Comparison of accuracy of breeding value for cow from three methods in Hanwoo (Korean cattle) population
In Korea, Korea Proven Bulls (KPN) program has been well-developed. Breeding and evaluation of cows are also an essential factor to increase earnings and genetic gain. This study aimed to evaluate the accuracy of cow breeding value by using three methods (pedigree index [PI], pedigree-based best lin...
| Main Authors: | , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Korean Society of Animal Sciences and Technology
2023-07-01
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| Series: | Journal of Animal Science and Technology |
| Subjects: | |
| Online Access: | http://www.ejast.org/archive/view_article?doi=10.5187/jast.2023.e5 |
| _version_ | 1797741470914969600 |
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| author | Hyo Sang Lee Yeongkuk Kim Doo Ho Lee Dongwon Seo Dong Jae Lee Chang Hee Do Phuong Thanh N. Dinh Waruni Ekanayake Kil Hwan Lee Duhak Yoon Seung Hwan Lee Yang Mo Koo |
| author_facet | Hyo Sang Lee Yeongkuk Kim Doo Ho Lee Dongwon Seo Dong Jae Lee Chang Hee Do Phuong Thanh N. Dinh Waruni Ekanayake Kil Hwan Lee Duhak Yoon Seung Hwan Lee Yang Mo Koo |
| author_sort | Hyo Sang Lee |
| collection | DOAJ |
| description | In Korea, Korea Proven Bulls (KPN) program has been well-developed. Breeding and evaluation of cows are also an essential factor to increase earnings and genetic gain. This study aimed to evaluate the accuracy of cow breeding value by using three methods (pedigree index [PI], pedigree-based best linear unbiased prediction [PBLUP], and genomic-BLUP [GBLUP]). The reference population (n = 16,971) was used to estimate breeding values for 481 females as a test population. The accuracy of GBLUP was 0.63, 0.66, 0.62 and 0.63 for carcass weight (CWT), eye muscle area (EMA), back-fat thickness (BFT), and marbling score (MS), respectively. As for the PBLUP method, accuracy of prediction was 0.43 for CWT, 0.45 for EMA, 0.43 for MS, and 0.44 for BFT. Accuracy of PI method was the lowest (0.28 to 0.29 for carcass traits). The increase by approximate 20% in accuracy of GBLUP method than other methods could be because genomic information may explain Mendelian sampling error that pedigree information cannot detect. Bias can cause reducing accuracy of estimated breeding value (EBV) for selected animals. Regression coefficient between true breeding value (TBV) and GBLUP EBV, PBLUP EBV, and PI EBV were 0.78, 0.625, and 0.35, respectively for CWT. This showed that genomic EBV (GEBV) is less biased than PBLUP and PI EBV in this study. In addition, number of effective chromosome segments (Me) statistic that indicates the independent loci is one of the important factors affecting the accuracy of BLUP. The correlation between Me and the accuracy of GBLUP is related to the genetic relationship between reference and test population. The correlations between Me and accuracy were −0.74 in CWT, −0.75 in EMA, −0.73 in MS, and −0.75 in BF, which were strongly negative. These results proved that the estimation of genetic ability using genomic data is the most effective, and the smaller the Me, the higher the accuracy of EBV. |
| first_indexed | 2024-03-12T14:27:35Z |
| format | Article |
| id | doaj.art-a68ca881d942499b8ebe4a798b1758ea |
| institution | Directory Open Access Journal |
| issn | 2672-0191 2055-0391 |
| language | English |
| last_indexed | 2024-03-12T14:27:35Z |
| publishDate | 2023-07-01 |
| publisher | Korean Society of Animal Sciences and Technology |
| record_format | Article |
| series | Journal of Animal Science and Technology |
| spelling | doaj.art-a68ca881d942499b8ebe4a798b1758ea2023-08-18T03:53:06ZengKorean Society of Animal Sciences and TechnologyJournal of Animal Science and Technology2672-01912055-03912023-07-0165472073410.5187/jast.2023.e5Comparison of accuracy of breeding value for cow from three methods in Hanwoo (Korean cattle) populationHyo Sang Lee0Yeongkuk Kim1Doo Ho Lee2Dongwon Seo3Dong Jae Lee4Chang Hee Do5Phuong Thanh N. Dinh6Waruni Ekanayake7Kil Hwan Lee8Duhak Yoon9Seung Hwan Lee10Yang Mo Koo11Genetic Information Division, Korea Animal Improvement Association, Livestock Hall, Seoul 06668, KoreaDepartment of Bio-AI Convergence, Chungnam National University, Daejeon 34134, KoreaDivision of Animal and Dairy Science, Chungnam National University, Daejeon 34148, KoreaTNT Research Co., Anyang 