은 건강에 대한 관심 고조로 염소고기 소비가 증가함에 따라 국내 사육두수는 2011년 248 천두에서 2017년 11월 기준 489 천두로 증가하는 추세이다. 염소고기 수입량도 2012년 789 톤에서 2017년 1,752톤으로 늘어나고 있다. 농림축산식품부는 2018년부터 염소를 가축개량 지원사업 대상 축종에 포함하였으며, 향후 국가단위 염소개량 정책을 수립할 예정으로 있다. 국가단위 염소개량 계획은 생산자와 소비자가 경제 적 이득을 취할 수 있는 방향으로 설정되는 것이 바람직하다. 본 연구는 국가단위 염소개량 방향 설정을 위한 기초자료 확보를 위하여 생산농가 및 소비자 측면에서의 개량 대상 형질 선호도와 농가에서 사육하고 있는 염소 집단의 품종 구성 및 유전적 관계 현황을 유전체 수준에서 분석하 였다. 소비자들은 흑염소를 선호하고 염소고기의 풍미와 마블링 개선을 요구하였다. 생산자들은 육량 개량을 원하고 있으나 종축 선정에 어려움 이 있고 혈통관리 부재로 근친에 대한 우려가 큰 것으로 조사되었다. 농가에서 사육하고 있는 염소는 여러가지 품종이 혼합된 교잡종 염소가 대 부분 사육되고 있는 것으로 조사되었고 재래흑염소와는 성장 특성이 구별되나 유전자 고정을 통한 품종으로 발전하지 못하고 있었다.
Key Words : goat, national level, improvement, field condition, policy support
PA-10
The comparison of the dairy industry and reproductive performance of dairy cows in Uganda and South Korea 1 2 1 3 Dae-Jin Kwon , Usama Kabuye , Jaeyoung Heo , You-Lim Choi 1 2 International Agricultural Development and Cooperation Center, Chonbuk National University, Jeonju 54896, Korea Department of 3 Animal Biotechnology, Chonbuk National University, Jeonju 54896, Korea Animal Genetics & Breeding Division, National Institute of Animal Science, RDA, Seonghwan 31000, Korea
ABSTRACT This study conducted a meta-analytic study on the productive and reproductive performance of the dairy cows in Uganda and South Korea as well as comparison of the dairy industry in two countries. National data ranging from 2014 through 2016 about the performance of dairy cows for two countries was analysed. Except the mean lactation length (LL) which was not significantly different for two countries, results indicated better productive performance in terms of daily average milk production (AMP), peak milk yield (PMY) and total lactation milk yield (LMY) for the dairy cows in South Korea. A similar trend was observed for the reproductive performance where the dairy cows of South Korea had a significantly shorter age at first service (AFS), shorter age at first calving (AFC), shorter calving interval (CI) and days open (DO) as well as less services per conception (SPC) with an above average conception rate (CR) in comparison with the dairy cows of Uganda. However there was no significant difference in the estrus / heat interval (HI) for the dairy cows in the two countries. Since reproductive traits have low heritability, from these results it can be concluded that the genetic potential and performance of the dairy cows in Uganda can fully be realised with improvement and modernisation of dairy management and production. Introduction, promotion, and adoption of modern dairy production technology and management like that of South Korea is one of the novel promising interventions in achieving a more profitable dairy industry in Uganda.
Key Words : Dairy Industry, Reproductive Performance, Dairy Cows, Uganda, Korea
5 • 2019 International Symposium & Conference PA-11
Production performance of 12 Korean native chicken varieties preserved as national genetic resources
Ki Gon Kim, Eun Sik Choi, Jae Hyun Kwon, Hyun Chul Jung and Sea Hwan Sohn
Department of Animal Science and Biotechnology, Gyeongnam National University of Science and Technology, Jinju 52725, Korea
ABSTRACT In this study, to determine the productive characteristics of 12 Korean native chicken varieties which have been collected and conserved for over 25 years in NIAS RDA, viability, growth performance and egg production performance were investigated. The 1,134 hens were tested and their production traits including survival rate, body weight, age at first egg laying, hen-day and hen-housed egg production, egg weight and egg quality were measured. In results, survival rate was highest in Korean Rhode-D and Korean White, and lowest in Korean Cornish Brown, 92.2% and 54.3%, respectively. Body weights from 4w to 50w were consistently high in order of Korean Cornish-, Korean Rhode-, Korean Chicken-, Korean Ogye- and Korean Leghorn-breed. There was no significant difference in weight between varieties within breed. Age at first egg laying was the shortest in Korean Leghorn, while was the longest in Korean Cornish. The hen-day egg production from 1 st egg to 57w was highest in Korean Leghorn-K, and lowest in Korean Cornish Brown, 76.7% and 10.8%, respectively. Egg weight was heaviest in Korean Leghorn-F and lightest in Korean White. The haugh unit was highest in Korean Rhode-C and lowest in Korean Ogye. Taken together, these results suggest that it is desirable that Korean Cornish is improved as Korean meat breed because of its excellent growth ability, Korean Leghorn is improved as Korean layer breed because of its good laying performance, and also Korean Rhode and Korean Chicken are improved as disease resistance breed because of theirs good survival rate.
Key Words : national conservation genetic resource, growth performance, egg production performance, Korean native chicken
PA-12
Estimation of combining abilities and heterosis effect of some economic traits in Korean Native Chicken strains † Eun Sik Choi, Ki Gon Kim, Jae Hyun Kwon and Sea Hwan Sohn
Department of Animal Science and Biotechnology, Gyeongnam National University of Science and Technology, Jinju 52725, Korea
ABSTRACT This study was conducted to develop a new synthetic breed of Korean native chicken. The combining ability and heterosis effect for economic traits were estimated with 1,157 hens of Korean native chicken used in 5×5 diallel cross mating. Body weight, survival rate, age at first egg laying, egg weight, and hen-day egg production were measured and analyzed. The heterosis effect was calculated according to formula and the combining ability was estimated by Griffing’s method. In results, the average heterosis effect was 5.4% for body weight at 12w, 16.9% for survival rate, -2.7% for age at first egg laying, 1.3% for egg weight, and 14.3% for hen-day egg production. Generally, the heterosis effect for viability and egg production traits was higher than that for growth trait. The values of general combining ability and specific combining ability were -209.7~162.2 and -52.5~79.4 in body weight at 12w, -9.6~11.1 and -1.7~12.4 in survival rate, -2.8~3.7 and -4.9~4.5 in age at first egg laying, -0.9~1.0 and -1.1~1.4 in egg weight, and -4.9~6.0 and -1.9~5.7 in hen-day egg production. The mean value based on combining ability was higher in WY and WF combinations for survival rate; GF and HF combinations for body weight; and GW and FW combinations for hen-day egg production. On the basis of these results, it is expected that the selection of the HF combination, which had excellent growth performance, is the most desirable as the paternal strain, and the selection of GW and FW combinations, which had excellent laying performance, are preferable as the maternal strain.
Key Words : Korean Native Chicken, combining ability, heterosis effect, diallel cross mate
Korean Society of Animal Breeding & Genetics • 6 PA-13
Utilizing text mining approach to detect fatty acid-related genes of Hanwoo cattle 1 1 1 1 1 1 1 1 Hyun Ji Choi , Dongwon Seo , Doo Ho Lee , Soo Hyun Lee , Ji Min Kang , Sung-Bong Jang , Yoon ji Chung , Hyo Jun Lee and 1 Seung Hwan Lee
1 Division of Animal & Dairy Science, Chung Nam National University, Daejeon, 305-764, Korea
ABSTRACT Text mining is defined as the automatic extraction of previously unknown and potentially useful information from text. It is very powerful method to detect specific genes which related economical traits of livestock. The object of this study is to compare the performance of Genome-wide association study (GWAS) using text-mined and commercial genotyped data in order to use genes to genomic selection. For this object, we extracted the appearance rate and frequency of genes related to each fatty acid in the research papers by text mining. As a result of the text mining, the number of genes related to myristic acid, palmistic acid, stearic acid, oleic acid, linoleic acid, and eicosapentaenoic acid were 119, 546, 241, 672, 669 and 512, respectively. Also, gene ontology (GO) analysis was performed to confirm the validity and reliability of our text mining results. Oleic acid is one of the most abundant fatty acids which has determined meat quality in Hanwoo cattle and it has a very strong positive correlation with intramuscular fat accumulation. In addition, the concentration of oleic acid in muscle lipid significantly increase the taste panel scores for tenderness, juiciness and flavor. Therefore, we focused on oleic acid and identified functions of genes for oleic acid. As a result, ‘GO:0006629, lipid metabolic process’ and ‘GO:0008610, lipid biosynthetic process’ terms were enriched on the top 10 with significant p-value. These results indicated that our text mining method properly detected fatty-acid related genes so that it could help us move on to the further analysis.
Key Words : Text mining, Oleic acid, Gene ontology and Fatty acid
PA-14
Identification of genetic component by multivariate reaction norm model with THI in Hanwoo 1 1 1 1 1 1 1 1 Yoon Ji Chung , Dongwon Seo , Doo Ho Lee , Soo Hyun Lee , Ji Min Kang , Sung-Bong Jang , Hyo Jun Lee , Seung Hwan Lee 2 and S. Hong Lee
1 2 Division of Animal & Dairy Science, Chung Nam National University, Daejeon, 305-764, Korea Australian Centre for Precision Health, University of South Australia Cancer Research Institute, University of South Australia, Adelaide, South Australia 5000, Australia
ABSTRACT The genetic architecture of Hanwoo (Korean brown cattle) has been dissected without considering genotype by environment interaction (GXE) and the performance of this breed tend to be affected by temperature of farm among various environment factors. We propose a multivariate reaction norm model (MRNM) considering GXE to estimate genetic parameters and predict breeding values more accurately. MRNM can solve the problem by correctly accounting for both genetic interaction and correlation with univariate reaction norm model. We applied MRNM to 58,990 SNPs of Hanwoo in analysis of economic traits using Temperature-Humidity Index (THI) as a covariate in comparing Genome-based restricted maximum likelihood (GREML) and random regression model (RRM) in MTG2. Furthermore, we used two-step approach using residual variance for efficiency of computing times. Significant G-C interactions were found for carcass weight and eye muscle area and the estimates using GREML were underestimated for genetic component. On the other hand, for back fat thickness, G-C interaction estimate was inflated in existing methods with highly significant G-C correlation. In addition, significant heterogeneity for carcass weight and marbling score identified in the estimated residual variance across levels of the different covariate, i.e., residual-covariate (R-C) interaction. Additionally, we showed that heritability of these traits indicates higher values compared to those of existing model except back fat thickness. In conclusion, these results indicate genetic component is broadened and we could calculate more accurate parameters. MRNM would be a powerful model for genomic selection in Hanwoo breeding program.
Key Words : Genotype by environment(GXE), Multivariate reaction norm model, THI, Hanwoo(Korean cattle)
7 • 2019 International Symposium & Conference PA-15
Using text-mining to increase the accuracy of genomic prediction in Hanwoo, Korean native cattle. 1 1 1 1 1 1 1 1 Hyo Jun Lee , Dong Won Seo , Doo Ho Lee , Soo Hyun Lee , Ji Min Kang , Yeoug Kuk Kim , Sung Bong Jang , Yoon Ji Chung , 1 1 1 1 Hasini Indrachapa Wijayananda , Hyun Ji Choi , Chandima Gajaweera and Seung Hwan Lee 1 Division of Animal & Dairy Science, Chung Nam National University, Daejeon, 305-764, Korea
ABSTRACT Text mining, also known as text data mining, is a good way to extracting valuable data from textual databases. In this study, text-mining was used to find gene associated with carcass and meat quality traits in previous papers. After mining genes, SNPs involved in Text-mined genes (TMG) and intergenic region of TMG were used for genomic prediction. the results showed a similar genomic prediction accuracy for carcass traits (i.e. carcass weight (CWT/ kg), backfat thickness (BF/mm), eye-muscle area (EMA/cm 2 )) using Text-mined SNPs (CWT : 0.207 ± 0.03, BF : 0.161 ± 0.03, EMA : 0.127 ± 0.03) and using imputed 777k SNPs (CWT : 0.184 ± 0.03, BF : 0.147 ± 0.04, EMA : 0.128 ± 0.03). Therefore, use of text-mining for carcass traits is expected to provide economic benefits in genomic selection. However, genomic prediction for Warner-Bratzler Shear Force of longissimus dorsi muscle (D_SF) and intramuscular fat content of semimembranosus muscle (S_IMF) shoed lower accuracy for text mined SNPs (D_SF : 0.124 ± 0.01, S_IMF : 0.073 ± 0.02) than the imputed 777k SNPs (D_SF : 0.135 ± 0.02, S_IMF : 0.195 ± 0.03). Because SF and S_IMF are not traits to consider in evaluating the degree of Hanwoo breed, selection of these two traits would not have been carried out actively. Therefore, linkage disequilibrium between causal maker for these traits and other markers would be weakened and this seems to be reduce the accuracy of genomic prediction using text-mined SNPs for these traits.
Key Words : genomic best linear unbiased prediction, genomic prediction, Hanwoo, text-mining.
PA-16
EFFECT OF DIVERGENT SELECTION FOR MARBLING AND HIGH ENERGY DIET ON CARCASS CHARACTERISTICS AND QUALITY GRADING STANDARDS OF HANWOO STEERS. 1 2* 1* 1 1 1 Chandima Jayanath Gajaweera , Ki Yong Chung , Seung Hwan Lee , Doo Ho Lee , Soo Hyun Lee , Yeong Kuk Kim , Hasini I. 1 Wijayananda 1 2 Division of Animal and Dairy Science, Chungnam National University, Daejeon, 34140, Republic of Korea. Hanwoo Research institute, National Institute of Animal Science, RDA, Pyeongchang, 25340, Republic of Korea.
ABSTRACT Focusing to develop a genomic based nutrition management model for Hanwoo steers, we evaluated the response to the divergent selection on genetic merit for marbling score(MS), under different dietary TDN(total digestible nutrient) levels. Total of 112 calves were genotyped and initially grouped for estimated breeding value (high and low) for marbling score(MS-EBV). Subsequently, managed under two levels of feed TDN%, over the calf period, early, middle, and final fattening periods following 2X2 factorial arrangement. Carcasses were evaluated for MS, Back fat thickness(BFT) and Korean beef quality grading standard. As the direct response to the selection was significant, the results confirmed the importance of initial genetic grouping of Hanwoo steers for MS-EBV. However, dietary TDN level did not show an effect (p>0.05) on the MS. Further, no genetic-by-nutrition interaction for MS (p>0.05) was also observed. The present results showed no correlation response on BFT (p>0.05), indicating that the selection based on MS-EBV can be used to enhance the MS without undesirable effect on BFT. Ultimate turnover of the Hanwoo feedlot operation is primarily determined by the QGs. The present model shows that the initial grouping for MS-EBV increased the proportion of carcasses graded for higher QGs (QG1 ++ and QG1 + ) by approximately 20%. Moreover, there appear to be a potential to increase the proportion of QG 1 ++ animals among the high-genetic group by further increasing the dietary energy content. The results showed the difference between mean predicted and real phenotype of MS were higher among the low genetic animals for MS compared to the high genetic animals. Overall, our results implying the importance of genetic based initial grouping for Hanwoo steers with a subsequent divergent management based on dietary energy level.
Key Words : Genetic merit for marbling, feed energy level, Carcass quality, Hanwoo
Korean Society of Animal Breeding & Genetics • 8 PA-17
Incorporating transcriptomic data to genomic prediction of marbling related traits in Hanwoo 1 1 1 1 2 1 1 Sungnbong Jang , Yoon Ji Chung , Ji Min Kang , Dongwon Seo , Dong-Joon Kim , Jun-Heon Lee , Seung Hwan Lee 1 2 Division of Animal & Dairy Science, Chung Nam National University, Daejeon, 305-764, Korea TNT Research, Anyang, Korea
ABSTRACT Marbling is an important trait which affects the meat quality of Hanwoo. Thus, Hanwoo breeding program considered marbling score (MS) as one of the main objective traits. Genomic prediction has a large potential on genomic improvement of MS which is difficult to measure and it would be more precise in prediction of genomic breeding value (GEBV) if biological knowledge is incorporated into the model. To identify the improvement of GEBV accuracy when biological information is included, we used results of the prior transcriptomic analysis. Total of 374 differentially expressed genes (DEGs) was used to perform genomic prediction. Also, we imputed 50k to 777k and WGS levels. The genomic prediction was performed to investigate the prediction accuracy of DEGs and other genotype panels (50k, imputed 777k, imputed WGS). A total of 1,160 Hanwoo cattle with MS and intramuscular fat (IMF) content were used as phenotype data. We then estimated GEBV with 50k, imputed 777k, imputed WGS, and DEGs panel using GBLUP and BayesR model. In the result of GBLUP, DEGs panel showed relatively lower accuracies (0.26 ~0.32) than other panels (0.33 ~0.42) for all the traits. The most remarkable results were that BayesR method showed higher prediction accuracies (0.41 ~0.52) than GBLUP method (0.26 ~0.42) and for the MS, DEGs panel showed higher accuracy (0.51) than other two panels (0.41, 0.45 respectively). This results showed that DEGs panel in BayesR model indicated high prediction accuracy of MS so that adding biological information can be a useful way to improve genomic prediction.
Key Words : Marbling, Transcriptomic data, Genomic prediction
PA-18
Prediction of breed composition in crossbred pigs
Soo Hyun Lee, Doo Ho Lee, Ji Min Kang, Yeoung Kuk Kim, Sung Bong Jang, Yoon Ji Chung, Hyo Jun Lee, Hyun Ji Choi, Chandima Gajaweera, Hasini Wijayananda and Seung Hwan Lee*
Division of Animal & Dairy Science, Chung Nam National University, Daejeon, 305-764, Korea
ABSTRACT Crossbred of Landrace, Yorkshire and Duroc has been occupied Korean pig market. In terms of crossbreeding, breed composition (BC) is important thing to know when considering hybrid vigor and selecting animals. BC can be roughly measured using admixture by ancestry in common. With this information, we can predict BC of unknown population through the reference population. Accordingly, this study focused on the prediction of validation animals using multiple reference sets. A set of 871 pigs (786 crossbred and 85 Landrace) was genotyped in this study. As mentioned above, ancestry mixture was taken from the admixture and optimal K level was chosen at 46. In this level, Landrace representative ancestry column was chosen as a phenotype. Reference set was divided by breed or ancestry threshold in the entire studied population. Using this genotype and phenotype, SNPs effect for BC was calculated from reference data sets. Finally, BC was predicted using the calculated SNPs effect for both reference and validation animals. Correlation between real and predicted BC was measured. In this results, BC accuracy predicted by crossbred reference to Landrace and Landrace reference to crossbred was 0.10 and 0.79 respectively. Accuracy of crossbred and Landrace using phenotype filtered Landrace or crossbred reference showed 0.71 and 0.46 each.
Key Words : Breed composition, Prediction, Accuracy
9 • 2019 International Symposium & Conference PA-19
Genome-wide association study for carcass traits and genetic diversity between Korean Hanwoo and Chikso breeds 1 1 1 1 1 1 2 Hasini I Wijayananda , Ji min Kang , Soo Hyun Lee , Doo Ho Lee , Chandima Jayanath Gajaweera , Sung Bong Jang , Mina Park , 2 2 1* Dajeong Lim , Byounghoho Park , Seung Hwan Lee 1 2 Department of Animal Science and Biotechnology, Chungnam National University, Daejeon, South Korea Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Rural Development Administration, Wanju, South Korea
ABSTRACT Hanwoo and Chikso are closely related Korean cattle breeds that can be distinguish by its coat color. Hanwoo considered as the most popular beef cattle with high economic value in Korean market that has well established breeding and selection program. Chikso or Korean Brindle cattle has lower population compared to Hanwoo, yet it is one of the major cattle breeds in Korea. Our main objective is to compare Hanwoo and Chikso by genotype and phenotype data to investigate genetic diversity and genome wide association study of meat quality traits (Back fat Thickness (BFT), Marbling Score (MS), Eye muscle area (EMA) and Carcass weight (CW)). The results will help to improve conservation and breeding practices of Hanwoo and Chikso. A total of 1216 Chikso and 11369 Hanwoo animals were used as the sample of the study. The sample was genotyped by Illumina BovineHD SNP 50k Bead chip. PLINK 1.9 was used to filter SNPs from quality control parameters and, finally 44,297 and 35,272 SNPs were used for the final analysis, respectively. Multidimensional scale (MDS) showed distribution of the Hanwoo always lies within Chikso breed while Chikso showed broad distribution within MDS plot. Admixture analysis illustrated, Chikso has little difference when compared to Hanwoo., while Chikso showed high introgression compared to Hanwoo. The GWAS was conducted to find out genomic regions associated with meat quality traits in Hanwoo and Chikso, separately. Meat quality related phenotypic data were adjusted for fixed effects. Then residual values for each phenotype that corrected for systematic effect were used to apply linear mixed model in GCTA with all candidate SNPs. GWAS revealed 76 SNPs in Hanwoo significantly associated (P value ≤ 1.42 × 10 -6 ) with 15 chromosomes in the Bos taurus genome (BTA 3, 6, 9, 13, 14, 17, 18, 19, 20, 22, 23, 25, 26, 27,28 ). Chikso GWAS results depicted one SNP in BTA 14 was significantly associated (P value ≤ 1.13 × 10 -6 ) with Carcass weight of Chikso. Further, investigations with more genotype data is necessary to investigate these associations more precisely.
Key Words : Hanwoo, Chikso, , Meat Quality traits, GWAS, Genetic diversity
PA-20
Epistatic effect of six candidate genes on fatty acid composition in Korean native chicken
Shil Jin, Seung Hwan Lee, Doo Ho Lee, Jun Heon Lee*
Division of Animal & Dairy Science, Chungnam National University
ABSTRACT The fatty acid composition is one of the important considerations for consumer's purchasing decisions to select high quality livestock products. However, the fatty acid composition is not a single trait and is not affected by one genetic factor, so it is difficult to apply in the animal breeding program. Therefore, this study examined the genetic relationships between nine SNPs in six genes (DEGS1, ELOVL6, FABP3, FABP4, FASN, and SCD) which previously known to affect the fatty acid composition in meats. The fatty acid composition of thigh and breast meat from 597 chickens were measured for this study. PCR-RFLP and Fluidigm array system were used for the SNP genotyping. The pairwise SNPxSNP interaction analyses were performed between the nine SNPs and five major fatty acids (C16:0, C16:1, C18:0, C18:1 and C18:2) using ASReml-W software. The results indicated that total 22 SNP pairs showed significant effects on fatty acid composition (P<0.5). Furthermore, we identified how the genotypes of each significant SNP pairs act on fatty acid traits. In future, the results of this study could be useful for the chicken breeding program to improve meat quality.
Key Words : Chicken, Epistatic effect, Fatty acid composition, SNPxSNP interaction
Korean Society of Animal Breeding & Genetics • 10 PA-21
Genomic prediction for body measurement traits in Yorkshire pigs 1 1 1 1 1 1 1 1 Tae Jeong Choi , Seung Soo Lee , Yun Ho Choy , Chang Gwon Dang , Hyuk Kee Chang , Jae Gu Lee , Mi Na Park , Youlim Choi , 1 2 SiDong Kim andJungjae Lee
1 2 Division of Animal Breeding and Genetics, NIAS, RDA, Cheonan, Korea Jung P&C Institute, Inc., Yongin, Korea
ABSTRACT The objectives of this study was to investigate and compare the accuracy of genomic prediction for body measurement traits in Yorkshire pigs. Phenotypic data on body height (BH), body length (BL) from 2,432 Yorkshire pigs were used to obtain breeding values including as response variable the estimated breeding value (EBV) and two types of deregressed EBVs—one including the parent-average (DEBVincPA), and the other excluding it (DEBVexcPA). A final genotype panel comprising 46,199 SNP markers was retained for analysis after quality control for common SNPs. The BayesB and BayesC methods— with various π and weighted response variables (EBV, DEBVincPA, or DEBVexcPA)—were used to estimate SNP effects. The accuracy of genomic prediction was estimated using a 5-fold cross-validation with the K-means clustering method. Genomic accuracy was measured as the genomic correlation between the molecular breeding value and the individual weighted response variables (EBV, DEBVincPA, or DEBVexcPA). Diversity π did not influence the accuracy of genomic prediction. The BayesB method showed slightly higher genomic accuracy for body measurement traits than did the BayesC method in this study. Additionally, the genomic accuracy using DEBVincPA as response variable was higher than that using other response variables. Therefore, the genomic accuracy using BayesB (π = 0.90) with DEBVinPA as a response variable was the most effective in this study. The genomic accuracy for BH, BL were calculated to be 0.52, 0.60, respectively.
