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Zoda A, Ogawa S, Kagawa R, Tsukahara H, Obinata R, Urakawa M, Oono Y. Single-Step Genomic Prediction of Superovulatory Response Traits in Japanese Black Donor Cows. BIOLOGY 2023; 12:biology12050718. [PMID: 37237533 DOI: 10.3390/biology12050718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/11/2023] [Accepted: 05/12/2023] [Indexed: 05/28/2023]
Abstract
We assessed the performance of single-step genomic prediction of breeding values for superovulatory response traits in Japanese Black donor cows. A total of 25,332 records of the total number of embryos and oocytes (TNE) and the number of good embryos (NGE) per flush for 1874 Japanese Black donor cows were collected during 2008 and 2022. Genotype information on 36,426 autosomal single-nucleotide polymorphisms (SNPs) for 575 out of the 1,874 cows was used. Breeding values were predicted exploiting a two-trait repeatability animal model. Two genetic relationship matrices were used, one based on pedigree information (A matrix) and the other considering both pedigree and SNP marker genotype information (H matrix). Estimated heritabilities of TNE and NGE were 0.18 and 0.11, respectively, when using the H matrix, which were both slightly lower than when using the A matrix (0.26 for TNE and 0.16 for NGE). Estimated genetic correlations between the traits were 0.61 and 0.66 when using H and A matrices, respectively. When the variance components were the same in breeding value prediction, the mean reliability was greater when using the H matrix than when using the A matrix. This advantage seems more prominent for cows with low reliability when using the A matrix. The results imply that introducing single-step genomic prediction could boost the rate of genetic improvement of superovulatory response traits, but efforts should be made to maintain genetic diversity when performing selection.
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Affiliation(s)
- Atsushi Zoda
- Research and Development Group, Zen-noh Embryo Transfer Center, Kamishihoro 080-1407, Japan
| | - Shinichiro Ogawa
- Division of Meat Animal and Poultry Research, Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization (NARO), Tsukuba 305-0901, Japan
| | - Rino Kagawa
- Research and Development Group, Zen-noh Embryo Transfer Center, Kamishihoro 080-1407, Japan
| | - Hayato Tsukahara
- Research and Development Group, Zen-noh Embryo Transfer Center, Kamishihoro 080-1407, Japan
| | - Rui Obinata
- Research and Development Group, Zen-noh Embryo Transfer Center, Kamishihoro 080-1407, Japan
| | - Manami Urakawa
- Research and Development Group, Zen-noh Embryo Transfer Center, Kamishihoro 080-1407, Japan
| | - Yoshio Oono
- Research and Development Group, Zen-noh Embryo Transfer Center, Kamishihoro 080-1407, Japan
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Ogawa S, Zoda A, Kagawa R, Obinata R. Comparing Methods to Select Candidates for Re-Genotyping to Impute Higher-Density Genotype Data in a Japanese Black Cattle Population: A Case Study. Animals (Basel) 2023; 13:ani13040638. [PMID: 36830425 PMCID: PMC9951718 DOI: 10.3390/ani13040638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 02/04/2023] [Accepted: 02/10/2023] [Indexed: 02/15/2023] Open
Abstract
As optimization methods to identify the best animals for dense genotyping to construct a reference population for genotype imputation, the MCA and MCG methods, which use the pedigree-based additive genetic relationship matrix (A matrix) and the genomic relationship matrix (G matrix), respectively, have been proposed. We assessed the performance of MCA and MCG methods using 575 Japanese Black cows. Pedigree data were provided to trace back up to five generations to construct the A matrix with changing the pedigree depth from 1 to 5 (five MCA methods). Genotype information on 36,426 single-nucleotide polymorphisms was used to calculate the G matrix based on VanRaden's methods 1 and 2 (two MCG methods). The MCG always selected one cow per iteration, while MCA sometimes selected multiple cows. The number of commonly selected cows between the MCA and MCG methods was generally lower than that between different MCA methods or between different MCG methods. For the studied population, MCG appeared to be more reasonable than MCA in selecting cows as a reference population for higher-density genotype imputation to perform genomic prediction and a genome-wide association study.