14059, KoreaDivision of Animal and Dairy Science, Chungnam National University, Daejeon 34148, KoreaInstitute of Agricultural Science, Chungnam National University, Daejeon 34134, KoreaDepartment of Bio-AI Convergence, Chungnam National University, Daejeon 34134, KoreaDivision of Animal and Dairy Science, Chungnam National University, Daejeon 34148, KoreaGenetic Information Division, Korea Animal Improvement Association, Livestock Hall, Seoul 06668, KoreaDepartment of Animal Science and Biotechnology, Kyungpook National University, Sangju 37224, KoreaDivision of Animal and Dairy Science, Chungnam National University, Daejeon 34148, KoreaGenetic Information Division, Korea Animal Improvement Association, Livestock Hall, Seoul 06668, KoreaIn Korea, Korea Proven Bulls (KPN) program has been well-developed. Breeding and evaluation of cows are also an essential factor to increase earnings and genetic gain. This study aimed to evaluate the accuracy of cow breeding value by using three methods (pedigree index [PI], pedigree-based best linear unbiased prediction [PBLUP], and genomic-BLUP [GBLUP]). The reference population (n = 16,971) was used to estimate breeding values for 481 females as a test population. The accuracy of GBLUP was 0.63, 0.66, 0.62 and 0.63 for carcass weight (CWT), eye muscle area (EMA), back-fat thickness (BFT), and marbling score (MS), respectively. As for the PBLUP method, accuracy of prediction was 0.43 for CWT, 0.45 for EMA, 0.43 for MS, and 0.44 for BFT. Accuracy of PI method was the lowest (0.28 to 0.29 for carcass traits). The increase by approximate 20% in accuracy of GBLUP method than other methods could be because genomic information may explain Mendelian sampling error that pedigree information cannot detect. Bias can cause reducing accuracy of estimated breeding value (EBV) for selected animals. Regression coefficient between true breeding value (TBV) and GBLUP EBV, PBLUP EBV, and PI EBV were 0.78, 0.625, and 0.35, respectively for CWT. This showed that genomic EBV (GEBV) is less biased than PBLUP and PI EBV in this study. In addition, number of effective chromosome segments (Me) statistic that indicates the independent loci is one of the important factors affecting the accuracy of BLUP. The correlation between Me and the accuracy of GBLUP is related to the genetic relationship between reference and test population. The correlations between Me and accuracy were −0.74 in CWT, −0.75 in EMA, −0.73 in MS, and −0.75 in BF, which were strongly negative. These results proved that the estimation of genetic ability using genomic data is the most effective, and the smaller the Me, the higher the accuracy of EBV. http://www.ejast.org/archive/view_article?doi=10.5187/jast.2023.e5Pedigree estimated breeding valuePedigree indexGenomic estimated breeding valueAccuracyHanwoo cattleEffective number of chromosome segments (M<sub>e</sub>) |
| spellingShingle | Hyo Sang Lee Yeongkuk Kim Doo Ho Lee Dongwon Seo Dong Jae Lee Chang Hee Do Phuong Thanh N. Dinh Waruni Ekanayake Kil Hwan Lee Duhak Yoon Seung Hwan Lee Yang Mo Koo Comparison of accuracy of breeding value for cow from three methods in Hanwoo (Korean cattle) population Journal of Animal Science and Technology Pedigree estimated breeding value Pedigree index Genomic estimated breeding value Accuracy Hanwoo cattle Effective number of chromosome segments (M<sub>e</sub>) |
| title | Comparison of accuracy of breeding value for cow from three methods in Hanwoo (Korean cattle) population |
| title_full | Comparison of accuracy of breeding value for cow from three methods in Hanwoo (Korean cattle) population |
| title_fullStr | Comparison of accuracy of breeding value for cow from three methods in Hanwoo (Korean cattle) population |
| title_full_unstemmed | Comparison of accuracy of breeding value for cow from three methods in Hanwoo (Korean cattle) population |
| title_short | Comparison of accuracy of breeding value for cow from three methods in Hanwoo (Korean cattle) population |
| title_sort | comparison of accuracy of breeding value for cow from three methods in hanwoo korean cattle population |
| topic | Pedigree estimated breeding value Pedigree index Genomic estimated breeding value Accuracy Hanwoo cattle Effective number of chromosome segments (M<sub>e</sub>) |
| url | http://www.ejast.org/archive/view_article?doi=10.5187/jast.2023.e5 |
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