Key Words : Yorkshire pigs, body measurement traits, Bayesian method, Genomic Prediction
PA-22
Acquisition of resistance to avian influenza virus through targeted gene editing of cellular host factor in chicken fibroblast DF-1
Young Hyun Park¹, Hong Jo Lee¹, Kelly Chungu¹, Su Bin Lee¹, and Jae Yong Han¹
1 Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
ABSTRACT Since the influenza viruses inevitably utilize the host cellular machinery during their life cycle, avian-origin influenza virus (AIV) generally replicate well in avian host but not in mammals, indicating that there are different host factors between birds and mammals. A profoundunderstanding of the host cellular factors that support or limit viral life cycle is both important for the development of antiviral drugs and the prevention of influenza viruses. Although there has been an increase in knowledge of interaction dynamics among the AIVs and their cellular host factors, which of the host factor that are involved in the species- specific differential viral polymerase (vPol) activity is still unclear. Here, we targeted the AIV-associated host factor using CRISPR/Cas9- mediated gene editing system to examine the functional role of the host factor on vPol activity of AIV in chicken. First, we established the mutant clones, which were verified by DNA sequencing. Next, we revealed that the knockout of the host factor resulted in significant reduction in vPol activity and replication of AIVs compared to wild-type DF-1 cells. Furthermore, we showed that the gene edited DF-1 clones has increased cell survival compared to wild-type DF-1 cells upon infection of AIVs. Finally, via knockdown and enforced expression experiments, we found that the host factor members between chicken and human could play differential role in supporting of vPol activity. Our findings provide the novel understanding of the species-specific host factors for vPol activity, and the implications for the development of antiviral drug and strategy for AIV-resistant animals.
Key Words : Avian influenza virus, Chicken, Gene editing, Host factor
11 • 2019 International Symposium & Conference PA-23
Genome modification technologies in chicken for bioactive protein production
Young Min Kim, Jin Se Park, Hong Jo Lee, Kyung Youn Lee and Jae Yong Han
Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
ABSTRACT In recent, genome modification technologies such as piggyBac transposition and clustered regularly interspaced short palindromic repeats (CRISPR)/ CRISPR-associated protein 9 (CRISPR/Cas9) system has been provided lots of advantages in basic biological research and industry filed. In avian species, the primordial germ cell (PGC)-mediated germline transmission system could be combined with genome modification technologies for production of genome modified models. Especially, chicken has been considered great model of bioactive protein production because of the short generation time, low maintaining cost, high productivity and simple composition of egg white (EW) proteins. Furthermore, half of the chicken egg white proteins were coded from single gene, and its properties made it possible to use the chicken as an efficient bioreactor. Using the genome modification techniques, we successfully introduced the exogenous therapeutic protein expressing gene cassettes with chicken promoter, and also edited the endogenous chicken egg white gene into exogenous gene in chicken PGCs. The protein products derived from genome modified chicken showed consistent expression level and more effective in target cells than commercial counterpart due to its specific glycosylation. These results suggest that chicken bioreactor is one of the optimal systems for producing bioactive proteins based on cutting edged genome modifying techniques.
Key Words : Primordial germ cell, Genome modification, Chicken bioreactor, bioactive protein
PA-24
Genetic association between sow longevity and social genetic effects on growth in pigs 1 1 1 1 1 Joon Ki Hong , Kyu Ho Cho , Eun Seok Cho , Young Sin Kim and Tae Jeong Choi 1 National Institute of Animal Science, Rural Development Administration, Cheonan 31000, Korea
ABSTRACT Sow longevity is important for efficient and profitable pig farming. Recently, there has been an increasing interest in social genetic effect (SGE) of pigs on stress-tolerance and behavior. The present study aimed to estimate genetic correlations among average daily gain (ADG), stayability (STAY), and number of piglets born alive at the first parity (NBA1) in Korean Yorkshire pigs, using a model including SGE. The phenotypic records of ADG and reproductive traits of 33,120 and 11,654 pigs, respectively, were evaluated. The variances and (co) variances of the studied traits were estimated by a multi-trait animal model applying the Bayesian with linear-threshold models using Gibbs sampling. The direct and SGEs on ADG had a significantly negative (–0.30) and neutral (0.04) genetic relationship with STAY, respectively. In addition, the genetic correlation between the social effects on ADG and NBA1 tended to be positive (0.27), unlike the direct effects (–0.04). The genetic correlation of the total effect on ADG with that of STAY was negative (–0.23) but non- significant, owing to the social effect. These results suggested that total genetic effect on growth in the SGE model might reduce the negative effect on sow longevity because of the growth potential of pigs. We recommend including social effects as selection criteria in breeding programs to obtain satisfactory genetic changes in both growth and longevity. (RDA Project number : PJ012636, PJ014289)
Key Words : Indirect Genetic Effects; Longevity; Pigs; Stayability; Social Genetic Effects
Korean Society of Animal Breeding & Genetics • 12 PA-25
Development of simple avian sexing model system by targeting Z chromosome in chicken primordial germ cells 1 1 1 1 1 1 1 Kyung Youn Lee , Hong Jo Lee , Kyung Min Jung , Young Min Kim , Jin Se Park , Young Hyun Park , Deivendran Rengaraj and 1 Jae Yong Han 1 Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
ABSTRACT Genome modification technologies including clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein 9 (cas9) in avian species is expected to strength the advantages of aves as an animal model as well as industrial resources. Here, we developed the new chicken models by targeting chicken primordial germ cells (PGCs) through CRISPR/Cas9- mediated nonhomologous end joining repair pathway. By introduction of donor plasmid containing short guide RNA recognition sequences and CRISPR/Cas9 plasmid targeting intergenic region of Z chromosome into chicken PGCs, the donor plasmid was precisely inserted into Z chromosome, and generation of genome-modified chickens was accomplished via transplantation of the Z chromosome-targeted PGCs into recipient embryos. Through this method, we succeeded in production of genome-modified chickens that accurately targeted sex Z chromosome without off-target mutations. Z chromosome targeting chickens strongly expressed green fluorescent protein (GFP), which could be used for chicken sexing during embryonic development stage. Taken together, our results suggest that CRISPR/Cas9 mediated genome modification can be applied to avian model for a wide range of purposes, and we anticipate this simple method will be applied not only to targeted gene insertion but also to gene disruption or gene tagging.
Key Words : CRISPR/Cas9, Genome modification, Primordial germ cells, Z chromosome
PA-26
Sequential disruption of viral host receptor genes by programmable genome editing technology 1 1 1 1 1 1 Soo Taek Han , Hong Jo Lee , Kyung Youn Lee , Kyung Min Jung , Kyu Hyuk Lee and Jae Yong Han 1 Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
ABSTRACT Wide spread of avian leukosis virus (ALV) has caused economic losses in poultry industry of asia and also threaten biodiversity of avian species. To confer resistant to the viral disease, we applied one of the programmable genome editing tools, clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9), for targeted gene disruption of ALV host receptors. By introduction of CRISPR/Cas9 vector which targeting ALV host receptor genes into chicken DF-1 fibroblasts, we successfully induced indel mutations on targeted locus. Viral challenge experiments revealed that the established DF-1 clones which having mutations on ALV host receptor genes confer resistant to ALV. Furthermore, we sequentially modified tva, tvb, and Na+ /H+ exchange 1 (chNHE1) genes in DF-1, which are the specific receptors for ALV subgroups A, B, and J, respectively. Sequential genome modifications of the host receptors and subsequent viral challenge experiments revealed that the tva, tvb, and chNHE1-modified DF-1 clones confer to resistant to ALV subgroups A, B, and J, simultaneously, and also the results suggest that ALV subgroups A, B, and J do not share host receptors. Collectively, this sequential disruption strategy could be used to generate cells resistant to multiple viral pathogens and also could contribute to develop viral disease resistant aves.
Key Words : Avian leukosis virus, CRISPR/Cas9, Genome editing, Host receptor
13 • 2019 International Symposium & Conference PA-27
Novel folding-upon-binding mechanism of chicken NANOG in Primordial germ cells 1 1 1 1 Hee Jung Choi , Hong Jo Lee , Yong Hyun Park and Jae Yong Han 1 Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
ABSTRACT Homeobox protein NANOG is a key regulatory factor for maintenance of pluripotency in embryonic stem cells (ESC) and it plays important role in maintenance of primordial germ cell (PGCs) characteristics. However, the molecular mechanism behind the maintenance of PGCs by NANOG is not fully understood. In this study, we found chicken NANOG (cNANOG) forms a high-order oligomer via a disorder-to-order conformational transition of its C-terminal domain (CTD). Moreover, we identified novel hydrophobic interaction motif, which is distinct from the dimerization of mammalian NANOG in its CTD. Mutation of interaction motif was completely prevented the self-association. We performed the impact of the self-association of cNANOG using sequential transfection of PGCs. Interestingly, the results indicated that self-association of cNANOG is required for maintenance of pluripotency related gene and proliferation of PGCs. Our results contributed to understanding the unique self-association mechanism of cNANOG and its function in PGCs.
Key Words : Primordial germ cells, NANOG, chicken, self-association
PA-28
Genome Editing in Bird 1 Jae Yong Han
1 Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
ABSTRACT The genome editing technology has been rapidly developed and provided numerous benefits in diverse areas of research as well as industry, and the genome editing technologies such as clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (CRISPR/Cas9) technology have been facilitated to develop genome-edited bird. Since the avian species have been recognized as ideal experimental models due to their distinctive developmental characteristics, the genome editing technology has been expected to maximize the values of bird. And also the technology is expected to enhance the value of bird as industrial resources by acquiring disease- resistance or promoting functional protein synthesis in bird’s egg. To generate genome-edited birds, primordial germ cell (PGC) has been used for germline transmission system. Because avian PGCs migrate to embryonic gonads through embryonic blood stream unlike to mammal PGCs, the production of germline chimeric birds can be achieved by transplantation of PGC into embryonic blood vessel of recipient embryo. Applying the genome editing technologies such as CRISPR/Cas9 to the PGC-mediated germline transmission system of bird, the production of genome-edited bird has been accelerated. In these regards, we developed novel chicken lines by applying CRISPR/Cas9 and non-homologous end joining (NHEJ) pathway-mediated (CRISPR/Cas9-NHEJ mediated) genome editing strategy to chicken PGCs. Based on the genome editing strategy, we developed the novel germ cell tracing chicken model by gene tagging into the germ cell-specific gene. And also we developed a chicken sexing model by targeted gene insertion of fluorescent protein expression cassette to chicken sex Z chromosome. Furthermore, we accomplished targeted gene disruption of sex determination factor, which play a major role in male sex determination. Collectively, these results suggest that the genome editing method mediated by CRISPR/Cas9- NHEJ is simple and powerful strategy for genome-edited birds, and it will facilitate the production of genome- edited birds for diverse purposes by gene tagging, targeted gene insertion and targeted gene disruption.
Key Words : Avian species, chicken, CRISPR/Cas9, genome editing
Korean Society of Animal Breeding & Genetics • 14 PA-29
Immunophysiological responses to exercise-induced stress of Jeju and Thoroughbred horses
Saichit Khummuang, Hyo Gun Lee, Sang Seok Joo, Jeong-Woong Park, Jae-Young Choi, Jin Hyeog Oh, Kyoung Hwan Kim, Hyun-Hee Youn, Myunghoo Kim, and Byung-Wook Cho
Department of Animal Science, College of Natural Resources and Life Sciences, Pusan National University, Miryang 50463, Republic of Korea
ABSTRACT Jeju and Thoroughbred horses are classified as Equus caballus which have some differences in anatomy resulting in different racing performance. This study was conducted to investigate the immunophysiological responses to exercise-induced stress in these breeds. The hematological, biochemical, and immunological profiles of the blood samples were analyzed of adult Jeju (N = 5) and Thoroughbred (N = 5) horses pre- and post-exercise. Both Jeju and Thoroughbred horses displayed with significantly increased in rectal temperatures, cortisol levels, and muscle catabolism- associated metabolites post- exercise. Moreover, red blood cell indices were significantly higher in Thoroughbred horses than in Jeju horses. In addition, exercise-induced stress triggered the formation of neutrophil extracellular traps (NETs) and reduced platelet counts in Jeju horses but not in Thoroughbred horses. HSP72 and HSPA6 expression, is rapidly modulated in response to exercise- induced stress in the PBMCs of Jeju horses whereas The CXCR4 expression in PBMCs was higher in Thoroughbred horses post-exercise. Taken together, the different immunophysiological responses of Jeju and Thoroughbred horses enlighten the differences in the physiological and anatomical properties of these breeds. The physiology of Thoroughbred horses makes them suitable for racing as less sensitivity to exercise-induced stress compared to Jeju horses. This study provides a basis for investigating the linkage between exercise-induced stress and the physiological alteration of horses. Hence, our findings show that some of assessed parameters could be used in breeding programs to improve the physical performance of horses and reduce associated exercise-related stress to endure horse racing performance.
Key Words : Jeju horse, Thoroughbred horse, Exercise, Blood analysis and Immunological gene expression
PA-30
Epigenetic regulation of moderate NANOG expression by REST/CoREST/HDAC co-repressor complex in chicken primordial germ cells 1 1 1 1 Ho Yeon Cho , Young Hyun Park , Deivendran Rengaraj and JaeYong Han
1 Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
ABSTRACT Primordial germ cells (PGCs) are the precursors of sperm and oocytes, which have ability of transmitting genetic information to the next generation. The transcription factor NANOG is an important for regulating pluripotency in embryonic stem cells (ESCs) and even differentiating PGCs. However, epigenetic regulations of NANOG with histone deacetylase (HDAC) complex have not been studied in chicken. In this study, we investigated the mechanism of NANOG expression with epigenetic regulations in chicken PGCs. We identified the upstream region of NANOG promoter is moderately suppressed by histone deacetylation while NANOG is highly activated in chicken PGCs through ChIP pcr results. Also immunocytochemical and western blot analysis indicated that H3 lysine 9 acetylation (H3K9ac) is induced by treatment of HDAC inhibitor resulting de-repression of NANOG expression. Furthermore, we confirmed HDAC complex members containing RE1-silencing transcription factor (REST) and REST corepressor 3 (RCOR3) is epigenetically modulating NANOG expression in chicken PGCs by knockdown studies. We revealed that moderate expression of NANOG is regulated by REST/CoREST/HDAC complex, and this mechanism could be crucial for maintaining integrity of chicken PGCs.
Key Words : chicken, primordial germ cells, NANOG, RE1-silencing transcription factor, REST corepresspr, histone deacetylation
15 • 2019 International Symposium & Conference PA-31
Digestive and metabolic pathway for production traits by genetic hitch-hiking effect of Hanwoo. 1 1 1 1 2 3 4 1 Dongwon Seo , Doo Ho Lee , Yoon Ji Chung , Soo Hyun Lee , Mina Park , Byoungho Park , Ho Baek Yun , Seung Hwan Lee 1 2 Division of Animal & Dairy Science, Chung Nam National University, Daejeon, 34134, Korea Animal Genetics & Breeding Division, 3 National Institute of Animal Science, Seonghwan, 31000, Korea Poultry Research Institute, National Institute of Animal Science, 4 Pyeongchang, 25342, Korea Hanwoo Research Institute, National Institute of Animal Science, RDA, Pyeongchang, 25340, Korea
ABSTRACT The Hanwoo has been used as a major labor force in the past, but recently it has become the representative meat of Korea by government animal breeding system for improvement of carcass traits including meat quality. Therefore, analyzing the selection signature of Hanwoo can not only find the genetic background of selection index phenotypes, but also detect a genetic evidence of unintended productivity traits. In this study, the signature of selection was analyzed with the integrated haplotype score (iHS), and as a result, a total of 9 ancestral alleles and 30 derived alleles were identified. Among these, the three SNP regions of BTA14 confirmed that consistent with the CW and EMA results of GWAS, but 34 SNP regions of BTA13 were newly identified SNPs which have no evidence of phenotype in the previous association studies. The highest iHS values of ancestral and derived alleles were analyzed gene ontology and KEGG pathway using selected gene list by their functions. As a result, one derived allele confirmed 45 functional pathways by 16 GO term genes. Of these, 14 pathways were significantly associated with selected gene list and most significant pathways were confirmed as salivary secretion, glucagon signaling pathway, and insulin signaling pathway. Moreover, other functional pathways also detected as digestive and energy metabolism by a total of five GO term genes. These results can be considered that digestive and metabolic functional traits were selected by hitch-hiking effect in the Hanwoo population and these traits can be used for improvement of nutritional factors by the genomic selection approach.
Key Words : Hanwoo, signature of selection, integrated haplotype score, pathway.
PA-32
Signaling pathways taking cover of acute asymmetric cellularization and lineage segregation are revealed by the transcriptome of chicken embryos 1 1 1 1 1 You Yun Kim , Hong Jo Lee , Young Hyun Park , Hee Jung Choi , and Jae Yong Han 1 Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
ABSTRACT In the Bird 10,000 Genomes (B10K) project, phylogenomics and comparative functional genomics of avian species were investigated. This was due to the significance of evolutionary position of birds and their value as a research model. However, because of the realistic difficulties in getting pre- oviposited eggs, the systematic profiling of transcriptional changes before oviposition has not been studied deeply in avian species. Here in this research, 137 pre- oviposited embryos were obtained from hen ovaries and oviducts, and RNA-sequencing analyses were performed. Chicken zygotic genome activation (ZGA) was observed by two waves. During cleavage and area pellucida formation, developmental processes were independently detected. These processes such as Notch, Wnt, MAPK and TGFβ signaling shows distinct function. Moreover, the early stages of chicken development and the human and mouse counterparts were compared emphasizing chicken signaling pathways. This also highlights the gradually analogous gene expression via ZGA. These results will now suggest a genome-wide understanding of avian embryogenesis and comparisons of amniotes.
Key Words : Aves, Amniotes, Early embryo, RNA-seq, Signaling pathways
Korean Society of Animal Breeding & Genetics • 16 PA-33
시계열 ARIMA 모형을 통한 국내 종돈장의 사육규모 변화 예측 1 1 1 1 1 1 1 2 2 3 4 5 손지현 , 차대협 , 구양모 , 이기환 , 김정일 , 김성수 , 정용호 , 임현태 , 이정규 , 서강석 , 이지홍 , 최태정 1 2 3 4 5 한국종축개량협회, 경상대학교, 순천대학교, 경북도립대학, 국립축산과학원
ABSTRACT 본 연구는 2014년부터 2017년 6월까지 한국종축개량협회의 3개 품종 농장 등록자료 546,473두의 자료를 이용하여 사육규모별로 100 두 미만, 100두 이상 300두 미만, 300두 이상 500두 미만, 500두 이상 및 전체두수의 5그룹으로 설정하였고 시계열 데이터 생성을 위해 1개월 단위로 세 분화하였으며 변화 추세의 예측을 위하여 SAS/ETS 프로그램의 시계열 ARIMA 모형을 통한 분석을 실시하였다. 사육규모에 따른 출생년도별 월별 사육두수의 변화 추세를 살펴보면 전체 농장의 사육두수는 월 평균 약 99두가 증가하는 것으로 나타났으며 100두 미만 농장의 경우 월평균 약 35두 가량 감소하는 것으로 나타났다, 이를 제외한 100두 이상 300두 미만 농장의 경우 월 평균 41두, 300두 이상 500두 이상 농장 월 평균 약 35두 및 500두 이상 농장에서 약 57두가 증가하는 것으로 나타나 500두 이상 대규모 농장은 지속적으로 사육두수가 증가하는 것으로 나타났다. 사육규모별 17년 6월 이후 향후 1년간 사육두수의 예측 추세 분석결과를 살펴보면 17년 7월 대비 18년 6월 예측 두수는 100두 미만 농장에서 약 430두(24.6%) 증가할 것으로 나타났고 100두 이상 300두 미만 농장에서는 약 389두(11.5%) 증가할 것으로 나타났으며 300두 이상 500두 미만 농장에서는 약 972두(21.6%) 증가할 것으로 나타났다. 500두 이상 농장에서 약 620두(10.6%) 증가할 것으로 나타났으며 전체 농장은 약 2,843두 (17.1%) 증가할 것으로 나타났다. 마지막으로 향후 사육규모별 추세를 살펴보면 100두 미만 농장의 경우 전체적으로 봤을 때 감소할 것으로 나 타났고 이를 제외한 모든 사육규모별 두수는 전체적으로 증가할 것으로 나타났다.
Key Words : 종돈, 시계역 분석, 사육규모
PA-34
Frame switch splicing of X-box binding protein 1 gene induced by heat stress in horse muscle cells
Saichit Khummuang, Hyo Gun Lee, Kyoung Hwan Kim, Hyun-Hee Youn, Jeong-Woong Park, Jae- Young Choi, and Byung-Wook Cho
Department of Animal Science, College of Natural Resources and Life Sciences, Pusan National University, Miryang 50463, Korea
ABSTRACT The unfolded protein response (UPR) is a well-known mechanism related to endoplasmic reticulum (ER) stress. ER stress is induced by various external and environmental factors such as starvation, ischemia, hypoxia, oxidative stress, and heat stress. Inositol requiring enzyme 1α (IRE1α)- X-box protein 1 (XBP1) is the most conserved signalling pathway involved in the UPR to downstream ER-associated degradation (ERAD) or UPR-related genes. Frame switch splicing of XBP1 transcription factor is a novel mechanism of splicing(s) XBP-1 nuclear translocation to maintain the refolding and degradation of protein. Horses were considered as exercise models of racing performance and their muscle is subjected to higher thermal stress after exercise than other tissues. Therefore, we examined the frame switch splicing of horse XBP1 and its dynamics using muscle cells exposed to heat stress. The results showed that the duration of thermal stress effected horse sXBP-1 mRNA by deletion 26 nucleotides in the exon 4 after heat stress. The protein sequence and the cis-regulatory elements on the promoter of horse XBP1 are highly conserved among the mammals. Induction of putative downstream genes of horse XBP1 was dependent on the duration of heat stress. We confirmed that both the mechanisms of XBP1 frame switch splicing and various binding elements found in downstream gene promoters are highly evolutionarily conserved. In conclusion, the frame switch splicing of horse XBP1 and its dynamics were highly conserved among species. This finding provide valuable information for the continuation of ER stress-related studies in horse in relation to various environmental stresses.
Key Words : Endoplasmic reticulum stress, Heat stress, X-box binding protein 1, Frame switch splicing and Horse muscle cells
17 • 2019 International Symposium & Conference PA-35
Quantitative proteomic analysis of poly (I:C)-induced differentially expressed proteins in chicken DF-1 cells by 2D-electrophoresis and LC-MS/MS 1 1 2 1 2 3 1 2 3 Ra Ham Lee , Wanjeong Ryu , Jae-Young Heo , Hak-Kyo Lee , , , Ki-Duk Song , , 1 2 Department of Animal Biotechnology, Cheonbuk National University, Jeonju, 54896, Republic of Korea, Korea International Agricultural 3 Development and Cooperation Center, Chonbuk National University, Jeonju 54896, Republic of Korea, Animal Molecular Genetics and Breeding Center, Cheonbuk National University, Jeonju, 54896, Republic of Korea, Korea
ABSTRACT With the development of the poultry industry, problems with viral diseases as well as inflammatory diseases caused by them are increasing. To date, molecular studies on poultry have not been undertaken at the same level of detail as those of mice. In the present study, a chicken embryonic fibroblast cell line (DF-1 cells) was treated with polyinosinic:polycytidylic acid (poly (I:C)), which engages with toll-like receptor 3 (TLR3) to induce inflammatory responses. Thirty differentially expressed proteins were screened using two-dimensional electrophoresis (2-DE). Further, the LC- MS/MS method was used for quantitative protein analysis. Additionally, the Gene ontology (GO) database was used to analyze the differentially expressed proteins. Our results indicated that Parkinson disease protein 7 (PARK7) is accessible as a potential inflammatory biomarker. Moreover, we observed that PARK7 expression is inhibited after poly (I:C) treatment using NF-κB or AP-1 inhibitors in chicken DF-1 cells. In sum, our results suggest that PARK7 may be a target gene for TLR3 signaling. and may provide the basis for identifying new inflammatory response mechanisms in chickens.
Key Words : chicken, TLR3, inflammation, proteomics, PARK7
PA-36
Characteristics and Genetic Polymorphism of Autosomal MS Marker in Sus scrofa domesticus
Hyun Ju Kim, Ju yeong Ham and Yong Teak Sim
DNA analysis laboratory, miDNA Genome Research Institute, Kunsan, 54156
ABSTRACT Pigs are one of the most important sources of protein for human, accounting for the largest share of meat consumption in Korea. To protect pig markets and monitor their deceptive distribution, microsatellite analysis has been applied for individual identifications been used for these purposes. However, there have been reported some disadvantages of the loci. Many of them were co-amplified with confusing stutter peaks from multiplex PCR and their allele distribution was out of Hardy-Weinberg equilibrium. In this study, we screened 12 tri-, 11 tetra-, 5 penta-nucleotied repeat microsatellites from 18 Sus scrofa automosal chromosomes and analysed their genetic parameters using 165 individuals consisting three races of pigs, Landrace, Duroc and Yorkshire. Of the twenty-eight loci, fifteen loci revealed a power of discrimination (PD) greater than 0.8 and six loci were Hardy- Weinberg equilibrium. In addition, the larger the repeating nucleotide sequence unit, the lower the occurrence rate of the stutter peak and the higher the discrimination power. These results demonstrated that some markers we studied could be used to improve pig microsatellite analysis for the individual and paternity identification.