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Affiliation(s)
- Shinichiro Ogawa
- Division of Meat Animal and Poultry Research, Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization (NARO), Tsukuba 305-0901, Japan
- Correspondence: ; Tel.: +81-29-838-8627
| | - Atsushi Zoda
- Research and Development Group, Zen-Noh Embryo Transfer Center, Kamishihoro 080-1407, Japan
| | - Rino Kagawa
- Research and Development Group, Zen-Noh Embryo Transfer Center, Kamishihoro 080-1407, Japan
| | - Rui Obinata
- Research and Development Group, Zen-Noh Embryo Transfer Center, Kamishihoro 080-1407, Japan
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Rostamzadeh Mahdabi E, Tian R, Li Y, Wang X, Zhao M, Li H, Yang D, Zhang H, Li S, Esmailizadeh A. Genomic heritability and correlation between carcass traits in Japanese Black cattle evaluated under different ceilings of relatedness among individuals. Front Genet 2023; 14:1053291. [PMID: 36816045 PMCID: PMC9928846 DOI: 10.3389/fgene.2023.1053291] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Accepted: 01/18/2023] [Indexed: 02/04/2023] Open
Abstract
The investigation of carcass traits to produce meat with high efficiency has been in focus on Japanese Black cattle since 1972. To implement a successful breeding program in carcass production, a comprehensive understanding of genetic characteristics and relationships between the traits is of paramount importance. In this study, genomic heritability and genomic correlation between carcass traits, including carcass weight (CW), rib eye area (REA), rib thickness (RT), subcutaneous fat thickness (SFT), yield rate (YI), and beef marbling score (BMS) were estimated using the genomic data of 9,850 Japanese Black cattle (4,142 heifers and 5,708 steers). In addition, we investigated the effect of genetic relatedness degree on the estimation of genetic parameters of carcass traits in sub-populations created based on different GRM-cutoff values. Genome-based restricted maximum likelihood (GREML) analysis was applied to estimate genetic parameters. Using all animal data, the heritability values for carcass traits were estimated as moderate to relatively high magnitude, ranging from 0.338 to 0.509 with standard errors, ranging from 0.014 to 0.015. The genetic correlations were obtained low and negative between SFT and REA [-0.198 (0.034)] and between SFT and BMS [-0.096 (0.033)] traits, and high and negative between SFT and YI [-0.634 (0.022)]. REA trait was genetically highly correlated with YI and BMS [0.811 (0.012) and 0.625 (0.022), respectively]. In sub-populations created based on the genetic-relatedness ceiling, the heritability estimates ranged from 0.212 (0.131) to 0.647 (0.066). At the genetic-relatedness ceiling of 0.15, the correlation values between most traits with low genomic correlation were overestimated while the correlations between the traits with relatively moderate to high correlations, ranging from 0.380 to 0.811, were underestimated. The values were steady at the ceilings of 0.30-0.95 (sample size of 5,443-9,850) for most of the highly correlated traits. The results demonstrated that there is considerable genetic variation and also favorable genomic correlations between carcass traits. Therefore, the genetic improvement for the traits can be simultaneously attained through genomic selection. In addition, we observed that depending on the degree of relationship between individuals and sample size, the genomic heritability and correlation estimates for carcass traits may be different.
