[논문]Comparison on genomic prediction using pedigree BLUP and single step GBLUP through the Hanwoo full-sib family

Eun-Ho Kim; Ho-Chan Kang; Cheol-Hyun Myung; Ji-Yeong Kim; Du-Won Sun; Doo-Ho Lee; Seung-Hwan Lee; Hyun-Tae Lim

doi:10.5713/ab.22.0327

Comparison on genomic prediction using pedigree BLUP and single step GBLUP through the Hanwoo full-sib family 원문보기

Animal bioscience, v.36 no.9, 2023년, pp.1327 - 1335

Eun-Ho Kim (Department of Animal Science, Gyeongsang National University) , Ho-Chan Kang (Department of Animal Science and Biotechnology, Gyeongsang National University) , Cheol-Hyun Myung (Department of Animal Science, Gyeongsang National University) , Ji-Yeong Kim (Department of Animal Science, Gyeongsang National University) , Du-Won Sun (Gyeongnam Animal Science and Technology, Gyeongsang National University) , Doo-Ho Lee (Department of Animal Science and Biotechnology, Chungnam National University) , Seung-Hwan Lee (Department of Animal Science and Biotechnology, Chungnam National University) , Hyun-Tae Lim (Department of Animal Science, Gyeongsang National University)

Abstract ▼ AI-Helper

Objective: When evaluating individuals with the same parent and no phenotype by pedigree best linear unbiased prediction (BLUP), it is difficult to explain carcass grade difference and select individuals because they have the same value in pedigree BLUP (PBLUP). However, single step GBLUP (ssGBLUP), which can estimate the breeding value suitable for the individual by adding genotype, is more accurate than the existing method. Methods: The breeding value and accuracy were estimated with pedigree BLUP and ssGBLUP using pedigree and genotype of 408 Hanwoo cattle from 16 families with the same parent among siblings produced by fertilized egg transplantation. A total of 14,225 Hanwoo cattle with pedigree, genotype and phenotype were used as the reference population. PBLUP obtained estimated breeding value (EBV) using the pedigree of the test and reference populations, and ssGBLUP obtained genomic EBV (GEBV) after constructing and H-matrix by integrating the pedigree and genotype of the test and reference populations. Results: For all traits, the accuracy of GEBV using ssGBLUP is 0.18 to 0.20 higher than the accuracy of EBV obtained with PBLUP. Comparison of EBV and GEBV of individuals without phenotype, since the value of EBV is estimated based on expected values of alleles passed down from common ancestors. It does not take Mendelian sampling into consideration, so the EBV of all individuals within the same family is estimated to be the same value. However, GEBV makes estimating true kinship coefficient based on different genotypes of individuals possible, so GEBV that corresponds to each individual is estimated rather than a uniform GEBV for each individual. Conclusion: Since Hanwoo cows bred through embryo transfer have a high possibility of having the same parent, if ssGBLUP after adding genotype is used, estimating true kinship coefficient corresponding to each individual becomes possible, allowing for more accurate estimation of breeding value.

주제어

표/그림 (5)

표 Table 1. Basic statistics of test and reference population used in the analysis
표 Table 2. Estimated genetic parameters and heritability according to the analysis method
표 Table 3. Genetic correlation and phenotypic correlation according to analysis method¹⁾
표 Table 4. Comparison of GEBV and EBV, phenotype according to population¹⁾
그림 Figure 1. Estimated kinship coefficient using the pedigree and genotype of the test population. (A) is a boxplot showing the kinship relationship matrix diagram used for PBLUP and ssGBLUP by dividing it into low relatedness population, half-sib population, full-sib population. (B) shows the kinship coefficient matrix diagram used for ssGBLUP by frequency by population (RT1, Low relatedness population; RT2, Half-sib population; RT3, Full-sib population).