Key Words : Microsatellite marker, Sus scrofa demesticus, Genotyping
Korean Society of Animal Breeding & Genetics • 18 PA-37
Improvement of genetic evaluation for genotyped and non-genotyped reference population using single step BLUP in Hanwoo 1 1 1 1 1 1 Dooho Lee , Dongwon Seo , Soohyun Lee , Sungbong Jang , Hyojun Lee , Seunghwan Lee
¹Division of Animal & Dairy Science, Chung Nam National University, Daejeon, 305-764, Korea
ABSTRACT As the development of genomic technology come out with many SNP panels and genotyping cost has been decreasing. Genomic selection utilizing genomic technology is actively studied. However, there are limitations on the use of all phenotypes as reference population because there are more individuals in the reference population that do non-genotyped than those that genotyped data. To solve this problem, a single step BLUP (ssBLUP) method has been studied to increase the reference population by using pedigree and genotype data with phenotype as a reference population. The purpose of this study is to compare the accuracy of genetic evaluation using BLUP, gBLUP and ssBLUP method in Hanwoo. A total of 12678 commercial Hanwoo data were genotyped with the Illumina bovine 50K v3 and Hanwoo v1 Beadchip and of these animals, 2678 animals were used as the test set and the remaining 10000 animals were used as the reference set consist of four scenarios (2500, 5000, 7500, 10000). Each scenario was compared with the accuracy of genetic evaluation using three different methods: traditional pedigree-based BLUP (BLUP), genomic BLUP (gBLUP), and single step BLUP (ssBLUP). The traits used in the analysis were four economic traits: back-fat thickness (BFT), carcass weight (CWT), eye muscle area (EMA), and marbling score (MS). Results showed that the accuracy of genetic evaluation increased from 14.3 (31.2)% to 45.7 (68.4)% as the increasing of the reference population size and in the three different methods, we found that the ssBLUP method accuracy differs about 20% from the BLUP and gBLUP method. Among the four economic traits, MS traits showed the greatest difference in accuracy according to the reference population size and the method. These results show that the ssBLUP method can be applied to genetic evaluation for economic traits in Hanwoo.
Key Words : Genomic selection, Pedigree, SNP chip, GRM, ssblup, Hanwoo
PA-38
고밀도 유전체 정보를 이용한 육종가 추정 소프트웨어 개발
이준호
주식회사 진앱스, 서울특별시, 06123, 대한민국
ABSTRACT 해외에서 개발된 유전체 육종가 추정 프로그램은 매우 느리거나, 자료의 수를 제한하거나, 학업 또는 연구용으로만 이용을 제한한 경우가 대부 분이다. 이과 같은 제한사항없이 상업적 이용이 가능한 프로그램은 일년에 약 육만불 정도로 매우 비싸기 때문에 외화 낭비를 막고 기술경쟁력 을 확보하고자 본 소프트웨어를 개발하였다. 유전체 정보가 있는 개체들과 없는 개체들 모두를 이용하여 육종가를 추정하는 Single-step GBLUP 방법을 적용하였으며, 대칭희소행렬(Sparse Symmetric Matrix) 로 구성된 혼합행렬방정식의 해를 구하는데 효율적인 PCG(Preconditioned Conjugate Gradient)를 적용하였다. 프로그램의 정확도 비교를 위하여 blupf90프로그램의 관계행렬의 원소들 및 육종가와 본 소프트웨어의 결과 치와의 상관계수를 계산하였다. 관계행렬 원소들의 프로그램별 상관계수는 유전체관계행렬, 혈통관계행렬 중 유전체부분, 그리고 이 행렬들의 역행렬에서 각각 0.99999, 0.99981, 0.99994, 0.99949 로 나타났으며, 방정식의 고정환경효과부분의 해 및 육종가부분의 상관계수는 각각 0.99997, 0.99979 로 나타나 blupf90와 개발된 소프트웨어가 같은 결과를 제공하는 것이 확인되었다.
Key Words : 고밀도 유전체 정보, 유전체 선발, Preconditioned Conjugate Gradient, Single-step GBLUP, 유전체 육종가
19 • 2019 International Symposium & Conference PA-39
A comparative study of estimated breeding value with Hanwoo cows using genomic information 1 2 1 1 Dong Jae Lee , Seung Hwan Lee , Sang Eun Park , Duhak Yoon 1 2 Department of Animal Science & Biotechnology, Kyungpook National University, Sangju, 37224, Korea Division of Animal & Dairy Science, Chungnam National University, Daejeon, 34134, Korea
ABSTRACT Genomic selection can be used for predicting the breeding values for non-phenotypic animals, from a large number of single nucleotide polymorphism (SNP) markers across the whole genome. This study was conducted to compare the accuracy of estimated breeding value (EBV), genomic estimated breeding value (GEBV) and single-step genomic estimated breeding value (ssGEBV) for carcass traits of 935 Hanwoo cows. The carcass traits considered in this study were carcass weight (CW), eye muscle area (EMA), backfat thickness (BFT) and marbling score (MS). The EBV analysis was performed using the best linear unbiased prediction (BLUP) method by constructing a numerator relationship matrix (NRM) with the pedigree information of 935 cows and phenotype data of the 9,849 Hanwoo in commercial farms. The GEBV analysis was performed using genomic best linear unbiased prediction (GBLUP) method by constructing a genomic relationship matrix (GRM) with SNP 50K information of 935 cows, and phenotypic and genomic data of Hanwoo used in BLUP analysis as reference population. The ssGEBV analysis was performed with single-step genomic BLUP (ssGBLUP) based on the relationship matrix H, which is constructed from the numerator relationship matrix (A) augmented by the genomic relationship matrix (G). As the results, the differences in accuracies of GEBV and EBV for CW, EMA, BFT and MS traits for 935 cows showed that the accuracies of GEBV were increased by 47.18%, 42.42%, 44.02% and 51.03%, respectively. The accuracies of ssGEBV compared to EBV for CW, EMA, BFT and MS were increased by 47.78%, 42.99%, 44.51% and 51.39%, respectively. When ssGEBV was compared with GEBV for CW, EMA, BFT and MS, there were increased by 0.41%, 0.40%, 0.34% and 0.23%, respectively. As conclusion, this study suggests that GBLUP and ssGBLUP methods for Hanwoo cows are able to improve the accuracy of the estimated breeding value using genomic information. It could to help the management of cows and the establishment of a breeding system in the Hanwoo farms.
Key Words : Hanwoo cows, SNP, GBLUP, Accuracy
PA-40
Characterization of gap junction protein alpha 4 (GJA4) gene variation in horse 1 1 1 1 1 2 1 Jae-Young Choi , In Cheol Cho , Nam Young Kim , Jae Hoon Woo , Sang Min Shin , Jong-Eun Park , Moon Cheol Shin , Ji Hyun 1 3,* 1,* Yoo , Byung-Wook Cho and Byoung Chul Yang 1 2 Subtropical Livestock Research Institute, National Institute of Animal Science, RDA, Jeju 63242, Republic of Korea Animal Genomics 3 and Bioinformatics Division, National Instituteof Animal Science, Rural Development Administration, Wanju55365, Korea The Animal Molecular Genetics and Breeding Center, Chonbuk National University, Jeonju 54896, Republic of Korea.
ABSTRACT The aim of this study was to analyze the novel single nucleotide polymorphisms (SNPs) of the horse GJA4 gene identified in horse muscle RNA-seq and to predict structural changes of proteins by SNPs. In previous studies, we found differentially expressed genes (DEGs) that using before and after exercise through RNA-seq analysis in Thoroughbred. We also conducted evolutionary analysis using Thoroughbred and Jeju horse re-sequencing data. As a result, we found a novel SNP present in the GJA4 (LOC22385534 C>G) from the evolutionarily selected gene in the Thoroughbred horse. Transcription factor (TF) binding sites in the 5′-regulatory region of this gene were identified through PROMO. Using bioinformatic tools, we predicted the influence of non- synonymous SNP (nsSNP) on the function and stability. In addition, we confirmed the change of protein structure due to the amino acid sequence change, proline to arginine according to nsSNP. Our analysis will be helpful as a basis for studying genes and SNPs that affect in horses.
Key Words : Horse, SNPs, Transcription factor, Protein structure
Korean Society of Animal Breeding & Genetics • 20 PA-41
Genotype-environment interactions for on-farm performance traits of Landrace population in Korea 1 2 2 2 1 1, 2 Donghyun Shin , KyeongHye Won , Young-Sup Lee , Seungwoo Son , Geewon Kim and Hak-Kyo Lee 1 2 The Animal Molecular Genetics and Breeding Center, Chon-buk National University, Jeonju,Korea Department of Animal Biotechnology, Chon-buk National University, Jeonju, Korea
ABSTRACT Due to the lack of statistical power and several confounding effects of population structure in Landrace population data, genotype-environment interactions for on-farm performance traits of Landrace population in Korea remain unknown. So we want to estimation of genotype-environment interaction for exploring how genotype and environmental factors interact to in their influence onto on-farm performance traits. We analyzed five on-farm performance traits in over thousands Landrace individuals in Korea using approximately 50,000 autosomal single nucleotide polymorphisms (SNPs) collected from GGP(Grand-Grand-Parents) farms. And we estimated the statistically significant proportion of variance that could be explained by genotype-environment interactions in economic Landrace traits. Our data suggested that the genotypes could have different effects on each traits in different environmental settings using Landrace genomic data. In this study, we could investigate the genotype groups of individuals with similar genetic profiles based on the additive genetic relationships among individuals using SNP data. We observed the norms of reaction in Landrace population, and the differential phenotypic response of a genotype to a change in environmental exposure. This significant estimate of genotype-environment interactions will lead to conceptual advances in Landrace genome study and could be ultimately applied to selection of superior piglet in GGP farm.
Key Words : Landrace, SNP, genotype-environment interactions
PA-42
국가단위 한우 당·후대 검정우 선발지수식 통일에 따른 영향 분석
박미나, 김시동, 최태정, 최유림, 최연호, 이승수, 당창권, 이재구, 장혁기, 아람마부
농촌진흥청 국립축산과학원 가축개량평가과
ABSTRACT 국가단위 한우 유전능력 평가는 1995년부터 현재의 BLUP(Best Linear Unbiased Prediction) 통계 모델을 이용하여 당·후대 검정우의 유전능력을 분석하고, 이를 이용하여 후보씨수소 및 보증씨수소를 선발하여 왔다. 2017년 하반기부터 혈통자료, 검정자료에 유전체 정보를 추가하여 유전 능력을 분석하는 Single-Step GBLUP 평가 체계를 구축하여 2018년부터 본격적으로 당대검정후보우 송아지, 당대검정우 , 후대검정우의 유전체 유전능력 평가를 진행하였다. 이에 따라 형질별 유전능력의 정확도가 향상되었고, 보다 효율적인 씨수소 선발을 위하여 후보씨수소 선발지수 (2×12개월령 체중 + 1×근내지방도)를 보증씨수소 선발지수(1×도체중 + 1×등심단면적 - 1×등지방두께 + 6×근내지방도)로 통일 할 경우 선발되는 보증씨수소의 유전능력 변화를 분석하였다. 분석대상은 2016년부터 2018년까지 최근 3년간의 당대검정우(70차~75차)이며, 각 차수 별 약 450두의 당대검정 우 중 후보씨수소로 선발되는 유전능력 상위 35두를 각 차수별로 선별한 총 210두이다. 각 후보씨수소 및 보증씨수소 선 발지수로 선별한 210두의 유전능력을 2019년 3월 국가단위 당대검정우 평가 결과를 이용하여 도체 중, 등심단면적, 등지방두께, 근내지방도의 유전능력을 비교하였다. 그 결과, 도체중 유전능력은 후보씨수소 선발지수로 선발한 집단은 평균 55.29kg, 보증씨수소로 선발한 집단은 33.81kg 이었고, 등심단면적은 각 10.74cm2, 8.73cm2, 등지방두께는 –0.9mm, -1.05mm, 근내지방도는 0.90점, 1.60점이었다. 후보씨수소 선발지수로 선발한 집단의 경우 도체중, 등심단면적의 유전능력이 우수하였고, 보증씨수소로 선발한 집단의 경우 등지방두께, 근내지방도의 유전능력이 우 수하였다.
Key Words : 한우, 후보씨수소, 보증씨수소, 선발지수식
21 • 2019 International Symposium & Conference PA-43
Result of Genetic Evaluation of Korean Native Chicken with Multiple Traits Animal Models
권일, 박병호, 허강녕, 차재범, 추효준
국립축산과학원 가금연구소
ABSTRACT 본 연구는 국립축산과학원 가금연구소에서 보유 중인 적갈색 재래닭 (R계통), 황갈색 재래닭 (Y계통)의 선발을 위해 8주령 체중, 40주 산란수에 대해 유전능력 평가를 실시하였다. 유전능력평가를 위하여 적갈색 재래닭의 8주령 체중 1,198수, 40주령 산란수 876수에 대해 능력 자료를 분석 하였고, 황갈색 재래닭의 경우 8주령 체중 1,245수, 40주령 산란수 804수에 대해 자료를 분석하였다. 분석에 사용한 모수는 ‘03~’13년 토종닭 집 단에서 추정한 150일령 체중과 270일령 산란수의 모수를 활용하였고, 체중 유전력은 적갈색 재래닭 0.35, 황갈색 재래닭 0.56, 산란수 유전력은 각각 0.28, 0.23로 나타났으며, 체중과 산란수의 유전상관은 –0.09로 나타났다. 육종가 추정을 위하여 다형질 개체모형을 이용하였고, 추정한 육 종가를 표준화하여 체중과 산란수에 1:4의 가중치를 두어 총 육종가를 추정하였다. 적갈색 재래닭의 8주령 체중의 평균과 표준편차는 733±141.6g 이었고, 40주령 산란수의 평균 및 표준편차는 92±11.9개로 나타났으며, 황갈색 재래닭의 8주령 체중은 710±114.2g, 40주령 산란수는 98±12.5 개로 나타났다. 2년간 (‘16~’18) 8주령 체중의 유전적 개량량의 경우 두 계통에서 각각 36.1g, 42.4g으로 나타났으며, 연간 개량량은 각각 18.1g, 21.2g으로 나타났다. 40주령 산란수의 경우 두 계통의 1년간(‘17~’18) 유전적 개량량은 각각 2.17개, 2.09개로 나타났다. 본 연구에서 수행된 유 전능력평가 결과는 가금연구소 토종닭 선발에 이용되었다.
Key Words : 토종닭, 재래닭, 체중, 산란수, 유전능력평가
PA-44
Positional candidate gene of purebred Landrace body legnth trait by Genome-wide association study 1 2 3 4 5 1, 3, 4 강호찬 , 이재봉 , 유채경 , 김은호 , 최태정 , 임현태
1 2 3 4 경상대학교 축산학과, 전북대학교 인수공통전염병연구소, 경상대학교 농업생명과학연구소, 경상대학교 응용생명과학과(BK21 plus), 5 국립축산과학원 양돈과
ABSTRACT 양돈산업에서 돈육의 생산량 증가와 번식 관련 형질의 개선을 위해 체장에 대한 선발육종을 진행해왔으며, 양돈의 체장은 척추 수와 높은 연관 을 보이는 것으로 알려져 있고 척추 수가 증가함에 따라 도체중, 유두 수 등이 함께 증가한다. 따라서 본 연구는 순종 랜드레이스의 체장 형질에 관한 Genome-wide association study (GWAS)를 실시하였다. 순종 랜드레이스 542두의 genomic DNA를 이용하여 MINITAB program의 Ryan- Joiner Method으로 normality test를 실시하고 이상치를 제거한 결과 471두가 분석에 사용되었으며, 평균은 103.3cm, 최대값은 120cm, 최소값은 94cm로 확인되었다. Porcine SNP 60K bead chip으로 SNP marker의 유전자형을 분석하였으며, Plink program Ver.1.07을 이용하여 quality control 과정을 통하여 최종적으로 상염색체상의 42,262개의 SNP marker가 분석에 이용되었다. GWAS 분석은 Genome-wide Complex Trait Analysis (GCTA) program에서 제공하는 mlma command를 이용하여 SNP marker와 표현형 형질의 관련성을 분석하였으며, 유의적인 marker의 임계수 준은 Bonferroni adjusted genome-wide suggestive (1/ 상염색체상의 SNP marker수)로 탐색하였다. 유의적인 SNP marker의 위치상 후보유전자는 National Center for Biotechnology Information에서 제공하는 dbSNP map ver.11.1을 이용하였고, GWAS 분석 결과 체장 형질의 유의적인 SNP marker는 염색체 6번에서 1개(ASGA0100434; P = 2.15 ｘ 10 -05 ), 염색체 8번에서 1개(ASGA0088957; P = 7.91 ｘ 10 -06 )로 탐색되었으며, 각 marker의 위치상 후보유전자는 GNG12, LOC110262082로 동정되었다. LOC110262082 유전자는 기능에 대하여 알려진 바 없으나, GNG12 유전자는 세포성장과 연관 있는 유전자로 알려져 있다. 따라서 GNG12 유전자는 체장 뿐만 아니라 성장의 전반적인 형질에 영향을 미칠 것으로 판단된다. 본 연구는 순종 렌드레이스 체장 형질의 GWAS 분석으로 위치상 후보유전자 탐색을 수행하였으며, 그 결과 GNG12 유전자는 추가적 인 기능 연구를 통하여 양돈 체장 형질에 대한 선발의 기초 연구 자료가 될 것으로 생각된다.
Key Words : Genome-wide association study, 위치상 후보유전자, 순종 랜드레이스, SNP
Korean Society of Animal Breeding & Genetics • 22 PA-45
재래돼지 산자수에 대한 근친퇴화 효과 1 1 1 1 홍준기 , 김영신 , 조은석 , 조규호
1 농촌진흥청 국립축산과학원, 충남 천안, 31000, 대한민국
ABSTRACT 근친에 따른 개체의 능력저하 현상은 다양한 식물과 동물에서 밝혀져 왔다. 재래돼지는 국내 유일 품종이며 소규모 집단으로 유지되고 있어 국 가 차원에서 중요한 유전자원이다. 본 연구의 목적은 총산자수와 생존산자수에 대한 근교계수, 유전모수 및 근친퇴화 효과를 분석하는 것이다. 국립축산과학원에서 보유한 재래돼지 혈통 2,806두와 483개(1~5산차)의 번식성적을 보유한 모돈 303두의 자료를 활용하였다. 각 형질에 대한 유전모수 추정 후 혼합모형으로 근교계수에 대한 근친퇴화 효과를 분석하였다. 유전모수 추정결과, 총산자수와 생존산자수는 고도의 유전력을 유지하였다. 근교계수는 1998년에서 2017~2018년까지 꾸준히 증가하였으나, 각 형질에 대해 1998년 대비 2017~2018년의 능력감소는 확인되 지 않았다. 근교계수 증가에 따라 총산자수의 유의적인 근친퇴화(p=0.03)가 확인되었지만, 생존산자수에서는 유의적인 근친퇴화가 없었다 (p=0.41). 또한 두 형질 모두 근교계수와 육종가의 긍정적 상호작용이 확인되었다(p<0.05). 본 연구 결과, 재래돼지 산자수에 대한 근친퇴화 효과 가 일부 확인되었지만, 세대가 지남에 따라 명확한 표현형 감소는 확인되지 않았다. 이는 현재까지 높은 유전효과로 근친퇴화를 극복할 수 있음 을 시사한다. (RDA Project number : PJ012636, PJ014289)
Key Words : 재래돼지, 근교계수, 근친퇴화
PA-46
Genetic diversity and phylogenetic status of Mongolian cattle 1 1 2 1 3 1 Onolragchaa Ganbold , Seung-Hwan Lee , Woon Kee Paek , DongwonSeo , Munkhbaatar Munkhbayar , Prabuddha Manjula , 1 and Jun HeonLee
1 Laboratory of Animal Molecular Genetics, Division of Animal & Dairy Science, Chungnam National University, Daejeon, Republic of 2 3 Korea Daegu National Science Museum of Korea, Daegu, Republic of Korea Department of Biology, Mongolian National University of Education, Ulaanbaatar, Mongolia
ABSTRACT Domestic cattle is one of the important livestock that ever domesticated. The majority of previous studies agreed that cattle was domesticated in the Fertile Crescent region around 9,000 years ago. Recently, high-density Bovine SNP BeadChips were widely used to trace its genetic structure and breeding selection. In this study, genotype information of Bovine 50K BeadChip of 417 cattle which included novel 28 Mongolian cattle were used to clarify their genetic diversities, population structures and phylogenetic statuses for identifying genetic relationships of East Asian cattle breeds. A total of 41,763 SNPs were used for population genetic diversity analysis including MDS plot, SNPhylo, admixture and Treemix. The mean observed heterozygosity for Mongolian cattle was 0.359 (±0.035), while mean coefficient of inbreeding was 0.023 (±0.103). The Mongolian Kalmyk cattle and Hanwoo breed was revealed genetically close populations by all of the diversity analysis. In addition, the relatively varied ancestry pattern was observed for Mongolian cattle. Approximately, 40% ancestry of Mongolian cattle was the same with Hanwoo in K= 12 and 13 (indeed other Ks), while the ancestry proportion of Japanese and Mongolian cattle breeds was lower similarity than relationship with Hanwoo. An initial hypothesis was raised for the origin of cattle in Mongolia based on findings obtained from this and previous genetic and archeological studies.
Key Words : Genetic diversity, Bovine 50K Beadchip, Mongolian cattle, Hanwoo, Kalmyk cattle
23 • 2019 International Symposium & Conference PA-47
The development of genetic identification marker combination using a machine learning algorithm for new Korean native chicken breeding stock 1 1 2 1 1* Sung Hyun Cho , Dongwon Seo , Hyuongyong Kim , Seung Hwan Lee , Jun Heon Lee 1 2 Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea Insilicogen inc., Korea
ABSTRACT A useful tool of genetic markers for identification of unique breed can not only authenticate Korean native breed but also protect property rights.. For this purpose, the SNP genotyping platform can provide fast and accurate information with easy customize marker combinations for breed identification. Therefore, the aim of this study is to select optimal marker combination that can distinguish new Korean native chickens breeding stock using SNP data with machine learning algorithm. The 600K SNP genotype data of 285 chickens (15 KNC lines and 5 commercial chicken lines) were analyzed case- control test for distinguishing core parental lines (HH and HF) to select minimum marker combination. Following the case-control test, the top significant 96 SNPs were selected as candidate markers. Then, seven different machine learning models (Random Forest, LDA, AdaBoost, Nearest Neighbors, Decision Tree, Naive Bayes, QDA) were applied to finiding optimal marker combinations. As a result, the optimum number of markers for AdaBoost and Random Forest models with the highest accuracy were 36(99.36%) and 40(34.30%), respectively. In particular, the AdaBoost model showed excellent feature as a marker for discriminating completely new KNC from foreign breeds and it would be more improved by additional training data. These results can provide useful information for developing a verification tool kit of new KNC breeding stock in the market.
Key Words : Breed identification, Korean native chicken, Machine learning , SNP
PA-48
Genetic improvement through nationwide pig genetic evaluation system
이승수, 장혁기, 당창권, 이재구, 최연호, 최유림, 박미나, 김시동
농촌진흥청 국립축산과학원 가축개량평가과
ABSTRACT 한국의 종돈 산업은 민간종돈업체의 자율적인 돼지개량과 종돈보급체계에 기반하고 있다. 그러나 중소규모의 다수의 종돈장이 독립적으로 육 종 사업을 진행하여 유전적개량량의 증대효과가 적고 중복투자 및 과당경쟁의 폐해가 있었다. 따라서 한국 고유의 육종목표에 따라 개량의 효과 를 최대화하여 우량 종돈을 선발하고 공유하며 혈통연결을 통해 핵군 종돈장간 유전적 연결성을 높여 평가를 지속하기 위하여 15개의 종돈장이 참여하여 국가단위 돼지개량 네트워크 사업을 수행해 왔다. 2008년부터 부계종돈으로 듀록종의 평가를 위해 90kg도달일령, 등지방두께, 등심단 면적, 정육율을 검정하여 각 형질에 대해 유전능력평가를 수행하여 육종가를 추정하고 선발지수식에 따라 종돈을 선발하여 공유하였다. 개량의 목표는 90kg도달일령을 빠르게 하는 것에 우선 순위를 두었고 다음으로 등지방두께는 얇아지도록 가중치를 주었다. 그동안 148두를 선발하여 공유하였고, 공유된 종돈의 자손은 90kg도달일령의 추정육종가가 2012년 –3.69에서 2017년 –7.62로 개량되었다. 모계종돈은 2016년부터 랜 드레이스와 요크셔종 종돈의 평가를 위해 총산자수와 생존산자수에 대해 유전능력평가를 수행하여 육종가를 추정하고 선발지수식에 따라 종돈 을 선발하여 공유하였다. 지난 3년간 13두를 선발하여 공유하였고, 공유된 종돈의 자손은 생존산자수의 추정육종가가 2018년 랜드레이스는 0.16, 요크셔는 0.23으로 개량되었다. 향후 참여 종돈장의 수를 늘리고 공유하는 종돈의 수를 늘려서 평가의 정확성과 개량량을 향상될 것으로 기대된 다.
Key Words : 종돈, 듀록, 랜드레이스, 요크셔, 유전능력평가
Korean Society of Animal Breeding & Genetics • 24 PA-49
Assessing the major histocompatibility complex (MHC)-linked microsatellite marker LEI0258 diversity in Asian and African chicken breeds
Prabuddha Manjula, Sung Hyun Cho, Dongwon Seo, Jun Heon Lee* 1 Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Republic of Korea
ABSTRACT Genetic diversity is a critical measure in population genetics because it can give information about the current and likely future health of a population. Adaptive genetic variation of a species more important because it is related to the selection of particular traits because the certain coding gene has been selected. Chicken MHC as an adaptive genetic region where its genes influence many biological traits in vertebrates. The microsatellite marker LEI0258 linked in MHC-B region provides relatively easy and consistent results to assess the diversity at MHC region in chicken. We used 1971 samples from 33 populations from four different countries (Sri Lanka, Bangladesh, Nigeria, and Korea). These populations were again divided into semi intensive-natural breeding and Intensive-selective breeding, based on the prevailing production system and breeding methods. Male and female groups of selected populations of the intensive group were also analyses for the difference in allele distribution and diversity measures. A total of 39 alleles, ranging from 191 bp to 539 bp were observed with 16 new allele sizes. Among populations, the Sri Lankan chicken populations indicated the highest mean alleles per ecotype (15.25) where as the lowest reported in Korean populations (8.13). Mean Polymorphic information content (PIC) and allele frequencies per population were 0.455 – 0.892, and 0.2 % - 69.0% respectively. Based on allele frequency distribution several alleles were shared. Particularly, alleles 249 (25) > 193 (24) > 309 (23) > 443 (19) > 357, 307 (18) > 205 (13) >295 (12) >381 (11). Overall Observed heterozygosity value estimated between 0.467 (Black Silkie) and 1.00 (Sri Lanka ecotypes TN). Majority of genetic variations, 81.99% is due to within individual’s differences and 14.95% variation from among the populations. A clear difference in a number of allele (Na) and allele richness value was observed between two production systems, indicating semi intensive system have higher mean allele number and allele richness values. No clear difference among sex was observed except for the observed heterozygosity difference. Overall, native chicken populations have high diversity, however, their production system and breeding strategy might cause these observed diversity differences. Information in the current study provide the roots to understand the effect of prevailing management strategies, breeding approach in both local ecotypes and pure breeds of chicken to make decisions for their further development, improvement or conservation.
Key Words : Chicken, MHC-B, LEI0258 Marker, Diversity.
PA-50
Evaluation of economic values and selection index for carcass traits in Hanwoo steers production
Chiemela Peter Nwogwugwu, Jun Heon Lee, Seung-Hwan Lee*
Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Republic of Korea
ABSTRACT Evaluation of livestock with carcass traits and auction price records is usually used in animal production. This study aimed at evaluation of economic values (EVs) and construction of selection index (SI) for carcass traits in Hanwoo steers. Assessment of EVs for carcass traits is important in the breeding scheme in order to estimate the economic weight attached to each trait. The EVs are helpful in selecting multiple traits through selection index method. Collection of phenotypic data on carcass traits was from different abattoirs within eight provinces from 2005 to 2012. A total number of animals used were 14,999. The measurements were carcass weight (CWT), eye muscle area (EMA), backfat thickness (BFT), marbling score (MS), and auction price. Estimates of the carcass traits and auction price were calculated in various years and age groups. The EVs, correlation and principal components analysis (PCA) were also performed with the data. The results of the slaughter year were notconsistent, however, increased values were observed among the traits. The average values for CWT, EMA, BFT, MS, and auction price were 420.54 kg, 90.91 cm 2 , 13.53 mm, 5.68, and 16,100 KRW, respectively. Higher MS and auction price were obtained on the animals slaughtered at 28 and 29 months. Estimated EV was higher in MS, which also indicates a strong association between MS and auction price. PCA revealed that principal component one (PC 1 ) is related to CWT and EMA, whereas principal component two (PC 2 ) is associated with BFT and MS in both age groups. As a result, both PCs could be interpreted as an index for respective traits. Therefore, the selection of animals with early maturity and high MS could be of great economic gain.
Key Words : Carcass traits, economic values, selection index, principal component
25 • 2019 International Symposium & Conference PA-51
Characterization of PR-39, a potent antimicrobial peptide of pigs, copy number variation and development of the typing method 1,† 1,† 1 1 1 1 Byeongyong Ahn , Hyoim Jeon , Minh Thong Le , Mingue Kang , Hye-sun Cho and Chankyu Park 1 † Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul, Korea These authors equally contributed to this work
ABSTRACT Proline-arginine (PR)-rich 39 is a porcine neutrophil antimicrobial peptide that plays an import role in immune responses against infiltrating pathogens including elimination of bacteria and modulating immune system in innate immunity. In our previous study, we suggested the multiple copy presence of PR-39 in the pig genome and reported a finding of PR-35, a different type of PR-39, which have 12 bp nucleotide deletion in exon 4 from PR-39. To further characterize the degree of copy number variations and sequence variations of different PR-39 alleles or loci, we developed a method for typing PR-39 copy number variation (CNV) using quantitative real time PCR and digital droplet PCR (ddPCR). We also amplified the complete genomic sequence of PR-39 using genomic PCR from multiple individuals and performed sequence analysis of cloned PCR products. From the results, we identified a total of 20 different types of PR-39 variants. Additionally, we carried out CNV typing of PR-39 for 48 individuals from 6 breeds. Surprisingly, there was a large variation in PR-39 copy numbers among individuals with the highest number of 13. The functional consequence of PR-39 copy number expansion could contribute to increasing the innate immune capacity of animals and improving resistance against pathogenic infection.
Key Words : antimicrobial peptides, PR-39, pigs, copy number variation, innate immunity, disease resistance.
PA-52
한우 암소의 도체형질에 대한 환경효과 분석 1 박상은, 이동재, 윤두학
1 경북대학교 축산BT학과
ABSTRACT 본 연구는 한우 암소의 도체형질에 미치는 환경요인을 추정하기 위하여 실시하였다. 2013년 4월부터 2014년 8월까지 국내 6개 지역(강원; 150, 경 남; 98, 경북; 150, 전남; 99, 전북; 150, 충남; 105)에서 출하·도축된 한우 암소 752두의 도체형질 자료를 이용하였다. 효과검정을 위해 도체중, 등 지방두께, 등심단면적, 근내지방도 및 성숙도 형질을 이용하였으며 도축년도-계절과 사육지역을 고정효과, 사육개월령을 공변이로 처리하여 분 석을 수행하였다. 각 형질에 대한 환경효과 분석결과, 등지방두께와 성숙도를 제외한 나머지 형질에서 모두 유의적인 결과가 확인되었다 (p<0.05). 도축년도-계절의 효과를 보면 도체중, 등심단면적, 근내지방도는 각각 337.86±3.810 kg, 82.07±0.945 cm 2 , 4.26±0.149점으로 2014 년 봄에 가장 높게 나타났으며 성숙도는 4.68±0.121점으로 2013년 겨울에 가장 높게 나타났다. 사육지역의 효과의 경우 도체중, 등심단면적, 근 내지방도가 각각 333.43±4.023 kg, 81.54±0.963 cm 2 , 4.32±0.189점으로 강원에서 가장 높게 나타났으며, 성숙도의 경우 4.76±0.132점으로 경북에서 가장 높게 나타났다. 본 연구결과는 한우 암소개량 및 사양관리를 위한 기초자료로 활용 가능할 것으로 사료된다.
Key Words : 한우 암소, 도체형질, 환경효과
Korean Society of Animal Breeding & Genetics • 26 PA-53
Analysis on the evolution of AMP repertoires between terrestrial and aquatic mammalian genomes 1 1 1 1 1 1 Mingue Kang , Byeongyong Ahn , Joori Yum , Hye-Sun Cho , Hyoim Jeon , Nagasundarapandian Soundrarajan , and Chankyu 1 Park
1 Department of Stem Cell And Regenerative Biotechnology Graduate School of Konkuk university, Seoul, Republic of Korea
ABSTRACT Antimicrobial peptides (AMP) are important innate-immune molecules to control pathogenic infection and good candidates to improve host resistance against pathogenic infection. We analyzed and/or compared the genome-level AMP repertoires of six terrestrial (human, cattle, pigs, goats, dogs, and African elephants) and five aquatic (minke whales, bottlenose dolphins, Yangtze river dolphins, walruses, and manatees) mammals. Our analysis resulted in the identification of 59 additional beta defensin genes (BD) for the aquatic mammals comparing to the current gene annotation from public databases. In contrast, the results for non-BDs were consistent to those of public databases. The average number of BD genes for terrestrial and aquatic mammalian species investigated in this study was 35.17 and 27.80, respectively, showing the number was lower in aquatic than terrestrial animals. Phylogenetic analysis showed a total of 350 BD genes from 11 species formed 27 clusters, suggestingthe expansion of gene subfamilies and the presence of large sequence variations in mammals. The synteny analysis of BD genes resulted in the identification of 8 conserved flanking genes which constitute four BD containing regions, PGK2-TFAP2D, BCL2L1-ZCCHC3, AGPAT5-GPM6A, and ADAM29-CTSB intervals. We observed the occurrence of chromosomal inversions and segmental deletions regarding to the intervals among different species, indicating the expansion of BD genes occurred before separating into terrestrial and aquatic mammals. In addition to BDs, the expansion of cathelicidins was also more active in artiodactyls than cetaceans although they are closely related phylogenetically. Our results show that AMPs were subject to different evolutionary pressure depending on their habitats.
Key Words : Aquatic mammals, Antimicrobial peptide (AMP) and Evolution
PA-54
Alteration in the expression level of keratin family genes is associated with longer hair phenotypes in hairy ear (Eh) mutant mice 1 Joori Yum , 김다영, 안병용, 최민경, 박찬규
1 Department of Stem Cell And Regenerative Biotechnology Graduate School of Konkuk university, Seoul, Republic of Korea
ABSTRACT Phenotypes showing variation in hair development and growth are important traits for animals and humans. The hairy ear (Eh) mutation in mice was caused by a paracentric inversion of a ~47Mb segment on distal half of chromosome 15. Heterozygotes (Eh/+) have longer and extra hairs on ears and a different shape of pinna compared to that of wild types (+/+). To investigate the mechanism underlying the hairy ear phenotypes of the mutant mice, we carried out RNA-seq analysis on ear tissues of four weeks old Eh/+ and +/+ mice, respectively. We then compared their gene expression profiles to identify differentially expressed genes between the wild-type and mutant mice. We also carried out gene ontology enrichment analysis. As a result, we found that the expression of keratin filament and hair cycle related genes differ significantly between wild-type and Eh/+ mice. Interestingly, hair follicle or hair- specific keratin genes including krt71 and krt81 showed increased expression in Eh/+ comparing to wild-type mice. The expression level of epithelial specific keratin gene, krt2, was rather decreased in the mutant mice. We also evaluate the pattern of gene expression from RNA-seq by real time PCR and the results were consistent between the two methods. This indicates that Eh mutation upregulates the expression of hair phenotype contributing keratin genes and changes the hair growth on ears, suggesting importance of hair keratin genes on hair growth. Further studies are necessary to illuminate the molecular mechanisms underlying the relationship between the level of keratin expression and hair growth.
Key Words : Mouse hairy ear (Eh), keratin, RNA-seq, Real-time PCR
27 • 2019 International Symposium & Conference PA-55
Identification and characterization of novel cathelicidins with potent antimicrobial activity and low cytotoxicity in Monodelphis domestica 1* 1* 1 1 Hye-sun Cho , Joori Yum , Hyoim Jeon and Chankyu Park 1 Department of stem cell and regenerative biotechnology, Konkuk University, Hwayang-dong, Kwangjin-gu, Seoul 143-701, Korea *H. Cho and J. Yum contributed equally to this work.
ABSTRACT Alternatives to conventional antibiotics have been required to combat increasing multi-drug resistance. Cathelicidin, a family of antimicrobial peptides, has emerged as possible candidate with broad-spectrum activity and specific mechanism to kill pathogens. In the genome of marsupials and monotremes, cathelicidin-encoding genes are expanded and have evolved to protect immunologically naïve young in the pouch or burrow expectedly rich in microorganisms. In this study, we carried out a genome-wide in silico analysis of cathelicidins of grey short-tailed opossum. Our results showed the presence of seven cathelicidins (namely ModoCATHs) with complete open reading frames bearing the antimicrobial domain. Therefore, they were considered biologically functional. We chemically synthesized three peptides (ΔModoCATH1, 5 and 6) according to their predicted antimicrobial activity core region. The synthesized peptides were subjected to cell viability assay against a panel of standard bacterial strains and mammalian cells. ΔModoCATH1 showed highly potent antimicrobial activity with a broad-spectrum, while ΔModoCATH5 and ΔModoCATH6 showed specific bactericidal activity against Gram-positive and Gram-negative bacteria in the tested strains, respectively. The antimicrobial activity of ΔModoCATH1 and ΔModoCATH5 was stable after incubation with 50% serum. ΔModoCATH1 and ΔModoCATH6 showed a minimal level of cytotoxic activity on chicken erythrocytes and mammalian cells. However, ΔModoCATH5 exerted a strongly cytotoxic influence on the cell viability. Taken together, ΔModoCATH1 or its derivatives showing a broad-spectrum antimicrobial activity with low cytotoxicity and high stability in serum could be an interesting candidate for pharmaceutical applications including controlling of multi-drug resistance pathogens and antibiotic alternatives.
Key Words : antimicrobial peptide, host defense peptide, cathelicidins, Monodelphis domestica, grey short-tailed opossum
PA-56
A study on the estimation and accuracy of genomic estimated breeding value of donor for Ovum Pick Up technuqe 1 1 2 3 3 1 김은호 , 강호찬 , 선두원 , 이두호 , 이승환 , 임현태 1 2 3 경상대학교 응용생명과학부(BK21), 경상대학교 농업생명과학연구원 충남대학교 동물자원생명과학과
ABSTRACT OPU(Ovum Pick Up)는 살아있는 공란우의 난소에서 초음파기구를 이용하여 미성숙 난자를 채취하여 수정란 대량생산이 가능한 기술로, 이에 이용되는 공란우의 경우 우수한 유전능력을 가지는 암소로 활용하면 효과를 극대화 시킬 수 있다. 따라서 본 연구로 OPU에 활용할 공란우의 유 전능력을 평가하고자 기존 OPU에 사용된 공란우 33두를 대상으로 GBLUP(Genomic Best Linear Unbiased Prediction)을 이용하여 유전체육종가 (Genomic Estimated Breeding Value, GEBV) 추정 및 정확도 분석을 실시하였다. 분석에 사용된 참조축군은 표현형정보와 유전체정보를 보유하 고 있는 한우 11,376두를 이용하였으며 유전체정보는 Hanwoo 50K Version.1을 사용하였고 Quality Control을 통해 32,086개의 SNP 유전자형을 선별하여 GCTA(Genomo-Wide Complex Trait Analysis)의 GRM(Genomic Relationship Matrix) command를 이용한 유전체혈연행렬을 구축하 고 ASreml 프로그램으로 분석하였다. 결과로 추정된 형질별 유전력은 도체중은 0.327, 등심단면적은 0.298, 등지방두께는 0.303, 근내지방도는 0.356이고 정확도는 도체중은 0.654, 등심단면적은 0.642, 등지방두께는 0.644, 근내지방도는 0.665가 나타났다.
Key Words : OPU, GBLUP, GEBV, 유전체정보, 유전력, 정확도
Korean Society of Animal Breeding & Genetics • 28 PA-57
두록과 교잡돈(두록×피어트레인×피어트레인)의 산육형질 및 도체 수율 비교 1 1 1 1 1 1 김영신 , 조규호 , 이미진 , 김정아 , 조은석 , 홍준기 1 농촌진흥청 국립축산과학원, 충남 천안, 31000, 대한민국
ABSTRACT 본 연구는 국내 비육돈 생산 시 종료종모돈으로 주로 이용되는 두록(Duroc)과, 유럽에서 많은 정육 생산의 장점으로 종료종모돈으로 사용되고 있는 피어트레인(Pietrain)을 이용한 교잡돈 (DPP)의 산육형질과 도체수율을 비교 분석하여 우수한 품종 개발에 필요한 기초자료를 얻고자 실시 하였다. 국립축산과학원 양돈과에서 보유한 돼지 총32두(D 16두, DPP 16두)를 공시축으로 이용하여 90kg 도달일령, 등지방 두께, 사료요구율, 도체 수율 등을 조사하였다. 90kg 도달일령은 D 135일, DPP 134일로 유의적인 차이를 보이지 않았고, 등지방 두께는 D 14.2mm, DPP 12.6mm 로 확인되었다(p<0.001). 사료요구율은 D 2.10, DPP 1.98로 유의적인 차이를 보였다 (p<0.05). 도체수율 중 어깨등심, 앞다리, 등심, 뒷다리에서 D는 5.12kg,10.00kg, 8.22kg, 19.90kg 으로, DPP는 6.01kg, 12.40kg, 9.71kg, 23.40kg 으로 확인되었다(p<0.001). 반면 삽겹살은 D 15.00kg, DPP 12.80kg으로 유의적인 차이를 보였다(p<0.001). 본 연구 결과, 교잡돈 DPP가 D에 비하여 등지방 두께, 사료요구율에서 긍정적은 수치를 보였다. 또한 도체수율 대부분에서 DPP가 높은 수치를 보였지만 삼겹살 수율은 낮은 수치를 보였다.
Key Words : 두록, 피어트레인, 산육형질, 도체수율
PA-58
한우연구소 보유 축군의 유전체 육종가 추정 및 보증씨수소와의 비교 1 1 1 2 2 윤호백 , 김현주 , 원정일 , 이두호 , 이승환 1 2 Hanwoo Research Institute, National Institute of Animal Science, RDA, PyeongChang, Korea Division of Animal & Dairy Science, Chung Nam National University, Daejeon, 305-764, Korea
ABSTRACT 한우연구소에서 2009년부터 10년간 보증씨수소 정액을 이용하지 않고 자체 수소를 선발하여 조성한 축군에 대하여 도체형질의 유전체 육종가 를 추정하고 보증씨수소 757두와 비교 하였다. 한우연구소에서 보유하고 있는 412두(암 287, 수 125)의 50k 유전체 자료를 분석하였으며, 국가 단위 후 대검정우 2,605두와 일반 상업축 8,291두의 자료를 참조집단으로 하여 Asreml 4.0 프로그램을 이용하여 도체중, 배장근단면적, 등지방두 께 및 근내지방도 4개 형질에 대하여 유전체 육종가를 추정하였다. 국가단위 후대 검정우 참조집단을 이용하여 분석한 유전체 육종가의 분포는 도체중 –85.18~88.47, 배장근단면적 –13.26~19.66, 등지방두께 –5.08~10.98, 근내지방도는 –2.76~2.48로 나타났으며, 상업축 참조집단의 경우 각 형질에 대하여 –86.37~ 111.7, –18.97~25.43, -6.67~9.9, -3.68~2.44로 나타나 상업축 참조 집단을 이용했을 때 육종가의 분포 범위가 넒은 것으로 나타났다. 분석에 활용한 참조집단별로 한우연구소 축군과 보증씨수소 집단의 유전체육종가를 비교한 결과 국가단위 후대검정우 참조집단을 사용했을 경우 모든형질에서 보증씨수소 집단이 높게 추정되었으나, 상업축 자료를 참조집단으로 한 경우 등지방두께와 근내지방 도에서 한우연구소 축군의 육종가가 높게 추정되었다. 각 참조집단에 대한 유전체 육종가 추정 정확도를 비교한 결과 국가단위 참조집단에서 보 증씨수소는 0.56~0.59, 상업축 참조집단에서 0.64~0.66을 나타내었고, 한우연구소 축군은 각각 0.33~0.37, 0.43~0.46으로 약 20~22% 낮은 정확 도를 나타내었다.
Key Words : 한우연구소, 유전체육종가, 도체형질, 보증씨수소, 정확도
29 • 2019 International Symposium & Conference PA-59
전장유전체연관분석을 이용한 개 슬개골탈구 연관 유전자 마커 탐색
권슬기, 박종은, 박원철, 차지혜, 채한화, 임다정, 최봉환
농촌진흥청 축산과학원 동물유전체과
ABSTRACT 본 연구는 개의 유전질환인 슬개골 탈구와 연관성이 높은 유전자 마커를 발굴하여 슬개골 탈구의 위험성을 갖는 개체를 조기 진단함으로써 반 려견 육성에 중요하게 적용하기 위해 연구를 수행하였다. 개의 유전자 정보를 분석하는 과정으로 먼저 개 124두의 혈액에서 genomic DNA를 확 보하여 canine 170K SNP chip을 이용해 단일염기다형(single nucleotide polymorphism, SNP)을 대량 확보하였다. 그리고 전장유전자연관분석법 (GWAS)을 통해 하디-바인베르그 평형(HWE)과 minor allele의 빈도(MAF)에 대하여 일정 조건에 맞지 않는 결과는 배제 (HWE; P<0.001, MAF; <1%) 하고 슬개골 탈구 위험성과의 연관성이 높은 SNP을 선발하였다. 그 결과, 개의 슬개골 탈구 위험성과 연관된 SNP 20개를 선발하였고, 유 의한 SNP 중 상위 그룹에 해당되는 SNP으로 염색체 7번의 BICF2S23625290(p > 0.0000111), 염색체 5번의 BICF2P415323(p > 0.0000382), 염색 체 17번의 BICF2S23153924(p > 0.0000424)등으로 확인하였다. 따라서, 확보한 SNP 20개는 개의 슬개골 탈구 위험성을 조기 예측 가능케하는 유 전자 마커로 활용될 수 있을 것이라 사료된다.
Key Words : Canine patellar luxation, Genome-wide association study (GWAS), single nucleotide polymorphism (SNP),
PA-60
Transcriptome analysis to identify candidate genes and pathways for adaptation of liver tissue in to two different climatic conditions 1 1, 2 2 3 1 1 1* Himansu Kumar , A.U. Iskender , Zhunushov Asankadyr , Hyojun Choo , Gul Won Jang , Youngjo Lim , J. E. Park
1 2 Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, RDA, Wanju 55365, Korea Institute of 3 Biotechnology, National Academy of Science of Kyrgyz Republic Poultry Research Institute, National Institute of Animal Science, RDA, PyeongChang, Korea
ABSTRACT RNA sequencing was utilized to profile a liver transcriptome of Korean commercial chicken line at two different locations as Korea and Kirgizstan. RNA- seq technology provides the mechanism involved in environmental response, as liver is highly metabolic tissue. We analyzed ten samples from each location to investigate the candidate genes which are involved in environmental response such as sea level, humidity, temperature etc. on liver transcriptome. At false discovery rate (FDR) < 0.05 and fold change (FC) > 2, we found 315 genes were differentially expressed (DE). Out of 315 DE genes, 174 were upregulated and 141 were downregulated between two different locations. The top five upregulated DE genes such as TSKU, PDXK, GSTA3, SERPINB10, and ANKRD22, similarly for downregulated VTG1, APOV1, PCK1, HMGCL, MBOAT2 genes were highly involved in liver metabolic activity. Gene ontology (GO) enrichment analysis showed that liver tissue is highly associated with the energy metabolism such as pyruvate and lactate metabolic processes, and glycerol catabolic process. Similarly, KEGG pathways analysis indicated pyruvate metabolism, PPAR signaling pathway, FoxO pathway, Glycolysis/Gluconeogenesis, Biosynthesis, Citrate cycles were differentially enriched. Multiple reports indicated that enriched genes like TSKU, VTG1, SGK, CDK2 etc. in such pathways are highly involved in adaptation of organisms into diverse climatic conditions. Through, Ingenuity Pathway Analysis (IPA), we created a network that combines the liver tissue related protein family with environmental response genes. The present study provides insights into transcriptome profile of liver tissue in chicken, which is a valuable resource for studies of chicken genomes.
Key Words : Transcriptome, liver tissue, FoxO and PPAR pathways, DE, IPA.
Korean Society of Animal Breeding & Genetics • 30 PA-61
DESeq2 소프트웨어 활용 한우 태아기 성장단계에 따른 잠재 마블링 관련 조직의 차등발현유전자 기능 분석 1 1 1 1 1 1 1* 정태준 , 정기용 , 박원철 , 박종은 , 손주환 , 채한화 , 임다정 1 국립축산과학원
ABSTRACT 축산물 가식 부위의 대부분을 차지하는 동물의 근육은 다수의 근섬유가 구조적으로 결합하여 형성하게 된다. 근섬유는 줄기세포에서 분화된 근세포의 연장이며 가축의 근섬유는 태아기에 주로 축적되어 근육을 형성하고 출생 후에는 근섬유의 순 축적 없이 크기가 커지는 것으로 근육을 성장시킨다. 태 아기의 여러 요인에 따라 근섬유 형성이 극적으로 변화한다. 결국 이 시기의 성장, 발달이 성체의 도체 형질에 많은 영향을 끼치게 된다. 본 연구에서는 임신 6, 9개월령 한우 태아의 복강 지방, 간, 사태, 등심 조직을 추출, RNA 발현량을 조사하여 성장단계에 따른 조직별 유전자 발현 변화를 살펴봄으로써 한우 태아기 유전적 발현 양상이 출하 시 도체 형질에 미치는 영향 등을 파악하고, 수정 이후 어미 소에서부터 이뤄지는 정밀 사양의 기초 자료로 활용될 수 있도록 하고자 한다. 한우 태아 6개월령 6두, 9개월령 9두에서 추출한 각 4개 조직, 전체 59개(6개월령 간 조직 1개 누락) 샘플에서 RNA sequence reads 를 추출하여 Salmon을 이용, 발현 값을 구하고 이를 DESeq2를 이용해 분석하였다. 조직별 6, 9개월로 비교 분석하여 log fold change 절댓값 1 초과, FDR 0.05 미만으로 differentially expressed genes(DEGs)를 파악한 결과 복강 지방에서 1,858개의 up-regulated genes가있었고, 975개의 down-regulated genes 가 있었다. 간은 up-regulated genes 1,403개, down-regulated genes 309개, 사태는 up-regulated genes 1,899개 down-regulated genes 886개, 등심은 up- regulated genes 2,165개, down- regulated genes 1,075개로 나타났다. 이를 바탕으로 DAVID로 조직별 차등 발현 DEGs를 이용하여 Gene Ontology 분석 결과 cell volume homeostasis, cell maturation 등과 같은 기능이 up-regulated genes에서 나타났고, lipid homeostasis, lipid transport, skeletal muscle tissue development 등이 down- regulated genes에서 볼 수 있었다. 이는 6개월에서 9개월령으로 넘어가면 서 태아가 근육, 지방과 같은 주요 조직들의 분화와 발달에 변화를 주는 것으로 보인다. 또한 간, 복강 지방의 down-regulation에서 immune response, innate immune response, fever generation 등과 같은 발 열, 면역 활동에 관한 term이 보이는데 이 시기에 면역 관련 유전적 기능이 변화를 나타내는 것으로 사료된다. KEGG pathways 분석에서도 up-regulated genes에서 p53 signaling pathway, AMPK signaling pathway 등의 경로가 나타나고, down-regulated genes에서 Metabolic pathways, Pyruvate metabolism, PPAR signaling pathway, Protein digestion and absorption 등의 경로가 나타나는데 역시 근육의 성장과 발달에 변화가 생기는 것으로 추측된다.