참고문헌 (30)

Henderson CR. Theoretical basis and computational methods for a number of different animal models. J Dairy Sci 1988;71:l-16. https://doi.org/10.1016/S0022-0302(88)79974-9？

상세보기
Jil TC, Rahman MM, Pitchayapipatkul J, Mashitah SM, Nor Azlina AA, Raja Ili Airina RK. Viability of bovine opuderived oocytes to honeybee as cryoprotectant. IOP Conf Ser: Earth Environ Sci 2021;756:012063. https://doi.org/10.1088/1755-1315/756/1/012063？

상세보기
Hayes BJ, Visscher PM, Goddard ME. Increased accuracy of artificial selection by using the realized relationship matrix. Genet Res (Camb) 2009;91:47-60. https://doi.org/10.1017/S0016672308009981？

상세보기
Goddard ME, Hayes BJ, Meuwissen THE. Using the genomic relationship matrix to predict the accuracy of genomic selection. J Anim Breed Genet 2011;128:409-21. https://doi.org/10.1111/j.1439-0388.2011.00964.x？

상세보기
Sullivan PG. Mendelian sampling variance tests with genomic preselection. In: Proceedings of the 2018 Interbull Technical Workshop; 2018 Aug 25-26; Dubrovnik, Croatia.？
Misztal I, Lourenco D, Legarra A. Current status of genomic evaluation. J Anim Sci 2020;98:skaa101. https://doi.org/10.1093/jas/skaa101？

상세보기
Meuwissen THE, Hayes BJ, Goddard ME. Prediction of total genetic value using genome-wide dense marker maps. Genetics 2001;157:1819-29. https://doi.org/10.1093/genetics/157.4.1819？

상세보기
R Core Team. R: A language and environment for statistical computing [Internet]. R Foundation for Statistical Computing [cited 2022 Aug 10]. Available from: https://www.R-project.org/？
Purcell S, Neale B, Todd-Brown K, et al. PLINK: A toolset for whole-genome association and population-based linkage analysis. Am J Hum Genet 2007;81:559-75. https://doi.org/10.1086/519795？

상세보기
Loh P. Eagle v2.4.1 User manual [Internet]. Loh Lab [cited 2022 Aug 6]. Available from: https://alkesgroup.broadinstitute.org/Eagle/？
Das S, Forer L, Schonherr S, et al. Next-generation genotype imputation service and methods. Nat Genet 2016;48:1284-7. https://doi.org/10.1038/ng.3656？

상세보기
Misztal I, Tsuruta S, Lourenco D, Aguilar I, Legarra A, Vitezica Z. Manual for BLUPF90 family programs [Internet]. University of Geonrgia, USA [cited 2022 Aug 6]. Available from: https://nce.ads.uga.edu/wiki/doku.php?iddocumentation？
VanRaden PM. Efficient methods to compute genomic predictions. J Diary Sci 2008;91:4414-23. https://doi.org/10.3168/jds.2007-0980？

상세보기
Zhang Z, Buckler ES, Casstevens TM, Bradbury PJ. Software engineering the mixed model for genome-wide association studies on large samples. Brief Bioinform 2009;10:664-75. https://doi.org/10.1093/bib/bbp050？

상세보기
Lee GH, Lee YS, Moon SJ, Kong HS. The accuracy of genomic estimated breeding value using a Hanwoo SNP Chip and the pedigree data of Hanwoo cows in Gyeonggi Province. J Life Sci 2022;32:279-84. https://doi.org/10.5352/JLS.2022.32.4.279？

원문보기 상세보기
Lee CW, Choi JW, Shin HJ, Kim JB. Genetic prediction of Hanwoo carcass traits in Kangwon regional Hanwoo cow test farms. Ann Anim Resour Sci 2020;31:1-12. https://doi.org/10.12718/AARS.2020.31.1.1？

상세보기
Jang JS, Beag SJ, Baek JS, et al. 2021 Animal products grading statistical yearbook. 16th ed. Sejong, Korea: Korea Institute for Animal Products Quality Evaluation; 2022.？
Choi TJ, Kim SD, Agapita JS, Baik DH. Genetic parameter estimation on the growth and carcass traits in Hanwoo (Korean Cattle). J Anim Sci Technol 2006;48:759-66. https://doi.org/10.5187/JAST.2006.48.6.759？

원문보기 상세보기
Cesarani A, Gaspa G, Correddu F, Cellesi M, Dimauro C, Macciotta NPP. Genomic selection of milk fatty acid composition in Sarda dairy sheep: Effect of different phenotypes and relationship matrices on heritability and breeding value accuracy. J Dairy Sci 2019;102:3189-203. https://doi.org/10.3168/jds.2018-15333？

상세보기
Esfandyari H, Thekkoot D, Kemp R, Plastow G, Dekkers J. Genetic parameters and purebred-crossbred genetic correlations for growth, meat quality, and carcass traits in pigs. J Anim Sci 2020;98:skaa379. https://doi.org/10.1093/jas/skaa379？