Key Words : DESeq2, Salmon, DAVID, Hanwoo(Korean cattle), prenatal transcriptome
PA-62
Differential gene expression analysis of chicken breast tissue by RNA-seq technology 1, 2 1 2 3 1 1 1 A.U. Iskender , Himansu Kumar , Zhunushov Asankadyr , Hyojun Choo , Gul Won Jang , Youngjo Lim , J. E. Park 1 2 Department of Animal Genomics and Bioinformatics, National Institute of Animal Science at RDA of Republic of Korea. Institute of 3 Biotechnology at National Academy of Science of Kyrgyz Republic,. Poultry Research Institute, National Institute of Animal Science, RDA, PyeongChang, Korea
ABSTRACT In this study we analyze differential gene expression in chicken breast muscle tissue from two different locations. We collected two groups of chickens, n = 10, first group located on territory of Republic of Korea and second group on territory of Kyrgyz Republic. The aim of chosen locations is to compare differential gene expression in two different climatic areas. The main indicators between these two locations were altitude and humidity. The average altitude on Korea is 250 meters above from sea level. While average altitude on Kyrgyzstan is about 2500 meters from sea level. The average humidity in Republic of Korea is 70% while in Kyrgyz Republic its about 40%. Sequences obtained from RNA-seq were processed by using FastQC to check quality control, Trimmomatic to trimming, Hisat2 to mapping, Featurecounts to counting, and EdgeR were used for DEG analysis (LogFC = 2/-2, FDR <0.05). As a results a total of 485 genes were identified. Out of it, 110 genes were identified as upregulated and 375 genes were downregulated. Top upregulated genes such as VTG2, APOV1, NETO2, DCDC2, MB, ISL1, CHAC1, matrixmetallopeptidase3, FOXL2, MYBPC1. Similarly, out of 375 downregulated genes top ten downregulated genes such as ENPEP, HNF4G, RF00012, ELF3, SLC5A8, SLC34A2, GRM1, TSPAN16, Hypothetical LOC427933, MSX2. KEGG pathways analysis indicates that Glycine, serine and threonine metabolism, Gap junction, Tryptophan metabolism, and Neuroactive ligand- receptor interaction are differentially enriched. Whereas, gene ontology analysis showed in terms of biological process, cellular component, and molecular function indicates that negative regulation of BMP signaling pathway, Apical plasma membrane pathway, and Glycoprotein binding pathways were differentially enriched respectively. Our results facilitate the understanding of transcriptomic profiling of chicken breast muscle at two different geographical locations and identified the candidate genes for environmental responses.
Key Words : RNA-seq, breast muscle, DEG, VTG2, APOV1.
31 • 2019 International Symposium & Conference PA-63
Integrated transcriptomes and interacting network analysis of immune responsible tissues by PRRSV infection in pigs reveal specific susceptibility mechanisms 1 1 2 1* Byeonghwi Lim , Do-Young Kim , Won-Il Kim and Jun-Mo Kim 1 2 Department of Animal Science and Technology, Chung-Ang University, Anseong 17546, Republic of Korea Department of Veterinary Medicine, Chonbuk National University, Iksan 54596, Republic of Korea
ABSTRACT Porcine reproductive and respiratory syndrome (PRRS) is an important viral disease affecting in pig productivity of the swine industry worldwide. To date, many studies have been conducted to identify and validate the causal gene associated with the host response to PRRS virus (PRRSV) infection using genome and transcriptome, but the biological function of the PRRSV susceptibility has not been well clarified. Therefore, current study investigated the host susceptibility mechanism for PRRSV infection using RNA-seq method. Viremia and body weight were measured at 5 time points (0, 7, 18, 25, and 32 days post infection (dpi)) in 40 pigs that were challenged with PRRSV (JA142), and 3 tissues (lung, alveolar lymph node, and tonsil) were collected by slaughtered 8 pigs in each time points (excluding 0 dpi). Thereafter, two groups (Good / Bad condition) with high / low PRRSV susceptibility were constructed based on viremia and body weight gain. RNA was isolated from all tissues and RNA-seq was performed. Differentially expressed genes (DEGs) were extracted with FDR < 0.05 and absolute log2 FC ≥ 1, resulting in that 2,466 DEGs in the Good condition, 2,121 in the Bad, and 1,155 in both at least one tissue and time point. Additionally, the DEGs (436 in Good and 499 in Bad) corresponding to stringent significant level (absolute log2 FC ≥ 3) were entered in the PCIT algorithm for gene co-expression network (GCN) analysis. The GCN was visualized in each of the Good (409 genes and 6,530 connections) and Bad conditions (477 genes and 14,465 connections). The DAVID enrichment analysis for KEGG pathway terms revealed that RIG-I-like receptor signaling pathway, which is directly related to antiviral signaling, is included only in the Good specific network. We suggested that the RIG-I-like receptor signaling pathway acts as a crucial biological role in PRRSV susceptibility and further studies are needed.
Key Words : PRRSV, RNA-seq, DEG, PCIT, GCN.
PA-64
PRRSV 감염에 따른 시점 별 폐포 림프절의 기능전사체 프로파일링
임치웅, 임남섭, 임병휘, 김도영, 김준모 *
중앙대학교 동물생명공학과 기능유전체 및 생물정보 연구실
ABSTRACT 돼지 생식기 호흡기 증후군(porcine reproductive and respiratory syndrome, PRRS)은 국내 양돈 산업뿐만 아니라 북미와 유럽을 포함한 전 세계적 인 피해를 주고 있는 대표적인 질병이며 모돈의 번식장애와 자돈의 호흡기 질환에 따른 성장률 감소 및 폐사율 증가의 피해를 유발한다. PRRS 바이러스(PRRSV)는 북미주(VR-2332)와 유럽주(Lelystad)로 구분되며, 형태학적으로나 유전체의 구조적인 측면에서 유사하지만, 항원은 약 60~70%의 염기상동성(sequence homology)을 보이는 차이가 있다. 현재까지 PRRSV 백신은 30여종류 이상 존재하지만, 바이러스의 높은 변이 율로 인하여 백신의 교차방어가 제한된다. 본 실험에서는 LYD 교잡종 40두의 4주령 이유돈에 대해서 PRRSV (JA142 형)를 공격접종하였고, 접 종기점으로 0, 7, 14, 25, 32일(D) 집단을 구성하여, 각 시점별로 도축 후, 면역반응의 중추적인 역할을 하는 폐포 림프절 조직을 채취하였다. 채취 한 조직은 전사체 관찰을 위해 RNA sequencing 분석을 진행하였다. 접종 0일령을 기준으로 각 접종 주령별 차등발현유전자(DEG)를 파악하였 다. 그 결과, 각 주령별로 416 (7D), 120 (18D), 17 (25D), 212 (32D) 개의 DEG를 보였으며, 그 중에서도 가장 많은 DEG를 보였던 7D 그룹에서 는 생물정보분석결과, 급성 면역반응과 관련된 유전자들이 유의적인 발현차를 보이는 것으로 관찰되었다. 또한 접종 18일까지는 유사한 면역반 응 향상 기작을 보였으며, 이후 25일에는 면역반응이 항상성 반응에 관련된 유전자로 전환되면서 32일차에는 다시 성장과 관련된 유전자의 발 현이 수치가 높음을 확인할 수 있었다. 결론적으로 본 연구를 통해서 PRRSV 접종에 따른 각 시기별 면역반응 양상을 전사체 수준에서 관찰하였 으며, 바이러스에 대한 면역 기작을 구명할 수 있었다.
Key Words : PRRSV, Alveolar lymph lode, RNA-seq, DEG, Transcriptome
Korean Society of Animal Breeding & Genetics • 32 PA-65
PRRSV 감수성 차이에 따른 시점 별 편도의 기능전사체 프로파일링
곽창희, 김동현, 임병휘, 김도영, 김준모*
중앙대학교 동물생명공학과 기능유전체 및 생물정보 연구실
ABSTRACT 돼지 생식기 호흡기 증후군(porcine reproductive and respiratory syndrome, PRRS)는 번식 장애와 호흡기 질병을 특징으로 하는 바이러스성 질병 으로 모돈의 생산성 감소와 자돈의 성장률 및 폐사율에 영향을 미쳐 결과적으로 돼지 생산성을 낮추는 주요 질병이다. 하지만 현재까지 PRRSV 숙주의 반응에 대한 mechanism이 명확하게 밝혀져 있지 않다. 따라서 본 연구에서는 호흡기 및 면역과 관련된 편도 조직에서 PRRSV 감염에 따 른 면역 반응 양상을 전사체 수준에서 조사하였다. 실험 집단은 PRRSV 공격 접종된 총 40마리의 돼지가 이용되었으며, 감수성에 따라 두 집단 (Good 20두, Bad 20두)으로 구성하였다. 편도 조직은 바이러스 접종 후 0, 7, 18, 25, 32일에 채취되었으며, RNA sequencing 분석이 수행되었다. 시점 별 Bad를 기반으로 Good의 발현량을 비교한 결과 차등발현유전자(DEG)는 25일에서 가장 많은 94개의 DEG가 존재하였다. 또한 다수의 DEG를 나타낸 25일을 Good과 Bad에서 0일을 기초로 하여 분석한 결과 각각 73개, 21개의 DEG가 추출되었다. 두 집단에서 공통으로 발현되는 유전자는 총 18개 였으며, 이들은 PRRSV 감염에 의한 숙주의 면역 및 회복 반응과 관련되어 있을 것으로 고려되었다. 공통 영역을 제외한 Bad 에서는 총 3개의 gene (RHCG, TCN1, ND4L)이 발현되었는데 RHCG, TCN1은 항상성 유지와 관련된 유전자로 알려져 있으며, ND4L은 ATP 생산을 저해하는 역할을 하는 유전자로 확인되었다. 따라서 ND4L은 돼지의 면역 반응에 부정적인 영향을 줄 수 있는 후보 유전자로 생각된다. 본 연구를 통해서 PRRSV 감염에 따른 각 시점 별 숙주 면역 반응 양상을 전사체 수준에서 조사하였으며, 감수성과 관련한 후보 유전자 ND4L을 제시하였다. 더 큰 집단에서 PRRSV 감염과 관련한 ND4L 유전자의 기능을 검증하는 추가 연구가 필요할 것으로 사료된다.
Key Words : PRRSV, RNA-seq, Tonsil, Transcriptome, ND4L
PA-66
PRRSV 감수성 차이에 따른 시점 별 폐의 기능전사체 프로파일링
임석원, 박은진, 임병휘, 김도영, 김준모*
중앙대학교 동물생명공학과 기능유전체 및 생물정보 연구실
ABSTRACT PRRSV(porcine respiratory and reproductive syndrome virus)는 돼지의 모돈 및 자돈의 생산성을 낮추는 주요 질병 중 하나이다. PRRSV는 높은 변이율로 인하여 다양한 유전자형의 바이러스가 존재하며 이러한 특성은 백신을 통한 면역 획득 또한 제한적으로 만든다. PRRSV는 폐포 대식 세포를 주 대상으로하는 바이러스이므로 본 연구에서는 PRRSV가 공격 접종된 돼지의 폐를 이용하여 숙주의 면역 반응에 대한 mechanism을 조 사하였다. 전체 40마리의 돼지가 PRRSV (JA142) 공격 접종 후 0, 7, 18, 25, 32일이 경과한 시점에 각각 8마리씩 조직이 채취되었으며, 감수성을 기반으로 두 집단(Good 20두, Bad20두)으로 구분되었다. 채취된 조직은 전사체 비교를 위해 RNA sequencing 분석이 수행되었다. 시점 별 Bad 를 기준으로 Good의 상대적 발현량을 관찰한 결과 7 (0D), 0 (7D), 23 (18D), 15 (25D), 10 (32D)개의 차등발현유전자(DEG)를 확인했으며, 전 시 점에서 DEG는 maturation, growth, ATP 생산에 관련한 geneontology (GO) term에 다수 포함되어 있었다. 또한 초기 면역 반응 차이를 보기 위하 여 Good과 Bad에서 각각 0일을 기준으로 7일의 mRNA 발현 차이를 확인한 결과 628(Good), 847(Bad)개의 DEG가 존재하였으며, 모두 면역반 응에 관련된 GO term (immune response, homeostatic process, response to virus등)을 나타내는 유사한 결과를 보였다. 결론적으로 본 연구를 통해 서 PRRSV 감염에 의해 폐에서 나타나는 숙주의 면역반응 양상을 시점 별로 전사체 수준에서 확인하였으며, 폐 외에 면역 기관에서의 반응 또한 추가 연구되어야 한다고 사료된다.
Key Words : PRRSV, Lung, Transcriptome, RNA sequencing, immune response
33 • 2019 International Symposium & Conference PA-67
한우거세우 참조집단을 이용한 제주흑우 도체형질 유전체 육종가 평가 1 1 2 2 3 4 1 이윤미 , Haque Azizul , 이승은 , 박세필 , 이승환 , 이학교 , 김종주 1 2 3 4 영남대학교 생명공학과, 경산시, 경상북도 제주대학교 생명공학부, 제주특별자치도 충남대학교 대전광역시 전북대학교 전주시, 전북
ABSTRACT 본 연구는 제주흑우 개체들의 도체형질들에 대한 유전 능력을 평가하고자 참조집단인 내륙한우 거세우를 이용하여 유전체 육종가를 추정 하고 자 수행하였다. 참조집단은 9,303두 출하거세우로 도체 중, 등심단면적, 등지방두께 및 근내지방도의 성적과 llumina bovine 54K SNP chip을 분 석하였고 제주흑우는 제주축산진흥원, 국립 축산과학원 난지축산연구소 및 제주흑우 농가에서 1,440두와 제주도 소재 한우로 혈통 등록된 656 두에서 고기를 이용하여 제주 흑우 품종 특이 (JJBC 120K) SNP chip을 이용하여 유전자형을 분석하였다. 유전자형과 표현형이 있는 참조집단( 내륙암소)과 유전자형 자료만 있는 검정집단(제주우) 모두 포함된 공통 SNP chip을 이용한 유전체혈연행렬로 GBLUP 모델을 이용하여 검정 집 단 개체의유전공분산을 이용하여 유전체 육종가를 추정하였다. 추정된 육종가 값은 실제 출하 도체성적 값들과 상관정도를 계산하였다. 분석결 과, 도체중, 등심단면적, 등지방두께 및 근내지방도의 상관계수는 각각 0.17, 0.17, 0.002 및 0.09으로 나타나 낮은 정의 상관관계 를 보였다. 이러 한 결과는 제주흑우 개체들로 구성된 참조집단 구축의 필요성을 제시하여 주며 향후 지속적 자료수집을 통하여 큰참조집단을 구축한다면 정확 도가 높은 도체성적 육종가 정보를 제공해 줄 것으로 사료된다.
PA-68
Development of fetal sex determination using DNA isolated from maternal plasma 1 1 2 1 1 1 1 Hyun-Joo Lim , Changgwon Dang , Hyun-Jong Kim , Ji-Hwan Lee , Dong-Hyun Lim , Min-Su Kim , Seung-Min Ha , Gyeong-Seok 1 1 Lee , Soo-Bong Park
1 2 Dairy Science, National Institute of Animal Science, RDA, Cheonan, Korea National Institute of Agricultural Science, RDA, Jeonju, Korea
ABSTRACT Gender selection is important to livestock produces because there are other advantages for the management and efficiency of livestock production. Cell free fetal DNA circulate in the bloodstream of pregnant animals. The presence of cell free fetal DNA in maternal plasma gives opportunities to detect prenatal sex using circulating fetal Y chromosome. Noninvasive prenatal testing (NIPT) using massively parallel sequencing of cell free fetal DNA in maternal plasma, has become clinically and commercially available. The aim of this study was to determine the fetal sex using z-scores of NIPT. We evaluated 5 pregnant dairy cattle with blood results. The fetal fraction is the amount of cell free fetal DNA divided by the amount of total cell-free DNA. The fetal fraction can be measured using molecular counting, amplification of differentially-methylated sequences, or detection of unique fetal polymorphisms. Z-score of Y chromosome is 1.323 ~ 2.795 in 3 samples. Other group’s z-score of Y chromosome is lower than 3 samples. The results showed that NIPT method is possible to determine of fetal sex using fetal DNA in maternal plasma. And cell-free fetal DNA is a new biomarker that can predict fetal ability.
Key Words : Dairy cattle, Fetal DNA, Fetal sex determination
Korean Society of Animal Breeding & Genetics • 34 PA-69
국내 토종 원종 계통별 육종가 정확도 평가 1 1 1 2 2 3 1 아람자한길 , 아지줄하쿠에 , 이윤미 , 추효준 , 박병호 , 손시환 , 김종주
2 3 ¹경북 경산시 대학로 280 영남대학교 생물응용과학대학 생명공학과 국립축산과학원 가금연구소, 경남과학기술대학교 동물생명과학과
ABSTRACT 본 연구는 한협(주) 소재 토종닭 12 계통(A, B, D, E, F, G, H, S, V, W, Y,Z) 들에 대하여 육종가 정확도을 규명하고자 각 계통별 988두, 1,112두, 2,466두, 2,194두, 2,132두, 2,233두, 4,293두, 7,655두, 2,630두, 6,721두, 5,385두 및 1,712두를 이용하여 혈통자료를 분석 대상형질인 생시체중, 4 주 체중, 8주 체중, 4주 정강이 길이 그리고 8주 정강이 길이에 대해서 혈연정보를 근거로 한 Animal model 이용하여 Asreml4.0 프로그램을 구동 하여 유전분산 추정하였다. 그 결과 유전력은 거의 0~ 0.76 값으로 나타났으며 E, G, S, Z 계통에서 분석형질에 대해 유전력이 다른 계통에서 보 다 높게 나타났다. 육종가의 정확도 평균 결과 0.29~ 0.54의 범위값을 가지며 D 계통에서 가장 낮은 정확도를 보였고 Y 계통에서 가장 높은 정확 도를 보였다.본 연구결과는 상용계통을 설정하는데 원종계의 유전적 능력을 평가하는 지표로 활용하는 정보를 제공하여 줄 것으로 사료된다
Key Words : Korean native chicken, Pure line, Body weight, Shank Length, Heritability
PA-70
개 행동학적 불안증 연관 유전자 변이에 대한 전장유전체 연관성 연구
김하나, 박종은, 박원철, 차지혜, 채한화, 임다정, 최봉환
농촌진흥청 국립축산과학원 동물유전체과
ABSTRACT 본 연구의 목적은 개의 스트레스성 행동장애로 인하여 유전적으로 발생되는 불안장애를 조기에 예측 및 불안장애의 위험성을 갖는 개체를 조기 에 진단 가능한 유전자 마커를 개발하여 유전적으로 우수한 개체를 선발 함에 있다. 연구 방법으로서 개의 유전자 정보 분석을 위해 50두의 개체 로부터 채취한 혈액 DNA에서 canine 170K SNP chip을 이용하여 대량의 SNP 발굴 및 유전자형을 분석하였다. 또한, 전장유전체연관분석 (GWAS)으로 개의 불안장애를 조기에 예측 가능한 SNP 7개를 선발 하였다. 유전자형 분석 및 선발 결과, 선발된 SNP 7개의 유전자형은 염색체 10번에서 BICF2P1411839(g59948159. A>G), 염색체 36번에서 BICF2G630758265(g29246033. G>C) 및 BICF2P280881(g28622504. G>A), 염색 체 9번에서 BICF2G630834875(g28622504. G>A) 및 BICF2G630834997(g34828682. G>A), BICF2G630834998(g35043288. A>G) 및 BICF2S2394588(g34358974. A>G)를 선발하였다. 결론적으로, 개의 SNP 유전자 정보 분석을 통해 유전적으로 발생되는 불안감을 나타내는 개 체를 조기에 예측할 수 있으며, 유전적으로 우수한 개체의 선발에도 유전자 마커가 유용하게 활용될 수 있을 것으로 사료된다.
Key Words : 개, SNP, chip, GWAS, 유전자형
35 • 2019 International Symposium & Conference PA-71
한우거세우 참조집단을 이용한 경북봉화 암소 집단의 유전체 육종가 평가 1 1 1 1 2 3 1 이윤미 , Haque Azizul , Alam Zahangir , 김나경 , 이승환 , 이학교 , 김종주 1 2 3 영남대학교 생명공학과, 경산시, 경상북도 충남대학교 대전광역시 전북대학교 전주시, 전북
ABSTRACT 본 연구는 검정집단인 경북 봉화 암소 개체들의 고급육 도체형질들에 대한 유전적 능력을 평가하고자 참조집단인 내륙한우 거세우를 이용하여 유전체 육종가를 추정 하고자 수행하였다. 내륙 거세우 한우의 참조집단은 9,303두로 도체중, 등심단면적, 등지방두께 및 근내지방도의 성적과 llumina bovine 50K SNP chip을 분석하였고 경북봉화 암소 및 비육거세우 1,985두에 대한 Illumina bovine 50K SNP chip의 유전자형을 분석하야 유전체혈연행렬로 GBLUP 모델을 이용하여 검정 집단 개체의 유전공분산을 이용하여 유전체 육종가를 추정하였다. 추정된 육종가 값은 실제 출 하 도체성적 값들과 상관정도를 계산하였다. 분석 결과, 도체중, 등심단면적, 등지방두께 및 근내지방도의 상관계수는 각각 0.32, 0.36, 0.34 및 0.41으로 나타나 정의 상관관계를 보였고 모델 적합성을 나타내는 결정계수가 0.9 이상으로 아주 높게 나타났다. 이러한 결과는 향후 지속적 자 료수집을 통하여 큰 참조집단을 구축한다면 한우 거세우 참조집단을 이용한 내륙 한우 검정집단의 정확도가 높은 도체성적 육종가 정보를 제공 해 줄 것으로 사료된다.
PA-72
Genome-wide association study on first-parity calving ease scores of Korean Holstein
Mahboob Alam, Choy Yun Ho, Lee Jae Gu, Dang Chang Gwon, Park Mi Na, Choi Tae Jeong, Lee Seung Soo, Chang Hyuk Kee, Choi Youlim, and Kim Sidong
Animal Breeding and Genetics Division, National Institute of Animal Science, Rural Development Administration, Cheonan, Korea 31000
ABSTRACT Calving ease (CE) is an important reproductive trait in dairy cattle. This genome-wide association (GWA) study was aimed to investigate the genomic association of calving ease traits in Korean Holstein heifers. A total of 903 Holstein heifers were genotyped using two high-density Illumina 50K BeadChip SNP panels (version 2 and 3). Their corresponding phenotypic records on CE was initially scored between 1 and 5, as an ordered categorical variable – from being the easiest to extreme difficulty in calving. To perform a GWA test for genomic regions, however, their phenotypes were converted into affection status variable (binary: 1/2), essentially converting CE of ≥ 2 as 2. Marker association test was performed by PLINK 1.07 software package, through a logistic regression model. Genotypes were pruned for commonly used quality control criteria. After that, 39,877 SNPs were left for the GWA. The association study showed 519 SNPs to be primarily significant at P<0.001 (without a p-value adjustment). After controlling for SNP false discovery rate (Benjamini and Hochberg’s FDR), about 39 SNPs remained significant at P<0.01. Although many chromosomes (BTA) tend to harbor multiple significant SNPs for CE in this study, BTA 3 and 23 were especially noticeable, residing the highest of 6 and 5 SNPs, respectively. Among other BTAs, BTA1, 5, 7, 9, 10, 14-16 and 28 also harbored two or more SNPs. This is the first study for GWA of CE in Korean Holstein, and we believe our outcomes would prove a better insight in future in understanding the calving ease trait.
Key Words : Calving ease, genome-wide association study, logistic regression, Korean Holstein, PLINK.
Korean Society of Animal Breeding & Genetics • 36 PA-73
SNP chip을 활용한 한우의 유전체 육종가 데이터 분석을 통한 우수 개체 선발 및 개량 방안 1 1 1 1 2 1 이광현 , 정지수 , 박병규 , 이윤석 , 오동엽 , 공홍식 1 2 경기 안성시 중앙로 327 한경대학교 유전정보연구소 경상북도 축산기술 연구소
ABSTRACT 본 연구는 경기지역 한우를 대상으로 실시하였으며 도체형질들에 대한 유전능력을 분석하기 위하여 실시하였다. 공시재료는 경기도에서 한우 를 사육중인 7개 농가에서 437두의 모근을 채취해 사용하였다. 채취한 모근을 SNP chip을 통해 유전체 데이터를 분석하였고 도체중, 등심단면 적, 근내지방도, 등지방두께에 대한 성적은 축산물품질평가원 데이터를 이용하여 수집하였다. 참조집단은 동물분자유전육종사업단 자료에 근 거하여 SNP chip분석을 통한 SNP들의 효과값을 GBLUP을 이용하여 추정하고, 추정된 값에 근거하여 경기한우 각 개체별로 SNP 유전자형에 따 른 효과 값들을 통합하여 유전체 육종가 값을 추정하였다. 네가지의 도체형질 중 근내지방도에 대한 유전체 육종가를 일정한 기준으로 나눠 분 석한 결과 A등급 64두, B등급 185두, C등급 94두, D등급 91두로 확인되었으며 A등급 64두중 도축된 17두의 도축성적과 비교 하였을 때 16두의 도축성적이 1++등급판정 받은 것으로 확인되었다. 이러한 결과로 볼 때 추정한 유전체 육종가 데이터를 기반으로 각 농가별로 개체를 분석하여 우수한 형질을 가진 개체들의 선발을 통하여 개량이 가능할 것으로 보이나 더 많은 자료들을 수집하여 정확도를 높여야할 것으로 사료된다.
Key Words : Hanwoo, Genome Breeding value, SNP chip, Carcass trait
PA-74
Estimation of heritability based on genomic and pedigree data for carcass traits in Hanwoo. 1 2 3 3 1 1 1 Swati Srivastava , Seunghwan Lee , Dong-Hyun Shin , Jae-Don Oh , Han-Ha Chai , Jong-Eun Park , WonCheoul Park , Na-Rae 1 1* An , Dajeong Lim 1 2 National Institute of Animal Science, Rural Development Administration, Jeonju, South Korea Department of Animal Science and 3 Biotechnology, Chungnam National University, Daejeon, Republic of Korea Department of Animal Biotechnology, Chonbuk National University, Jeonju, Republic of Korea
ABSTRACT Hanwoo is the most expensive and palatable breed of beef in South Korea. It’s among the four aboriginal breed: Chikso, Heugu and Jeju Black. Various studies were conducted and still ongoing to increase the meat production, improve the quality and heritability of its featured trait. Current study aims at selection of better candidates for future progeny. Evaluation is based on four carcass traits i.e. BFT (Back fat Thickness), CWT (Carcass weight), EMA (Eye Muscle area) and MS (Marbling score). Genomic and pedigree based evaluation was performed with the help of BLUPF90 family of program. Various models were built, evaluated and compared for best prediction. Phenotype data comprise of 10,215 commercial Hanwoo population with age around 30 months, out of these animals, genotype were available for 7,991 animals with 53,866 single nucleotide polymorphisms (SNPs). Quality checks for SNPs were performed with the help of PREGSF90 module of BLUPF90 programs. Through ANOVA, herd year months (HYM), age and sex were analyzed which were significant fixed effect. AIREML was used to calculate genetic variance and residual variance. Breeding values (estimated breeding value and genomic breeding value) for each animal were also predicted. Genomic selection emerged as one of the best method for genetic evaluation of these traits as they include genetic information along with pedigree and phenotypic information. Genomic based heritability estimate was more for CWT (0.39), EMA (0.39) and MS (0.46) as compared for pedigree based estimate for CWT (0.30),EMA (0.35) and MS (0.30) except for BFT(genomic heritability=0.38 & pedigree heritability=0.41). Even the accuracy of prediction for genomic selection model is more as compared to pedigree based model. Hence, inclusion of genomic information in form of SNPs can make the prediction of breeding value more accurate.
Key Words : carcass traits, BLUPF90, genomic selection, heritability
37 • 2019 International Symposium & Conference PA-75
Exome-seq and machine-learning based integrative diagnosis marker selection for dog degenerative diseases including diabetes, obesity, patella luxation and progressive retinal atropy 1 1 2 2 1 1 Ki-Eun Hyeong , Jae-Yong Nam1 , Bong-Whan Choi , Seulgi Kwon , Byeong-Chul Kang and Hyung-Yong Kim 1 2 Data Science Center, Insilicogen, Inc., Yongin, 16954, Korea National Institute of Animal Science, RDA, Wanju, 55365, Korea
ABSTRACT As dogs evolve to the present dogs, they became vulnerable to hereditary disease due to excessive inbreeding for fixation of breed. Especially, degenerative genetic diseases are a factor that greatly deteriorates the quality of life. If we know in advance whether the dog has genetic risk, we can take precautions before the onset or prevent the symptoms from getting worse. Genetic testing can be used to diagnose this early, and genetic markers that cause disease should be identified. The next-generation sequencing method enables more detailed selection of genetic markers than high-density SNP chips. In the case of Exome-seq, genetic markers that directly affect protein function can be selected based on the biological considerations. In this study, causative genetic mutations (markers) of 4 diseases were selected by association study of Exome-seq results for 83 dogs of 18 breeds and phenotypes including degree of patellar luxation, blood glucose, index of obesity and progressive retinal atropy. 86,863 mutations were obtained by GATK best practice for variant calling and QC including HWE. Candidate 20 genetic markers per disease were selected by machine learning and feature selection method rather than univariate GWAS. This allowed for a high discrimination with smaller number of markers due to the consideration of inter-marker relations. This work was carried out with the support of "Cooperative Research Program of Center for Companion Animal Research (Project No. PJ01283301)" Rural Development Administration, Republic of Korea.
Key Words : Patella luxation, Dog, Degenerative disease, SNP markers, Exome-seq, Diabetes, Obesity, Progressive retinal atropy
PA-76
한국토종닭 순계집단에 대한 유전능력평가 적용 연구
추효준, 박병호, 허강녕, 차재범, 권 일
국립축산과학원 가금연구소
ABSTRACT 닭의 육종체계는 능력이 우수한 순계집단으로부터 생산된 원종계간 최적교배조합을 통하여 종계단계에서 대량 증식을 하게 되며 이들 종계로 부터 생산된 실용계가 상업적으로 이용되게 된다. 따라서 종계 및 실용계의 생산성 향상 및 산업경쟁력 확보를 위해 순계집단의 유전적 능력에 대한 개량이 필수적이다. 이에, 본 연구는 토종닭 실용계의 산업 경쟁력 향상을 위하여 한국토종닭 순계집단 및 현재 조성 중에 있는 재래닭 GGP 집단의 능력개량에 필요한 유전능력평가체계 구축 및 적용 연구에 활용하고자 수행되었다. 유전능력 분석에 이용된 자료는 2015년부터 2018년 까지 국립축산과학원 가금연구소에서 수집된 토종닭 순계의 능력검정 자료 중 산업 활용 목적에 따라 부계통으로 활용 가능한 코니쉬 순계 2 계 통 및 6,413수의 혈통자료 및 능력검정자료를 이용하였으며 평가형질은 8주령 체중과 40주령까지 집계된 산란 수 기록을 사용하였다. 체중 및 산란수의 육종가 추정을 위하여 다형질 개체모형(Multiple Traits Animal Model)을 적용하여 Wombat program(Mayer,2010)으로 분석을 실시하 였다. 부계로 활용되는 흑색 및 갈색 코니쉬 2계통은 2015년 재 복원된 이래 8주령 체중의 경우 1세대 당 약 50∼60g의 체중이 증가하였고 40주 시 산란 수는 0.2개 개량되는 것으로 분석되어 체중 증가 중심의 개량방향 설정과 부합되는 결과로 사료된다. 본 연구 수행 결과 8주령 체중 및 산 란 수에 대한 유전적 능력은 4세대가 경과되는 동안 개량되고 있는 추세로 나타났으나 향후 세대당 유전적 개량량을 증대시킬 수 있는 개량 체 계 설정이 필요할 것으로 사료된다. 따라서 현재 적용되고 있는 교배방법, 선발비율, 집단의 크기, 평가형질의 확대 등을 검토해 볼 수 있으며 아 울러, 신뢰도 높은 혈통과 검정자료 확보를 위한 닭 개량시스템의 고도화를 위한 노력이 필요하다.
Key Words : 한국토종닭, 순계, 다형질 개체모형, 유전능력평가
Korean Society of Animal Breeding & Genetics • 38 PA-77
Development plan of a calibration method according to the upper limit of pig's test end weight
장혁기, 이승수, 당창권, 이재구, 최태정, 최연호, 최유림, 박미나, 김시동, 강연희, 류은아, 아람마부
농촌진흥청 국립축산과학원 가축개량평가과
ABSTRACT 현재 우리나라 가축검정기준 내 농장검정의 검정종료는 70~110kg에 도달하였을 때 90kg도달일령, 1일평균 증체량, 등지방두께, 등심단면적 등 을 측정하여 90kg대로 보정하고 있다. 하지만 비육돈의 출하체중이 과거 90kg대에서 100~110kg으로 상향되면서 기존 검정종료체중인 90kg을 초과할 경우 정확한 보정이 어려울 수 있다. 따라서 출하체중과 가까운 적정검정종료 체중 설정 및 적정 보정 방법을 개발하기 위해 본 연구를 실 시하였다. 10개의 종돈장에서 듀록 548두, 랜드레이스 648두, 요크셔 1493두의 개시 체중과 성별에 따른 체중 및 초음파 형질 자료를 수집하였 다. 각 형질은 현 검정종료시점인 90kg을 기준으로 2~3주 전·후를 측정하여 총 3회를 측정하였고 회귀분석을 통하여 성장곡선을 추정하였다. 적 정검정종료체중에 맞는 새로운 보정 방식 개발로 돼지 개량을 촉진하고 주요 종돈장의 품종 및 성별에 따른 종돈장 효과를 분석하여 효율적인 개량 방향을 설정할 수 있을 것으로 사료된다.
Key Words : 종돈, 듀록, 랜드레이스, 요크셔, 보정방법
PA-78
Duroc종에 대한 등지방두께와 지방산 조성 연구
강현성, 고대영, 이일주
다비육종 육종연구소
ABSTRACT Duroc 종은 우리나라에서 삼원교잡시 교배 종료웅돈으로 이용되며 원료 돈 출하시 소비자의 식감 및 영양에도 큰 영향을 미치는 품종 중 하나 이다. 돼지고기 등급판정은 품질의 정도와 도체중·등지방두께 등을 종합적으로 고려하여 평가되기 때문에 도체중 및 등지방두께가 등급 기준에 적당한 수준에서 적합한 개량이 이루어져야한다. Duroc 종의 등지방두께가 매년 감소하고 있는 가운데 돼지고기의 지방산 조성도 변화하고 있 다. 2010~2018년도 Duroc종 1004두에 대한 지방함량은 4.53%에서 3.09%로 점차 감소하고 있는 추세이며 도체 등지방두께의 경우 25mm에서 21.69mm로 얇아지는 추세를 보이고 있다. 도체 등지방두께는 지방산 조성에 영향을 미치며 불포화지방산의 경우 필수지방산(linoleic, linolenic, arachidonic, oleic acid)을 구성하고 있다. 다불포화지방산을 도체중에 회귀하여 보정한 결과에서 다불포화지방산과 도체 등지방두께는 –0.288 의 상관을 보였으며 포화지방산은 0.161의 상관을 보였다. 등지방두께가 얇아질수록 지방내 불포화지방산이 높아지는 결과값을 나타냈다. 도체 중의 경우 포화지방산과 불포화지방산에 각각 0.157, -0.147의 상관을 나타냈다. 또한 매년 도체중도 줄어드는 양성을 보였는데 돼지고기 등급 판정 및 도체중량 기준적합을 위해 규격돈(115kg) 측정 출하를 실시하는 것으로 사료된다. 또한 등지방두께가 얇을수록 등급은 높아지는 현 등 급판정 기준에 맞춰 추후등지방두께는 더 얇아질것으로 예상된다.
Key Words : Backfat thickness, Fat contents, Carcass weight, Unsaturated fatty acid
39 • 2019 International Symposium & Conference PA-79
Weighted single-step genomic BLUP for carcass traits in Hanwoo Cattle 1 2 3 3 1 1 1 Lopez, Bryan Irvine , Seunghwan Lee , Dong-Hyun Shin , Jae-Don Oh , Han-Ha Chai , Jong-Eun Park , WonCheoul Park , Na-Rae 1 1 An , Dajeong Lim 1 2 National Institute of Animal Science, Wanju, Republic of Korea Department of Animal Science and Biotechnology, Chungnam National 3 University, Daejeon, Republic of Korea Department of Animal Biotechnology, Chonbuk National University, Jeonju, Republic of Korea
ABSTRACT Single-step genomic best linear unbiased prediction (ssGBLUP) method has been widely used in routine genomic evaluation. However, this method assumes that all single nucleotide polymorphism (SNP) explain the same fraction of genetic variance, which is unlikely in the case of traits influenced by major SNP. This study investigated the predictive ability of weighted ssGBLUP (WssGBLUP) and compared with traditional pedigree-base method (BLUP) and ssGBLUP method for various carcass traits: backfat thickness (BF), carcass weight (CW), eye muscle area (EMA), and marbling score (MS) in Hanwoo cattle. Phenotypic data from 10215 animals that were slaughtered at approximately 30-month-old of age from different commercial herds were used. All animals were genotyped using Illumina Bovine 50k SNP chip. Training set and validation set were divided by random allocation, and the predictive ability were evaluated using 5-fold cross validations. The average predictives using BLUP were 0.21, 0.27, 0.24 and 0.22 and increased to 0.37, 0.43, 0.39 and 0.41 using ssGBLUP for BF, CW, EMA and MS, respectively. With WssGBLUP, predictives were 0.59, 0.61, 0.59 and 0.61 for BF, CW, EMA and MS, respectively. The results indicate that the WssGBLUP method provides improved predictions for all carcass traits contrary to BLUP and ssGBLUP methods.
Key Words : genomic prediction, weighted single-step genomic best linear unbiased predictor, carcass traits, Hanwoo
PA-80
젖소 국제유전체평가(InterGenomic-HOLstein, IG-HOL) 결과 활용계획
당창권, 이재구, 최연호, 아람마부, 최태정, 이승수, 장혁기, 박미나, 최유림, 강연희, 류은아, 김시동
농촌진흥청 국립축산과학원 가축개량평가과
ABSTRACT 젖소는 종축의 국가간 교역이 빈번하여 나라별 보유 씨수소에 대한 유전평가 결과를 각 나라 환경에 맞게 객관적으로 평가할 필요성이 있다. 그 래서 국제젖소유전능력평가기구(Interbull, 인터불)가 설립되어 전 세계 37개국의 씨수소를 평가하여 각 나라 환경에 맞게 평가결과를 환류하고 있다. 우리나라도 2011년부터 평가에 참여하고 있다. 최근 평가기법의 발전으로 유전체선발(Genomic Selection, GS)가 축산선진국에서 실용화 되어 평가되고 있지만 유전체 참조집단을 소규모로 가진 국가에서는 정확도 등의 문제로 평가를 하지 못하고 있다. 그래서 인터불에서는 유전체 참조집단을 소규모로 가진 국가간 유전체 정보를 공유하여 유전체선발을 할 수 있는 국제유전체평가(InterGenomic-HOLstein, IG-HOL) 프로 젝트를 ’17년도 처음 시험평가를 하였고 우리나라도 ’18년도에 참여하여 평가결과를 받았다. 현재 참여하고 있는 국가는 한국, 남아프리카공화 국, 슬로베니아, 아일랜드, 우루과이, 이스라엘, 크로아티아, 포루투갈 총 8개국이다. ’18년도에 이용된 유전체 정보는 우리나라 2,049두를 포함 하여 총 26,875두이며 유전체 유전평가를 통하여 평가의 정확도가 형질별 17~21%가 향상되었다. 향후 이 결과를 활용하여 후보씨수소 후보우 선발 등에 활용될 수 있을 것으로 기대한다.
Key Words : 젖소, 국제유전체유전평가, 인터불, IG-HOL
Korean Society of Animal Breeding & Genetics • 40 PA-81
국내 홀스타인 젖소의 유생산능력에 대한 로봇착유기 이용 효과
최연호, 당창권, 이재구, 장혁기, 최유림, 박미나, 이승수, 아람마부, 류은아, 강연희, 최태정, 김시동
국립축산과학원 가축개량평가과, 충남 천안시 서북구 신방1길 114, 31000
ABSTRACT 국내 로봇착유기 도입의 증가에 따라 주요 젖소 품종인 홀스타인 젖소의 검정기록에서 유생산형질 능력에 미치는 영향을 보고자 로봇착유기 사 용 농가의 사용 전후 성적을 비교하였다. 검정기록 중 이상치를 제거한 2000년 분만부터의 기록 2,077,676개의 자료를 이용하였으며, 로봇착유 기 사용농가는 도입일자가 파악된 검정농가 35호의 기록을 분석하였다. 이 중 기존착유기만을 사용하는 농가는 총 7,300호로 2,057,691개의 검 정자료가 분석되었으며, 로봇착유기 도입농가의 자료 수는 19,985개였다. 로봇착유기 사용 개시년도부터의 착유기록을 보면, 305일 보정유량과 유단백질 및 유지방량에 있어서 4산차까지 뚜렷한 증가 현상이 보였으나, 5산차 이후(5-10산차)의 성적에서는 그리 큰 차이를 보이지 않았다. 체세포점수에 있어서는 전 산차에 걸쳐 로봇착유기 사용에 따른 차이가 거의 없었다. 전통 착유기를 계속 사용하는 농가만을 봤을 때, 305일 보 정 유량, 유단백질 및 유지방량에 있어서 (1-10)산차까지 유의한 차이를 보였으나, 체세포점수에 있어서는 1-4산차까지는 유의한 차이를 보이 다가 5산차 이후는 유의적인 차이가 없었다. 한편 로봇착유기 도입농가의 착유기록에서 305일 보정 유량, 유단백량, 유지방량에 대해서 주로 1, 2산차에서 로봇착유기의 유의적인 효과가 나타났으며, 3산차 이후로 갈수록 그 차이는 유의성 정도에 차이가 있었다. 또한 체세포 점수에 있어 서는 로봇착유기 사용 전후와 산차간 상호작용 효과에서 일정한 경향을 보이지 않았다.
Key Words : 젖소, 유량, 유지방량, 유단백량, 체세포점수, 로봇착유기
PA-82
한우 칩 활용 한우 산업축군의 도체형질의 유전체 예측 1 1 2 3 3 1 1 1 1* 안나래 , 손주환 , 이승환 , 신동현 , 오재돈 , 박종은 , 박원철 , 채한화 , 임다정 1 2 3 국립축산과학원 동물유전체과 충남대학교 동물자원과학부 전북대 동물생명공학과
ABSTRACT 유전체 예측은 집단 개념에서 대용량의 단일염기다형성(SNP) 유전체 정보와 검정을 통해 얻어진 표현형 정보 간 연관성 분석을 통해 개체의 유 전체 유전능력을 평가하고 이를 기반으로 개체를 선발에 이용하는 것을 말한다. 유전체 예측을 통해 질병의 예후 및 약물반응 예측 연구, 육종가 추정을 통해 동물의 번식과 개량에 활용하면 보다 효율적이고 유용하게 사용될 수 있다. MTG2는 유전자 정보를 기반으로 다변량 선형 혼합 모 델 분석을 위한 효율적인 알고리즘을 사용하여 유전체 예측을 하는 프로그램이다. 본 연구에서는 MTG2 프로그램을 활용하여 30개월 전후 사 이의 비육우와 비육거세우의 유전자형이 결정된 한우 총 10,215두의 Hanwoo Chip(version 1) 데이터를 기반으로, 한우의 4가지 양적형질인 도 체중(CWT), 등지방 두께(BFT), 등심 단면적(EMA), 근내 지방도(MS)에 대해 10배 교차검증(10-fold cross validation)을 실행하여 유전체 예측 분석을 하였다. 나이와 성별을 고정효과(fixed effect)로 주었고, 대립유전자형빈도(MAF)는 0.01이하, 하디-와인버그 평형(HWE)은 10 -6 이하 로 품질관리(Quality Control)를 진행하였다. 그 결과 양적 형질의 유전력(h 2 )은 도체중 0.33, 등지방 두께 0.31, 등심 단면적 0.33, 근내 지방도 0.41였으며, 유전체 예측 정확도는 도체중 85%, 등지방 두께 92%, 등심 단면적 90%, 근내 지방도 89%였다.
41 • 2019 International Symposium & Conference PA-83
한우 혈통오류에 따른 육종가 변화 추정
당창권, 이재구, 최연호, 아람마부, 최태정, 이승수, 장혁기, 박미나, 최유림, 강연희, 류은아, 김시동
농촌진흥청 국립축산과학원 가축개량평가과
ABSTRACT 한우 농가에서는 개체의 능력을 추정하기 위하여 국가단위 유전능력평가 결과를 이용하는 한우교배계획길라잡이 등을 활용하여 개체능력을 추 정하고 있다. 하지만 프로그램은 혈통에 의존하여 자손의 능력을 계산하는 혈통지수로 농가에서 생성되는 도축기록 등을 활용하지 못하고 있다. 최근 한우농가에서 혈통이외에 도축성적 등을 보유하고 있는 농가가 증가함에 따라 이를 활용하여 혈통지수 보다 정확한 개체의 유전능력을 알 아보고자 하는 농장주들이 많아지고 있는 추세이다. 본 연구는 혈통 이외에 개체능력정보(도축, 분만, 체중기록 등)를 보유한 농가가 활용할 수 있도록 오류에 변화가 적은 유전능력평가 모형을 개발하기 위하여 수행되었다. 자료는 농협경제지주 한우개량사업소 후대검정우 검정자료 17,695두와 한국종축개량협회의 혈통자료 66,488두를 이용하여 분석하였다. 혈통오류는 농가에서 쉽게 발생할 수 있는 아비의 혈통을 엑셀 (VBA)을 활용 난수를 이용하여 오류(10, 20, 30%)를 발생시키고 아비의 목록 중에서 임의의 아비 중 자신보다 혈통이 빠른 아비만 찾아 오류만 큼 변환시켜 분석하였다. 아비에 대한 육종가 상관은 0과 10은 0.95, 0과 20은 0.91, 0과 30은 0.85, 10과 20은 0.89, 10과 30은 0.83, 20과 30%는 0.80으로 나타났고, 정확도 상관은 0과 10은 0.99, 0과 20은 0.97, 0과 30은 0.96, 10과 20은 0.98, 10과 30은 0.97, 20과 30%는 0.98으로 나타났다. 이 결과는 향후 농가에서 개체의 능력을 농장에서 가지고 있는 자료를 이용하여 추정할 수 있는 유전평가 알고리즘에 기초자료로 활용될 수 있 고 모형 개발을 위하여 데이터 오류 등 추가분석이 필요할 것으로 사료된다.
Key Words : 한우, 혈통오류, 육종가, 정확도, 상관
PA-84
Genetic diversity and population structure of Jeju Black cattle using 50K SNP chips. 1 1 1 1 2 1 Alam Zahangir , Azizul Haque , Yun-Mi Lee , Hyo-Jeong Sohn , Se-Pil Park , Jong-Joo Kim
1 2 Department of Biotechnology, Yeongnam University, Gyeongsan, Gyeongbuk, 38541, Korea School of Biotechnology, Jeju National University, Jeju, Korea
ABSTRACT Conservation and genetic improvement of cattle breeds requires to know the information about genetic diversity and population structure of existing animal. Jeju Black cattle are an endangered landrace heritage breed of cultural importance to Jeju Island of Korean peninsula. This study investigated genetic diversity and the population structure of Jeju Black (n = 78) cattle along with other breed namely Hanwoo (n = 66), Holstein (n =76), Angus ( n = 27), Hereford (n = 25), Brown Wagyu (n = 10), Black Wagyu (n = 50), Brahman (n = 15) and Nellore (n = 26). The measures of genetic diversity studied namely minor allele frequency (MAF), observed and expected heterozygosity (H O and H E ), inbreeding coefficient (F IS ). Genetic distances between breed pairs were also evaluated using Nei’s genetic distance (D A ), Weir and Cockerham’s F ST and past effective population size(N e ). Analysis of molecular variance and population structure was performed among nine cattle breeds using model-based clustering (ADMIXTURE). Results of this study revealed that Jeju Black cattle had lowest level of heterozygocity (H E = 0.21) among studied taurine breed ranges from 0.25~0.30, MAF of Jeju Black was 0.16 which is 0.11~0.21 in other breed. The level of inbreeding was -0.076 in case of Jeju Black as compared to other breed (-0.018 ~ -0.118). PCA analysis and neighbor-joining (NJ)- tree revealed a separation of Jeju Black cattle from other local and studied cattle breed. Model-based clustering also revealed a distinct pattern of admixture of Jeju Black cattle with no cluster of studied population. The F ST values of Jeju Black cattle with Hanwoo was 0.106 but other studied breed ranged from (0.161~0.274) which indicate some degree of closeness with Hanwoo. The N e of Jeju Black cattle was 42 as compared to Hanwoo was 214 in the most recent 13 generation ago. Thus, a sustainable breeding policy should be implemented to increase the population of Jeju Black cattle.