상세보기
Khanal P, Maltecca C, Schwab C. Gray K, Tiezzi F. Genetic parameters of meat quality, carcass composition, and growth traits in commercial swine. J Anim Sci 2019;97:3669-83. https://doi.org/10.1093/jas/skz247？

상세보기
Abdalla EEA, Schenkel FS, Begli HE, et al. Single-step methodology for genomic evaluation in Turkeys (Meleagris gallopavo). Front Genet 2019;10:1248. https://doi.org/10.3389/fgene.2019.01248？

상세보기
Park MN, Alam M, Kim SD, Park BH, Lee SH, Lee SS. Genomic selection through single-step genomic best linear unbiased prediction improves the accuracy of evaluation in Hanwoo cattle. Asian-Australas J Anim Sci 2020;33:1544-57. https://doi.org/10.5713/ajas.18.0936？

원문보기 상세보기
Powell JE, Visscher PM, Goddard ME. Reconciling the analysis of IBD and IBS in complex trait studies. Nat Rev Genet 2010;11:800-5. https://doi.org/10.1038/nrg2865？

상세보기
Bonk S, Reichelt M, Teuscher F, Segelke D, Reinsch N. Mendelian sampling covariability of marker effects and genetic values. Genet Sel Evol 2016;48:36. https://doi.org/10.1186/s12711-016-0214-0？

상세보기
Hill WG, Weir BS. Variation in actual relationship as a consequence of Mendelian sampling and linkage. Genet Res 2011;93:47-64. https://doi.org/10.1017/S0016672310000480？

상세보기
Lee SH, Goddard ME, Visscher PM, Werf JH. Using the realized relationship matrix to disentangle confounding factors for the estimation of genetic variance components of complex traits. Genet Sel Evol 2010;42:22. https://doi.org/10.1186/1297-9686-42-22？

상세보기
Veerkamp RF, Mulder HA, Thompson R, Calus MPL. Genomic and pedigree-based genetic parameters for scarcely recorded traits when some animals are genotyped. J Dairy Sci 2011;94:4189-97. https://doi.org/10.3168/jds.2011-4223？

상세보기
Christensen OF, Madsen P, Nielsen B, Ostersen T, Su G. Singlestep methods for genomic evaluation in pigs. Animal 2012;6:1565-71. https://doi.org/10.1017/S1751731112000742？

상세보기
Jang SB, Kim SY, Lee SH, et al. The effect of progeny numbers and pedigree depth on the accuracy of the EBV with the BLUP method. Korean J Agric Sci 2019;46:293-301. https://doi.org/10.7744/kjoas.20190015

원문보기 상세보기

표제어: PCR

동의어: Packet Collision Rate

용어 설명 출처 목록 (6)

용어 설명: PCR은 세균 특이성이 있는 primer를 이용하여 적은 수의 세균이 있을지라도 쉽게 검출할 수 있는 유용한 방법이며, 이를 이용하여 구강 내 치면세균막이나 타액에서 직접 세균을 검출할 수 있게 되었다[8].

내보내기 구분	파일저장 인쇄 메일전송
구성항목	기본정보 상세정보 관리번호, 논문명, 저널/프로시딩명, 저자 , 발행년, 권, 호, 시작페이지, 끝페이지, 발행기관 관리번호, 논문명, 대등논문명, 저자 , 저널/프로시딩명, 발행기관, 발행년, 발행언어, 권, 호, 시작페이지, 끝페이지, ISBN, ISSN, 주제분야, 키워드, 초록(한글), 초록(영문), 저자(소속기관)
저장형식	Text(ASCII format) Excel format RefWorks Direct Export RIS format (for Reference Manager, ProCite, EndNote), Scholar's Aids, Mendeley
메일정보	받는사람 (필수) @ 보내는사람 (선택) @ 제목 내용 KISTI 검색결과 이메일 서비스
안내	총 건의 자료가 검색되었습니다. 다운받으실 자료의 인덱스를 입력하세요. (1-10,000) 검색결과의 순서대로 최대 10,000건 까지 다운로드가 가능합니다. 데이타가 많을 경우 속도가 느려질 수 있습니다.(최대 2~3분 소요) 다운로드 파일은 UTF-8 형태로 저장됩니다. 파일의 내용이 제대로 보이지 않을실 때는 웹브라우저 상단의 보기 -> 인코딩 -> 자동선택 여부를 확인하십시오. ~ Text(ASCII format) Excel format

연합인증