Key Words : Genetic diversity, Jeju Black cattle, Population parameter
Korean Society of Animal Breeding & Genetics • 42 PA-85
Selection signature of Korean Hanwoo, Jeju black and Holstein cattle 1 1 1 2 3 1 Alam Zahangir , Azizul Haque , Seong-Ryong Baik , Se-Pil Park , Chang-Kown Dang , Jong-Joo Kim
1 2 Department of Biotechnology, Yeongnam University, Gyeongsan, Gyeongbuk, 38541, Korea School of Biotechnology, Jeju National 3 University, Jeju, Korea Naitonal Livestock Research Institute, JeonJu, Jeonbuk, Korea
ABSTRACT The purpose of this study was to detect selection signature in Hanwoo, Holstein and Jeju Black cattle using high density SNP chips and to find QTL and functional genes on the selection signal regions that were associated with economic traits. Genotypes were analyzed with the use of the customized Jeju Black cattle Affymetrix 150K SNP arrays. Pair-wise IBS (identical by state) and quality control tests were performed to remove the individuals with very identical genetic makeup, low SNP call rate (<0.90) and to remove the SNPs with minor allele frequency less than 0.01, resulting 112,193 available SNPs in 518 Hanwoo, 76 Holstein and 1,345 Jeju Black cattle respectively. The extended haplotype homozygosity (EHH) test was conducted to detect chromosomal regions with selection signature with the thresholds of a frequency of 25% or more and P-value of <0.01. A total of 1327, 693 and 603 core regions over the whole genome in Hanwoo, Holstein and Jeju Black cattle was detected for selective signature analysis. On the regions of selection signal, QTL and functional candidate genes were searched on the significant core haplotypes (P-value <0.001). In Hanwoo, 13 candidate genes found on QTL, among which AMPD1, SIRT6, SREBF1, KCNJ11, FABP4 and RORC gene were identified. In Holstein, 16 QTL were found on the core regions and six candidate genes related to milk production and fertility were detected, including SND1, LEP, IGF1R, BTN1A1, FOXO1 and PTGER2. In Jeju Black cattle QTLs for carcass weight were detected on the core regions, in which two candidate genes HGD and ADAMTS4 were found, and QTL for milk components were detected, in which two functional candidate genes such as SLC7A5 and GSK3B were retrieved. Our results show that the core regions of selection signal were in general consistent with the genetic improvement program that have been performed since several decades in Hanwoo and Holstein in Korea. However, in Jeju Black cattle, less QTL were found in the core regions of selection signature that were different from the former two breeds proving that the cattle breed has been isolated in Jeju Island for a long time without implementing artificial selection. This findings significantly improve the selection signature map of Korean cattle, and helps to identify functional candidate genesunder positive selection for future genetic improvement.
Key Words : Jeju Black cattle, Selection signature, Extended Haplotype Homozygosity (EHH) test, selective sweep.
PA-86
Genome-wide Association Study for Four Carcass Traits in Korean Hanwoo Cattle Using Imputed High-density SNP Chip Data. 1 1 2 3 1 Azizul Haque , Yun-Mi Lee , Seung-Hwan Lee , Hakkyo Lee , Jong-Joo Kim
1 2 Department of Biotechnology, Yeongnam University, Gyeongsan, Gyeongbuk, 38541, Korea Chungnam National University, Daejeon, 3 Korea Chonbuk National University, JeonJu, Korea
ABSTRACT The main objectives of this study was to identify the carcass traits (CWT, EMA, BF and MS) associated genes and genomic regions using a high-density SNP chip of Korean Hanwoo cattle breed. The genome-wide association study was conducted with the use of Illumina BovineSNP50K Beadchip. We used a total of 9,293 Korean Hanwoo population. Samples with identical genotype were removed from the dataset through pairwise identity by state (IBS) distance test (>0.95) to avoid confounding in our analysis. A total of 41,498 (79.62 %) single nucleotide polymorphisms (SNPs) were selected after applying quality control tests of genotyping call rate (<0.90), SNP call rate (<0.90), allele frequency (<0.05) and Hardy-Weinberg equilibrium (0.000001). Before performing GWAS analysis, a linear mixed model was applied, in which birth year season and slaughter age were fitted as a fixed effect while slaughter farm and slaughter person were fitted as a covariate to obtain adjusted phenotype by using ASReml v4.1. GWAS was performed under a single marker regression model by regressing residuals on each genotype to estimate additive effects for each trait. The heritability estimates for CWT, EMA, BFT and MS were 0.335±0.018, 0.311±0.019, 0.312±0.019 and 0.418±0.019, respectively. A total of 99 significant SNPs (p<0.001) were detected for the four carcass traits. Candidate genes were screened from NCBI web database, and some significant SNPs for the carcass traits were closely located to functional candidate genes. The SNP identified in this study may help to improve beef production in Korean Hanwoo cattle.
Key Words : SNP, GWAS, candidate gene, carcass traits, Hanwoo cattle.
43 • 2019 International Symposium & Conference PA-87
한우 참조집단에 따른 도체형질의 유전모수 추정 및 유전체 육종가 상관분석 1 1 1 2 2 원정일 , 김현주 , 윤호백 , 이승환 , 이두호 1 2 농촌진흥청 국립축산과학원 한우연구소 충남대학교
ABSTRACT 본 연구는 국가단위 및 상업축 각각 2,605두 및 8,291두를 참조집단으로 이용하여, 국가단위집단과 한우연구소 계통축집단 1,718두와 412두에 대해 도체형질에 대한 유전모수를 추정하고, 유전체 육종가를 계산하였으며, 참조집단간의 유전체 육종가 상관을 추정하였다. 국가단위 참조집 단 을 이용한 유전력은 등지방두께, 도체중, 등심단면적 및 근내지방도에 대해 각각 0.449, 0.526, 0.419, 0.431로 추정되었으며, 상업축 참조집단 을 이용해 추정한 등지방두께, 도체중, 등심단면적 및 근내지방도의 유전력은 각각 0.351, 0.358, 0.329 및 0.390으로 나타났다. 보증씨수소집단, 농가암소집단, 계통축 수컷집단 및 계통축 암컷집단 등 4개 집단의 도체형질 대해 참조집단에 따른 유전체 육종가 상관분석을 실시하였는데, 등 지방두께는 보증씨수소집단, 농가암소집단, 계통축 수컷집단 및 계통축 암컷집단에 대해 각각 0.56, 0.49, 0.46 및 0.50의 상관을 나타냈고, 도체 중은 보증씨수소집단, 농가암소집단, 계통축 수컷집단 및 계통축 암컷집단에 대해 각각 0.64, 0.64, 0.63 및 0.62의 상관을 보였으며, 등심단면적 은 보증씨수소집단, 농가암소집단, 계통축 수컷집단 및 계통축 암컷집단에 대해 각각 0.62, 0.56, 0.16 및 0.34의 상관을 나타냈다. 그리고 근내지 방도는 보증씨수소집단, 농가암소집단, 계통축 수컷집단 및 계통축 암컷집단에 대해 각각 0.61, 0.54, 0.49 및 0.55의 상관을 보였다.
Key Words : Hanwoo, Carcass traits, Genetic parameter, Genomic breeding value
PA-88
Quantile regression analysis of carcass quality and sensory evaluation traits in Korean Pigs
Mahboob Alam, Lee Seung Soo, Chang Hyuk Kee, Choy Yun Ho, Dang Chang Gwon, Lee Jae Gu, Park Mi Na, Choi Tae Jeong, Choi Youlim, and Kim Sidong
Animal Breeding and Genetics Division, National Institute of Animal Science, Rural Development Administration, Cheonan, Korea 31000
ABSTRACT The objective of this study was to investigate the impact of various factors on different quantiles of the meat qualitative traits and sensory evaluations in Korean Duroc pigs. A total of 1,035 pigs that were raised under Korean Pig Improvement Project from 2012 to 2018 were used in this study. Traits included for analysis were meat pH (field & lab), meat color measures L, a, b (field & lab), shear force, fatty acids (palmitic, oleic, stearic, linoleic, and linolenic), and various sensory evaluations (observed meat-color, taste, flavor, tender, and juiciness. Animal’s parity, slaughter-house, slaughter year, slaughter age, and date of slaughter were fitted as fixed effects and analysis of variance components using least squares regression and quantile regression models were performed on each trait. The averages of Lab pH and Field pH were 5.78 and 5.66. The averages of lab (a), (b) and (L) were 1.43, 5.99 and 4.86, respectively. Mean field (a), (b) and (L) values were measured as 1.71, 9.2, and 4.92, respectively. Linoleic, linolenic and oleic acids means were as 8.55, 0.52 and 0.428, respectively. Variance of traits on various quantiles (0.25, 0.5 and 0.75) were measured. The quantile regression methods showed significant differences at different quantiles in terms of regression parameters for several traits. As of principles, general linear regression models are not able to effectively explain the variances at different levels of quantiles. In this regard, quantile regression estimates could provide a better understanding for the significance of factors on different quantiles of these studied traits.
Key Words : Meat pH, meat color, quality traits, sensory evaluation, Korean Duroc pigs.
Korean Society of Animal Breeding & Genetics • 44 PA-89
A simulation study of the effect of male selection methods on inbreeding and genetic trends in a small population
차재범, 허강녕, 추효준, 권일, 박병호
국립축산과학원 가금연구소
ABSTRACT 소규모 집단에서 근교계수가 빠르게 상승할 확률이 높으며 근친에 영향을 미치는 요인은 집단의 크기, 선발강도, 선발되는 수컷과 암컷의 수 등 다양하다. 본 연구에서는 특정 아비의 자손들만 선발되는 것을 제한하기 위해 한 수컷에서 선발되는 수컷 자손을 1, 2, 3, 4, 5수로 제한하여 집단 을 선발했을 때 근교계수와 유전적 개량량의 변화를 모의시험을 통해 분석하였다. 모의시험 집단 디자인은 수컷 30수, 암컷 210수가 다음세대의 암/수컷 각 1,050수를 생산하고, 다시 수컷 30수, 암컷 210수를 선발하였다. 체중(8주령)과 산란수(~40주령)에 대해 다형질 개체모형으로 육종 가를 추정하고 표준화한 육종가에 4(체중):1(산란수)에 가중치를 두어 선발하였다. 각 모의시험 당 100회 반복을 실시하였고 근교계수, 체중과 산란수 유전적 개량량을 제시하였다. 한 수컷에서 선발되는 수컷 자손 수를 1, 2, 3, 4, 5마리로 제한을 두어 20세대 선발한 경우 유효집단크기(수) 는 각각 81.0, 56.0, 46.5, 41.7, 38.6으로 나타났으며, 8주령 체중 유전적 개량량(g)은 각각 878, 969, 992, 999, 998로 나타났으며, 40주령 산란수 유 전전 개량량(개)은 각각 23, 29, 30, 31, 32개로 나타났다. 한 수컷에서 3마리 이상의 수컷 자손을 선발하면 50이하로 감소하는 것으로 나타났으 며, 유전적 개량량 측면에서는 3마리까지 의 수컷에서 체중 및 산란수가 증가하는 것으로 나타났다. 이 분석 결과는 향후 가금연구소 토종닭 집 단 근친 관리를 위한 교배 프로그램을 설계하는데 활용될 것이다.
Key Words : 소규모 집단, 근친, 교배방법, 선발방법, 모의시험
PA-90
Comparison for Genetic Diversity Before and After the Reconstruction of five Korean Native Chicken lines 1* 1 1 1 1 1 Jihye Cha , Krishnamoorthy Srikanth , Bong-Hwan Choi , Jong-eun Park , Won-Chul Park , Haesu Ko , Mi-Rim Park, nayeon Kim 2 and Gulwon Jang 1 2 Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, Korea Research Policy Bureau, RDA, Wanju, Korea
ABSTRACT With the outbreak of AI in 2014, KNC(Korean Native Chicken) population(5 native breeds with 9 lines) held by NIAS were decimated. KNP breeds were restored from preserved samples from other regions between 2014 to 2016, but the size of the samples held were small, which might have resulted in the loss of genetic diversity in the restored KNP population. This study is aimed to analyze the genetic diversity and population structure of 5 KNP lines (C, H, R, S, Y) which were compared with the population before the reconstruction. A total of 50 heads from 5 KNC lines were whole genome sequenced at 10X coverage and were mapped against GallusGallus 5.0 reference genome using BWA 0.7.13 MEM. Variant calling was performed with GATK 3.5. The VCF files were then manipulated with PLINK 1.9 and PCA analysis was performed with GCTA. Admixture analysis was performed using ADMIXTURE. The PCA result showed that lines R and Y were genetically very similar, while the other breeds were genetically distinct. Also, admixture analysis showed that the five lines with the least error were divided into the five groups, and that each group had little mixture of genetic information from the other group, which could confirm that the reconstruction of the five lines was carried out normally. This study may provide the background for future studies to identify the genetic uniqueness of the KNP breeds.
45 • 2019 International Symposium & Conference PA-91
한우의 개량방법에 따른 개량효율에 관한 연구 1 4 4 3 1, 2, 3 2, 3 김현권 , 선두원 , 최병현 , 진종인 , 공일근 , 이정규 1 2 3 4 경상대학교 응용생명과학과(BK21 plus) 경상대학교 농업생명과학연구소 경상대학교 축산생명학과 경상대학교기업 GAST
ABSTRACT 최근 한우에 있어서 우량 송아지 생산 및 우수축군 조성이 매우 중요한 부분으로 자리잡고 있다. 경매시장에서도 같은 월령의 송아지라도 100만 원 이상의 가격차이를 보이는 경우를 많이 볼 수 있다. 그만큼 개량의 중요성이 대두되고 있는 상황이라고 생각한다. 한우의 개량을 위해서 수정 란이식 방법이 많이 활용되고 있는 실정이다. 이에 본 연구는 인공수정과 수정란이식의 개량 효율을 알아보기 위해 실시하였다. 수정란 이식은 인공수정과는 달리 우량암소의 난자를 수정란 이식 기술을 통해 그 유전자를 가진 후대를 대량 생산이 가능하다는 장점을 가지고 있다. 인공수 정과 수정란이식으로 태어난 개체들의 데이터를 수집하여 각 수정방법에 따른 표현형 형질의 차이와 육종가를 비교하고 개량효율에 대한 고찰 을 해 보았다. 연구를 위해 특정 보증종모우 후대의 도축 데이터를 이용하였으며 조사 두수는 총 1,470두이고, 도체형질은 도체중, 등지방두께, 배최장근단면적, 근내지방도 등 4가지 형질을 분석하였다. 분석결과를 살펴보면 표현형 형질의 분석결과 등지방두께를 제외한 도체중, 배최장 근단면적, 근내지방도는 모두 수정란 이식으로 태어난 후대가 유의적으로 우수하게 나타났고, 육종가는 조사된 모든 형질이 수정란이식으로 태 어난 개체가 유의적으로 높게 나타났다. 대체적으로 수정란이식으로 태어난 개체의 표현형과 육종가가 높게 나타난 것은 비교적 우수한 유전자 를 보유하고 있는 암소가 이용된 것이 주된 이유라고 사료된다. 이는 우수한 암소의 유전자가 확보 된다면 수정란이식은 농가의 수익증대와 한 우개량에 긍정적으로 작용할 수 있다고 사료된다.
Key Words : 개량, 인공수정, 수정란이식, 도체형질, 유전력
PA-92
홀스타인 젖소집단에서 대용량 SNP chip을 이용한 imputation 평가 1 1 1 2 1 Alam Zahangir , 김유삼 , 이윤미 , 당창권 , 김종주 1 2 영남대학교 생명공학과, 경산시, 경상북도 국립축산과학원, 개량평가과, 전주, 전라북도
ABSTRACT 본 연구는 국내 홀스타인 젖소집단 2016을 대상으로 대용량 Illumina 54K bovine SNP chip을 바탕으로 상용적으로 적용할 수 있는 저밀도 SNP chip을 활용하였을 때 imputation의 효율성을 평가하고자 수행하였다. 개체의 부모 또는 한쪽 부모의 유전자형 정보가 있는 690두를 실험집단으 로 설정하였고 나머지 1,314두에 대하여 참조집단1으로, 부모개체 270두를 참조집단2로, 부모가 아닌 개체들 270두를 참조집단3으로 설정하여 참조집단에 대한 SNP 밀도를 각각 5, 10, 15, 20K로 설정한 후 각 참조 SNP panel간의 imputation 정확도를 Beagle(4.0)과 Fimpute(2.2) 소프트웨 어를 이용하여 평가하였다. 분석결과 참조 SNP panel이 클수록 imputation 정확도가 높게 나타났으며 Beagle을 이용하였을때가 Fimpute를 이 용했을 때 보다 정확도가 다소 높게 나타났지만 분석시간이 500배이상 소요되어 Fimpute 소프트웨어를 통한 imputation 분석이 더 효율성이 높 게 나타났다. 또한 참조집단의 크기가 가장 큰 참조집단1을 이용하였을 때 가장 높은 정확도를 보였으며 부모개체들로 구성된 참조집단2을 이 용하였을 때 비부모로 구성되어진 참조집단 3 보다 정확도가 높게 나타났다. 이러한 결과는 SNP imputation 향상을 위한 최적의 저밀도 SNP set 선별에 대한 기본 정보를 제공하여 줄 것이다.
Korean Society of Animal Breeding & Genetics • 46 PA-93
A Genome-Wide Association study for meat and carcass quality traits in Hanwoo cattle using imputed whole genome sequence data 1 1 1 2 1 1 JuWhan Son , Krishnamoorthy Srikanth , Ki-Young Jang , Seung Hwan Lee , JongEun Park , Dajeong Lim
1 2 Animal Genomics & Bioinformatics Division, National Institute of Animal Science, RDA, Republic of Korea Department of Animal Science and Biotechnology, Chungnam National University, Daejon, Republic of Korea
ABSTRACT A genome-wide association study (GWAS) was conducted to identify major loci associated with four meat quality traits; Eye-Muscle area (EMA), carcass weight (CW), Marbling Score (MS) and Backfat thickness(BFT) in Hanwoo bulls. A total of 2,664 male animals were genotyped, out of which 480 animals were genotyped on illumina 777K BovineHD chip, 528 animals were genotyped on illumina Bovine SNP50 beadchip and a further 1,656 animals were genotyped on customized Hanwoo 50K chip. The data was imputed to sequence level in a two-step process, by first imputing with 777K single nucleotide polymorphism (SNP) data and then with sequence level SNP data which was generated from a reference sample of 311animals. After quality control and correcting for population stratification, a total of 2,450 animals and 11,493,197 SNPs remained for further analysis. The association analyses were performed using a mixed linear model (MLMA) approach implemented in GCTA, the largest chromosomal region found to be associated with BFT, MS,CW and EMA where located on BTA27, BTA23 and BTA14. The heritability estimated by considering all the SNPs together for BFT, CW, EMA and MAR were 0.45±0.04, 0.40±0.04, 0.38±0.04 and 0.45±0.03 respectively, suggesting moderate level of heritability .
PA-94
A Genome-Wide Association study for new meat quality traits in Hanwoo cattle using imputed whole genome sequence 1 1 1 2 1 1 Krishnamoorthy Srikanth , JuWhan Son , Ki-Young Jang , Seung Hwan Lee , JongEun Park , Dajeong Lim
1 2 Animal Genomics & Bioinformatics Division, National Institute of Animal Science, RDA, Republic of Korea Department of Animal Science and Biotechnology, Chungnam National University, Daejon, Republic of Korea
ABSTRACT A genome-wide association study (GWAS) was conducted to identify major loci associated with six new meat quality traits; Marbling percentage (MP), Fat Percentage (FP), Fineness of Marbling (FM), Number of marbling particles (NMP), Number of Fine marbling particles (NFP), and Marbling Area (MA) in Hanwoo bulls. A total of 2,664 male animals were genotyped, out of which 480 animals were genotyped on illumina 777K BovineHD chip, 528 animals were genotyped on illumina Bovine SNP50 beadchip and a further 1,656 animals were genotyped on customized Hanwoo 50K chip. The data was imputed to sequence level in a two-step process, by first imputing with 777K single nucleotide polymorphism (SNP) data and then with sequence level SNP data which was generated from a reference sample of 311animals. After quality control and correcting for population stratification, a total of 2,450 animals and 11,493,197 SNPs remained for further analysis. The association analyses were performed using a mixed linear model (MLMA) approach implemented in GCTA, large chromosomal region found to be associated with the targeted traits were located in BTA1 (MP, FP, FM), BTA12 (NMP), BTA1 and BTA28 (NFP) and BTA1, BTA10, BTA13 and BTA 14 for MA. The heritability estimated by considering all the SNPs together ranged from low; 0.17±0.03, 0.18±0.03 and 0.19±0.03 for MP, FP and MA to relatively moderate level for NMP, FM and NFP, 0.36±0.04, 0.40±0.04, 0.40±0.04 respectively.
47 • 2019 International Symposium & Conference PA-95
A comparative study of single and multi trait genomic prediction model for carcass traits in Hanwoo cattle. 1 2 3 3 1 1 1 Swati Srivastava , Seunghwan Lee , Dong-Hyun Shin , Jae-Don Oh , Han-Ha Chai , Jong-Eun Park , WonCheoul Park , Na-Rae 1 1* An , Dajeong Lim 1 2 National Institute of Animal Science, Rural Development Administration, Jeonju, South Korea Department of Animal Science and 3 Biotechnology, Chungnam National University, Daejeon, Republic of Korea Department of Animal Biotechnology, Chonbuk National University, Jeonju, Republic of Korea
ABSTRACT Korean beef cattle, Hanwoo farming is streamlined due to high customer demand and competition with other types of meat. It’s high meat quality, taste, juiciness etc. is granted by carcass traits such as Back Fat thickness (BFT), Carcass weight (CWT), Eye Muscle area (EMA) and Marbling score (MS). Therefore a study is conducted in order to analyze effect of one trait over other through multitrait animal model. Genetic parameters for above four carcass traits were estimated for 10,215 commercial Hanwoo populations with age around 30 months. 7991 animals with 53,866 SNPs (Single nucleotide polymorphism) were considered for genomic selection. A mutitrait model is built with the help of BLUPF90 program. Analysis is done by AIREML (Average Information Restricted Maximum Likelihood). A comparative study is done between single trait model and multi trait model. An increase in genetic correlation was observed for multitrait analysis (MT) as compared to bi-trait analysis (BT) on pedigree data BFT-CWT (BT-0.43, MT-0.45), BFT- EMA (BT-0.04, MT-0.08), CWT-EMA (BT-0.46, MT-0.49), CWT-MS (BT-0.38, MT-0.40) and EMA-MS (BT-0.62, MT-0.63). Whereas for genomic based data, there was slight decrease in correlation except for BFT-MS (BT-0.01, MT-0.2). Heritability was estimated and compared for pedigree based data, the result shows an increase from BFT(0.41),CWT(0.30),EMA(0.35),MS(0.30) to BFT(0.42),CWT(0.32),EMA(0.37),MS(0.34), whereas similar heritability was obtained for genomic data. The probable reason of similar genomic selection result for single trait and multi trait is consideration of SNPs (Single Nucleotide polymorphism).
Key Words : Multitrait model, genetic parameters, heritability, genetic correlaton
PA-96
Genome-wide association study and genomic prediction using two commercial medium- density SNP genotyping platforms for growth- and production-related traits in Korean Duroc pigs
Eun seok Cho, Kyu Ho Cho, Jun Ki Hong, Young Sin Kim, Hak-Jae Chung, Sun-Young Baek, Mi-Jin Lee, Jeong A Kim, Soo jin Sa
National Institute of Animal Science, RDA, Cheonan-si, 31000, Republic of Korea
ABSTRACT This study investigated the efficiency of genomic prediction by using two moderate-density single nucleotide polymorphism (SNP) genotyping panels in Korean Duroc pigs. We genotyped 1,026 individuals with growth and production records using two medium-density SNP genotyping platforms: Illumina PorcineSNP60 version 2 and GeneSeek-Neogen PorcineSNP80 BeadChip. These platforms consisted of 61,565 and 68,528 SNP markers, respectively. The deregressed estimated breeding values (DEBVs) derived from estimated breeding values (EBVs) and their reliabilities were taken as response variables. Two Bayesian approaches, BayesB and BayesC, were implemented to perform the genome-wide association study and genomic prediction. Our results indicate that the accuracies of genomic predictions slightly increased by using the GeneSeek-Neogen Porcine80K SNP panel for days to 90 kg body weight (DAYS) and loin muscle area (LMA) with two response variables. Significant differences in accuracies of genomic prediction were not identified based on the Bayesian approaches in four growth and reproduction-related traits. The largest differences in accuracies of genomic prediction were identified when comparing the results using DEBVs without parental information (DEBVexcPA) or with parental information (DEBVincPA) for all studied traits. In most situations, the choice of BayesB and BayesC following the mixture model were not significant. We recommend using genomic prediction derived from the use of DEBVincPA for genomic prediction accuracies in Korean Duroc pig breeding.
Key Words : Single Nucleotide Polymorphism; Porcine SNP panel;DEBVincPA
Korean Society of Animal Breeding & Genetics • 48 PA-97
Estimation of Genetic Parameters on Litter Size Traits by Parity in Landrace Pig
D. H. Lee, Y. G. CHO, D. H. Weon, B. M. Lopez, C. W. Song and K. S. Seo
Department of Animal Science and Technology, Sunchon National University, Suncheon, 57922, South Korea
ABSTRACT This study was conducted to estimate genetic parameters for litter size traits by parity using least square method (Harvey, 1979) in Landrace. For the study, 21,278 records for litter size traits were collected between the year 2000 and 2018 from 10 farms. The effects of environmental factors such as farm, and calving year-month group affected on litter size traits viz. Total number born (TNB), Number of born alive (NBA), Number accidents (NA), Mummy (MUM), Total number born excluding mummy (TBM), and Number accidents excluding mummy (NAM) significantly. The heritability of six traits was estimated 0.06~0.17, 0.07~0.21, 0.05~0.13, 0.13~0.19, 0.12~0.19 and 0.12~0.19 for NA, NAM, MUM, NBA, TNB, and TNBM, respectively. All phenotypic and genotypic correlation among parity were positive. However, the genotypic correlation varied widely from 0.03 to 0.99. The phenotypic correlation had lower range than genotypic correlation. Accordingly, it showed genetic parameters among parity on the same traits differ highly.
Key Words : Landrace, Litter size traits, Genetic parameters, Parity
PA-98
Relationship between Immune Antibody in Dairy cattle Using gBLUP
Y. G. Cho, D. H. Lee, D. H. Weon, B. M. Lopez, C. W. Song and K. S. Seo
Department of Animal Science and Technology, Sunchon National University, Suncheon, 57922, South Korea
ABSTRACT The study was conducted to investigate the association of dairy cattle immunity between birth. In totally, 107 dairy cattles were examined under this study whose were borned from 2013 to 2016, and blood samples from each cattle were collected at 0, 1, 4, and 24 weeks after vaccination on April 25, 2017. ELISA was performed on collected samples and analyzed the immunodomic cytokines of BVDV, BRSV and TNF-alpha, IFN-gamma, IL-17A, IL-1b, IL-2, IL-4 and IL-6. Using the genomic studio program and plink plugin program of Illumina, we analyzed gBLUP through Genetic Estimated Breeding Values(GEBV), and calculated correlations between traits. We found that BVDV antibody showed significant difference (p <0.05) for individuals borned in 2015 and 2016, and the highest value was observed in cattles bornead in 2016. The BRSV antibody showed the significant difference (p <0.05) for the individuals borned in 2013 and 2014, and after the vaccination, they were maintained after being reduced. Immune cytokines generally showed a tendency to rise at the first week of vaccination, then decreased at the fourth week, and later rose again at the 24th week. However, IL-2 decreased after vaccination and tended to increase after 4th week. Except for some of the immunocytokines, the levels of immune factors in individuals born in 2016 were generally higher. The correlation between the estimated GEBV of the BVDV antibody and the BSVS antibody were analyzed and the correlation coefficient were 0.31, 0.28, 0.27 and 0.27 respectively per week of 0, 1, 4 and 24 indicating the correlation of the middle, and it is considered that simultaneous breeding will be possible. Therefore, the results of the study suggests that the robustness of dairy cattles can be increased. However, additional research on the immune system of dairy cattle may be required furthermore.
Key Words : Immune Antibody, ELISA, gBLUP, Dairy cattle
49 • 2019 International Symposium & Conference PA-99
In silico analysis to identify functional and structural impact of non-synonymous SNPs in Ogye chicken genome 1 2 2 1 1 Seungwoo Son , Jihye Cha , Jongeun Park , Donghyun Shin , Ki-Duk Song 1 2 Animal Molecular Genetics and Breeding Center, Cheonbuk National University, Jeonju, Republic of Korea; Animal Genomics Division, National Institute of Animal Science, Rural Development Administration, Jeonju, Republic of Korea,
ABSTRACT Ogye, one of indigenous Korean native chickens, is notable for its black feather, skin, and bone. Comparing to other western chickens like Cornish or White Leghorn, it is less fatty but contains more essential fatty acids and total collagen as well as higher protein content. In this study, we aimed to identify using whole-genome sequencing data which were generated by National Institute of Animal Science, RDA, and composed of 120 chickens with 10 Ogyes obtained from Illumina Hiseq2000 platform, we identified total 89,701 non-synonymous single nucleotide polymorphisms (nsSNPs). Among them, we found 45,359 nsSNPs and 6,432 genes associated with these variations in Ogye genome. SIFT (Sorting Intolerant From Tolerant) and Polyphen-2 analyses identified 231 deleterious nsSNPs and 112 related genes to have significant biological impacts. Through the gene ontology analysis using WEB-based Gene Set AnaLysis Toolkit (http://www.webgestalt.org/), DAVID (https://david.ncifcrf.gov/), and ClueGO, we were able to identify steroid, arginine biosynthesis, flemming body, and brush border membrane in various categories of biological function. AGRN, HMMR, CEP55, DTL, FBF1, and HMMR genes could be predicted to be related to these pathways. Through this study, we were able to explore the genomic mechanisms which might be related to the domestication of Ogye. These results will help to support previous studies and provide the basis for future research on properties of Ogye genome.
Key Words : Ogye, Single nucleotide polymorphisms, Sorting Intolerant From Tolerant, Polyphen-2, Biological function
PA-100
Genome wide association study (GWAS) using the 170K CanineHD BeadChip for blood glucose in dogs
Bong-Hwan Choi, Jihye Cha, Haesu Ko, , Young-jo Lim, Jong-Eun Park, and Won-Chul Park
Animal Genomics & Bioinformatics, National Institute of Animal Science, RDA
ABSTRACT Blood glucose is the concentration of glucose in the blood. As with humans, dogs should always keep their blood glucose levels within a certain range to maintain homeostasis. Glucagon, adrenaline, insulin, and thyroid hormones are the hormones that contribute to maintain blood glucose levels, and blood glucose levels in the body are always maintained at about 74-143mg/dl. If such hormone secretion is abnormal, the blood glucose level becomes unstable. A typical example of this phenomenon in diabetes. Diabetes is accompanied by serious complications such as cardiovascular disease, chronic renal failure, and diabetic retinopathy. The objective of this survey is understanding association and correlation between single nucleotide polymorphism (SNP) and the blood sugar in dogs. SNPs were tested for Hardy-Weinberg equilibrium (HWE) to identify possible genotyping errors using the Chi-square test in the R/ SNPassoc Package (R Development Core Team). SNPs with HWE (P<0.05), fail to call (> 80%), monomorphic SNPs and minor allele frequency (< 0.01) were removed in this study. As a result, optimal SNP markers of 20 loci for canine blood glucose were found on chromosome 5, 8, 30, 34, and 35 using the 170K CanineHD BeadChip that was more than 170,000 evenly spaced and validated SNPs derived from the CanFam2.0 assembly. In particular, genetic markers that are present on chromosome 8 and 30 are placed nearby pinin, desmosome associated protein and microRNA (mir-147), respectively.
Key Words : Dogs, Genome-wide association study (GWAS), SNP, Blood glucose
Korean Society of Animal Breeding & Genetics • 50 PA-101
Genetic diversity and differentiation among Korean-Holstein, Hanwoo, Uganda-Holstein breeds 1, 2 3 3 1, 3, 4 Godfrey Bigirwa , Do-Hyun Kim , Jae-Don Oh , Ki-Duk Song
2 ¹Department of Agricultural Convergence Technology, Chonbuk National University, Jeonju 54896 Korea College of Veterinary Medicine, 3 Animal Resources and Biosecurity, Makerere University, Uganda Department of Animal Biotechnology, Chonbuk National University, 4 Jeonju 54896, Korea Animal Molecular Genetics and Breeding Center, Chonbuk National University, Jeonju 54896, Korea
ABSTRACT This was study was done to assess the genetic diversity of Korean-Holstein, Korean Hanwoo and Ugandan-Holstein breeds. A total of 226 DNA samples were extracted from either blood or hair of Korean-Holstein, Korean-Hanwoo and Ugandan-Holstein using AccuPrep® PCR Purification Kit. The DNA samples were amplified by multiplex polymerase chain reaction, using GeneTrack TM Hanwoo Genotyping Kit. Full genotyping, determining the number of alleles, the expected heterozygosity (H ex ), the observed heterozygosity(H ob ) and the polymorphism information content (PIC) from 10 microsatellite loci in the three breeds of cattle were obtained using ABI Genetic Analyzer 3130XL. Furthermore, GENETIX (v.4.02) program was used perform Factorial Correspondence of allele frequencies from 10 microsatellite loci genotypes in the 3 breeds. Clustering assignments of the three breeds were obtained by using STRUCTURE analyses. A total of 124 alleles were detected at 10 microsatellite loci across the three study breeds. The number of alleles varied between 8(TGLA126) and 22 (TGLA122), with an overall mean allele number of 12.2 per locus. The expected heterozygosity (H ex ) ranged between 0.617 (SPS115) and 0.854 (TGLA53) with an average of 0.761. The observed heterozygosity (H ob ) varied between 0.6 (SPS115) to 0.859 (TGLA53); and a mean of 0.761. The mean PIC was 0.723. Although, FCA of allele frequencies from the 10 microsatellite loci revealed the very clear separation between the Uganda-Holstein, Korean-Holstein and Hanwoo; clustering assignments revealed genetic admixture between Ugandan dairy cattle (Uganda-Holstein) and Hanwoo. All the identified alleles in this study were able to categorize the three breeds into three distinct groups. The allele admixture between Uganda-Holstein and Hanwoo suggest a genetic lineage of the Ugandan dairy cattle that could be linked to Hanwoo.
Key Words : Uganda-Holstein, Korean-Holstein, Hanwoo, Genetic diversity, Genetic differentiation
PA-102
번식과 육종 기법을 활용한 흑우 신품종의 개발과 유전적 우수성 1 2 3 정연길 , 서성보 , 김관석 1 2 3 전북 장수군 천천면 싸리재로 560-34 이티바이오텍(주) 한우유전자연구소 충북 청주시 흥덕구 오송읍 오송생명1로 194-41 ㈜코쿤 충북 청주시 서원구 충대로 1번지 ㈜블루진라이프사이언스
ABSTRACT 우리 한민족은 수천년동안 소를 키우고 이용해 왔다. 그리고 다양한 한우들이 한반도의 기후풍토에 맞게 적응해 왔지만, 일제강점기에 강제로 적갈색으로 외형적인 통일을 정한 정책은 지금도 이어져서 한우의 근대화 과정에 황갈색으로 열성 유전 모색을 고정한 결과 다양하게 있었던 한 우들은 사라지게 되었다. 특히 일본에서 개량한 우성 외모형질의 흑우가 세계적인 육우품종으로 인기가 있는 것은 일본 와규와 유전적으로 유사 한 한우를 기반으로 하여 새로운 흑우 품종을 개발하고 산업화하여서 한우농가의 수익증대와 한우산업의 발전에 도움이 된다. 하지만 현재 국가 에서 정한 획일화된 제도로 한우를 개량하고 있다보니 선발강도와 정확도가 낮고, 높은 비용이 들어가는 비효율성과 단일품종으로 소비자의 다 양한 요구를 반영하는 것도 한계가 있다. 현재 유전적으로 분리된 한우와 칡소, 그리고 흑우가운데 우량한 개체들을 선발하여 수정란 생산과 이 식을 통해 하나의 계통을 확립하였다. 한우의 우량유전자 선발과 고정을 통해 후대의 유전적 균일성도 증대시켰다. 한우와 칡소에 기반한 새로 운 흑우는 해외시장에서 높은 수출경쟁력도 가지고 있으며, 품종 차별화를 통해 지역 한우농가의 경쟁력을 강화하여 지역기반 한우산업이 될 수 있는 새로운 육종체계 모델이 되고있다.
Key Words : 신품종, 흑우개발, 수정란, 유전자 선발
51 • 2019 International Symposium & Conference PA-103
에티오피아 저·고지대 재래닭의 맹장내 미생물 유전체 및 항생제 내성 유전자 비교분석 1 1 1 1 1 2 3 3 3 장명진 , Himansu Kumar , 박원철 , 임다정 , Krishnamoorthy Srikanth , 김준모 , Jia, Xinzheng , Han Jianlin , Oliver Hanotte , 3 1* Samuel O. Oyola , 박종은 1 2 3 농촌진흥청 국립축산과학원 동물유전체과, 중앙대학교 안산캠퍼스 생명자원공학부 동물생명공학 Faculty of Medicine & Health Sciences, 4 University of Nottingham, UK, International Livestock Research Institute (ILRI) Nairobi, Kenya.
ABSTRACT 닭의 장내미생물은 숙주의 능력, 소화, 영양소의 흡수, 병원균에 대한 방어 등의 중요한 역할을 한다. 이러한 장내미생물의 조성은 면역력 및 사 료 효율을 포함한 전체적인 생산과 성장 능력에 있어 중요하다. 본 연구에서는 닭의 장내미생물 유전체 정보 분석을 통하여 환경과 장내미생물 의 기능적 연결 관계를 확인하고자 하였다. 시료는 에티오피아 Hugub(AF, 해발 730m)와 Menz Gera Midir(AM, 해발 3300m) 두 지역에 닭의 맹 장액을 이용하였다. 닭 10수의 게놈·장내미생물 유전체 정보를 생산 및 장내미생물 생물정보 분석을 수행한 결과, 두 지역 닭의 2,210개 공통 유 전자를 확인하였으며, 지리적 위치에 따라 장내미생물 조성에 차이를 관찰하였다. 또한, 생물학적 기능, 경로 및 다양한 장내미생물에 존재하는 항생제 내성 유전자를 탐색하였다. 선형 차별 분석 효과 크기(Linear discriminant analysis effect size)를 확인한 결과, Coprobacter, Geobacter, Cronobacter, Alloprevotella 및 Dysgonomonas의 분포가 AM에 비해 AF에서 큼을 확인하였다. 미생물군의 기능분석에는 KEGG, eggNOG, CAZy 데이터베이스를 이용하였으며, 환경정보처리(environmental information processing), 유전정보 처리(genetic information processing)와 세 포과정(cellular process) 등의 생물학적 기능이 유의적인 차이를 보였다. 또한 LSM, cephalosporin, tetracycline과 같은 항생제 내성 유전자가 AM 에 비하여 AF에서 상대적으로 많이 발견되었다. 따라서, 본 연구를 통해 확인된 미생물은 다양한 환경 및 기후 조건에 대한 닭 적응에 있어 장내 미생물 유전체에 생물학적 기능에 대한 기초 자료를 제공할 것으로 사료된다.
Key Words : AF, AM, LEfSe, KEGG, eggNOG, CAZy
PA-104
Estimation of lactation curve by parity in domestic Holstein
D. H. Weon, Y. G. Cho, D. H. Lee, C. W. Song, T. I. KIM and K. S. Seo
Department of Animal Science and Technology, Sunchon National University, Suncheon, 57922, South Korea
ABSTRACT The purpose of this study was to exploit the milk yield to parity with milking days in relation to estimate lactation curve of Holstein cattle in Korea. The data with daily milk yields 706 cows were collected from 251,862 to fifth parity from first parity cows, from 2005 to 2018 recorded at 15 farms in Korea. The lactation curves were using Wood (Wood, 1967) gamma model based on actual milk records, and Procedure NLIN of SAS program (ver.9.4). The functions formula of the estimate lactation curve using Wood model were , , , , , respectively. Peak milk yields about milking days of parity were 113.98 kg, 71.78 kg, 64.59 kg, 70.22 kg, 81.84 kg and peak milk yields time to reach were 33.44 day, 41.42 day, 44.67 day, 45.91 day and 43.02 day, respectively. The first parity of milking days of peak milk yields was turned out to be about 40 kg higher than other parity and also peak milk yields time was measured about 10 days fast. The first parity of milking days of peak milk yields was turned out to be about 40 kg higher than other parity and also peak milk yields time was measured about 10 days fast. Third parity of milking days of peak milk yields was about 50 kg lower than compare to first parity and also peak milk yields time was measured about 10 days slow. This study can be used as a basic data to confirm inflection point in the lactation stage of cow.
Key Words : Milking Days, Wood model, Estimate Lactation Curve, Dairy Cattle
Korean Society of Animal Breeding & Genetics • 52 PA-105
돼지의 사료요구율에 미치는 환경요인의 효과 추정
고대영, 이일주, 강현성
다비육종 육종연구소
ABSTRACT 국내 양돈산업에서 높은 사료가격은 생산비에 많은 부분을 차지하지만 정확한 개체별 사료섭취량 측정이 이루어지지 않기에 개선하기에 많은 어려움 있다. 본 연구는 사료섭취량 측정기를 통하여 수집된 개체별 사료 섭취량 측정 자료를 활용하여 사료요구율을 포함한 검정형질에 대하여 환경요인 효과를 분석하여 유전모수 추정에 활용하고자 실시하였다. 두록, 랜드레이스 및 요크셔에서의 수퇘지 검정돈 각 99두, 444두 및 684두 에 대한 자료를 수집하여 사료요구율을 계산하고 자가검정을 통하여 검정자료를 수집하였다. 사료섭취량 측정 개시 일령과 체중은 두록, 랜드레 이스 및 요크셔 각각 평균 76.33일령, 35.80kg, 80.84일령, 36.82kg 및 81.31일령, 36.54kg으로 나타났다. 품종별 하루 평균 사료 섭취량과 사료요 구율은 각각2.34kg, 2.24kg 및 2.18kg 그리고 2.11, 2.27 및 2.18로 유의적인 차이를 보였으며, 검정년도와 검정계절에서 또한 유의적인 차이를 나 타냈다.
Key Words : 사료섭취량 측정기, 사료요구율, FCR, 환경요인
PA-106
Unraveling the Genomic Signatures of the Mitochondria – Nucleus Conflict in African Cattle Admixture 1 1 2, 3 1 Taehyung Kwon , Kwondo Kim , Olivier Hanotte , Heebal Kim 1 2 Seoul National University, Seoul, South Korea School of Life Sciences, University of Nottingham, Nottingham, United Kingdom 3 LiveGene, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
ABSTRACT The mitochondria - nucleus conflict is a major barrier to cross-species hybridization affecting the fitness of hybrid progenies. Despite the admixed zebu- taurine nature of the majority of African cattle, only taurine mitochondrial haplotypes are found on the continent. Here, we proposed and investigated two evolutionary hypotheses as the bases of this observation, asymmetric admixture in zebu-taurine hybridization and selection pressure driven by the mito- nuclear discordance. We firstly confirmed the phylogenetic inconsistency based on mitochondrial DNA (mtDNA) and nuclear DNA (nucDNA), using public data and 162 African indigenous cattle whole genome sequences. In addition, estimation of demography and ancestry has concurred with the previous evidences of African zebu introduction and the admixture. We simulated various demographic scenarios and presumed that the current preponderance of taurine mtDNA necessitates the mito-nuclear selection as well as the population structure. Therefore, we identified mito-nuclear selection signatures on the genome of African zebu cattle, such as TRAK2 involved in neurodegenerative mitochondrial dysfuction. This illustrates the impact of mito-nuclear discordance on organismal function in the context of the population admixture. Our results indicate that the combination of selective pressure and population structure was likely the main driving forces of evolution behind the only presence of taurine mtDNA. We believe that our findings provide a new stepping stone toward the full understanding of the evolution of cattle population and their adaptation to the African continent.
53 • 2019 International Symposium & Conference PA-107
Genome-Wide Analysis for Population Structure in Korean Native Chickens 1 1 2 2 1, 3 Bongsang Kim , Byung June Ko , Han-Ha Chai , Dajeong Lim , Heebal Kim 1 Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University Seoul, 2 3 Republic of Korea National Institute of Animal Science, RDA, Wanju, Republic of Korea Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
ABSTRACT The Korean native chicken (KNC), comprised by five breeds and originated from China and South East Asia for about 2000 years ago, is endangered in extinction due to the wars on Korea in the 20th century and the importation of exotic species. In order to obtain useful traits and maintain species biodiversity, efforts to conserve and utilize the native breed have been emphasized as one of the key ways. For this reason, the efforts for restoration have been carried out on five KNC breeds with identifying genetic structure and useful feature of KNC. Although many studies on microsatellite or mtDNA have been conducted as well as SNPs from whole genome sequencing data, identification of the population structure using the entire region of the genome will be a great help to the restoration of KNC. Therefore, with whole genome sequencing, consisting of five Korean native and Yeonsan Ogye populations, one Chinese native population, and one outgroup (Red Jungle Fowl), we examined the population structure of Chinese and Korean native chickens and genetic features of Korean native chickens. The results of PCA and admixture analysis showed that the differences between KNC and Chinese groups were distinguished and also differences within KNC breeds were distinguished. In addition, F ST value and phylogenetic tree also indicate the differences between KNC and Chinese and within KNC breeds. Based on this population structure, we detected breed specific SNPs that were used for annotation and Gene Ontology (GO) analysis. Thus, by confirming KNC specific genetic structure, the results in the comparative genome-wide analysis of Chinese native chicken and KNC are expected to provide basis in the preservation and population genetics features of endangered native chickens.
Key Words : Native Chicken, Whole Genome Analysis, population structure, genetic feature
PA-108
Detection of Copy Number Variation in Three Different Chicken Breed by Focusing on Domestication 1 1 1 1 2 2 1, 3 Donghyeok Seo , BongGyu Min , Byung June Ko , Bongsang Kim , Han-Ha Chai , Dajeong Lim and Heebal Kim
¹Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 2 3 Republic of Korea National Institute of Animal Science, RDA, Wanju, Republic of Korea Interdisciplinary Program in Bioinformatics, Seo ul National University, Seoul, Republic of Korea
ABSTRACT Establishing a breeding strategy should be accompanied by an understanding of the genome of livestock. Among the livestock, chickens have evolved in specific directions, such as increased productivity of meat or eggs and improved disease resistance over the past few decades. A variety of studies have been actively conducted to identify genetic mechanisms associated with such trait changes and to apply them to the breeding system. In particular, with the help of genome-wide association studies (GWAS), numerous SNPs related to a specific trait have been uncovered, and the quantitative trait locus (QTL) database (https://www.animalgenome.org/cgi-bin/QTLdb/GG/summary) have been also being continually updated. However, genetic variants affecting traits include a large-scale variation of copy number variation (CNV) as well as a small-scale variation of SNV or indel. Although the importance of CNV has been emphasized through the study of CNV in human, there is a lack of CNV research in chickens. Furthermore, most of the studies already completed are microarray-based: array-based comparative genomic hybridization and SNP-based microarrays, which are known to be relatively inaccurate than NGS-based. Therefore, in this study, using total of nine samples from Cornish (broiler), White Leghorn (layer), and Rhode Island Red (hybrid), we identified breed-specific CNV through NGS data. As a result, a number of CNV regions related to transcription regulation were found in common, the metabolic pathway in Cornish, and calcium metabolism, retinoic-related pathway in White Leghorn. In conclusion, this study has helped to understand the genetic characteristic of domestic chicken at CNV level, which may provide useful information for the future chicken breeding system.
Key Words : Copy Number Variation (CNV), NGS, Cornish, White Leghorn, Rhode Island Red
Korean Society of Animal Breeding & Genetics • 54 PA-109
비드에 의해 성 분리된 돼지 정자의 단백질 동정 1 1 1 1 2 1 1 1 1 정학재 , 사수진 , 백선영 , 홍준기 , 손중호 , 박준철 , 김영신 , 조은석 , 조규호 1 2 국립축산과학원 양돈과, 노아 바이오텍
ABSTRACT 정자의 성 분리 기술은 가축의 개량 가속화를 촉진 가능하게 하는 매력적인 연구방법 중에 하나이다. 우리는 돼지 정자를 마그네틱 비드를 이용 해서 X-정자와 Y-정자를 분리(sperm sexing)하여, 각각의 정자에서 발현되고 있는 단백질의 분리 동정을 실시하였다. 마그네틱 비드에 X-chromosome 특이적 물질을 binding하여 성 특이적 정자를 접착시켜 마그네틱 비드를 강한 자성을 이용해서 분리하였다. 정자 분리에 필요한 자력의 범위는 약 5,000 가우스가 적용되었으며, 정자 분리 시 가장 효율적인 부착력을 고려한 막대자석이 사용되었다. 단백질 분리는 LC-MS/ MS analysis 방법을 이용됐다(Proteme tech Inc. Seoul). 본 연구 결과는 돼지 정자를 비드에 의한 성 분리 후 각각의 정자에서 발현되고 있는 단백 질 분리가 진행되었으며, 각각의 단백질 표적 marker들은 커다란 분자량의 단백질들을 차등으로 포착할 수 있었다. X-정자 group에 비하여 Y- 정자 group에서는 비교적 큰 분자량의 단백질들이 발현되고 있는 것이 분석되었으며, 반면, 작은 분자량의 단백질 분포는 X- 정자 group에 서 보다 많이 발현되고 있는 것이 분석되었다. 또한 동결 정자에서의 단백질 발현 양상은 무 처리 정자에 비하여 큰 분자량의 단백질 발현 양상 은 적게 분석되었다. 본 연구를 기초 근거로 하여 돼지 정자의 성 분리에 따른 정자의 활력 및 생존성에 관련된 연구를 추후 진행될 예정에있다.
Key Words : 돼지 정자, 비드, 정자 성 분리, 차등 단백질 발현, Proteomic analysis
55 • 2019 International Symposium & Conference