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Affiliation(s)
| | - Rugang Tian
- Institute of Animal Husbandry, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China,*Correspondence: Rugang Tian, ; Ali Esmailizadeh,
| | - Yuan Li
- Institute of Animal Husbandry, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Xiao Wang
- Institute of Animal Husbandry, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Meng Zhao
- Institute of Animal Husbandry, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Hui Li
- Institute of Animal Husbandry, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Ding Yang
- Institute of Animal Husbandry, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Hao Zhang
- Institute of Animal Husbandry, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - SuFan Li
- Institute of Animal Husbandry, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran,*Correspondence: Rugang Tian, ; Ali Esmailizadeh,
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Ogawa S, Taniguchi Y, Watanabe T, Iwaisaki H. Fitting Genomic Prediction Models with Different Marker Effects among Prefectures to Carcass Traits in Japanese Black Cattle. Genes (Basel) 2022; 14:24. [PMID: 36672767 PMCID: PMC9859149 DOI: 10.3390/genes14010024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/16/2022] [Accepted: 12/20/2022] [Indexed: 12/25/2022] Open
Abstract
We fitted statistical models, which assumed single-nucleotide polymorphism (SNP) marker effects differing across the fattened steers marketed into different prefectures, to the records for cold carcass weight (CW) and marbling score (MS) of 1036, 733, and 279 Japanese Black fattened steers marketed into Tottori, Hiroshima, and Hyogo prefectures in Japan, respectively. Genotype data on 33,059 SNPs was used. Five models that assume only common SNP effects to all the steers (model 1), common effects plus SNP effects differing between the steers marketed into Hyogo prefecture and others (model 2), only the SNP effects differing between Hyogo steers and others (model 3), common effects plus SNP effects specific to each prefecture (model 4), and only the effects specific to each prefecture (model 5) were exploited. For both traits, slightly lower values of residual variance than that of model 1 were estimated when fitting all other models. Estimated genetic correlation among the prefectures in models 2 and 4 ranged to 0.53 to 0.71, all <0.8. These results might support that the SNP effects differ among the prefectures to some degree, although we discussed the necessity of careful consideration to interpret the current results.
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Affiliation(s)
- Shinichiro Ogawa
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
- Division of Meat Animal and Poultry Research, Institute of Livestock and Grassland Science, Tsukuba 305-0901, Japan
| | - Yukio Taniguchi
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Toshio Watanabe
- National Livestock Breeding Center, Fukushima 961-8511, Japan
- Maebashi Institute of Animal Science, Livestock Improvement Association of Japan, Inc., Maebashi 371-0121, Japan
| | - Hiroaki Iwaisaki
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
- Sado Island Center for Ecological Sustainability, Niigata University, Niigata 952-0103, Japan
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Zoda A, Kagawa R, Obinata R, Urakawa M, Oono Y, Ogawa S, Uemoto Y, Satoh M. Genetic relationship between superovulatory response traits and carcass traits in Japanese Black cattle. Anim Sci J 2022; 93:e13731. [PMID: 35537852 DOI: 10.1111/asj.13731] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/30/2022] [Accepted: 04/07/2022] [Indexed: 11/30/2022]
Abstract
We estimated the genetic correlations between superovulatory response traits and carcass traits in Japanese Black cattle. As regards the superovulatory response traits in cows, we analyzed the phenotypic records of the total number of embryos and oocytes (TNE) and the number of good embryos (NGE) collected from 1532 donors between 2008 and 2018. As regards the carcass traits in fattened animals, we analyzed the phenotypic records for cold carcass weight, rib eye area, rib thickness, subcutaneous fat thickness, estimated yield percent, and marbling score for 1448 progenies derived from 596 donors and slaughtered between 2004 and 2020. Variance components were estimated using single-trait and two-trait animal models and the restricted maximum likelihood approach. The estimated genetic correlations with the carcass traits ranged from -0.05 to 0.04 for TNE and from -0.14 to 0.04 for NGE, and their standard errors ranged from 0.10 to 0.14. These results imply that the genetic relationship between the superovulatory response traits in Japanese Black donor cows and the carcass traits in their fattened progenies was weak to negligible. Therefore, we concluded that selecting donors with superior genetic ability for superovulatory responses would not have antagonistic effects on carcass performance in their fattened progenies.
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Affiliation(s)
- Atsushi Zoda
- Research and Development Group, Zen-noh Embryo Transfer Center, Kamishihoro, Hokkaido, Japan.,Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, Japan
| | - Rino Kagawa
- Research and Development Group, Zen-noh Embryo Transfer Center, Kamishihoro, Hokkaido, Japan
| | - Rui Obinata
- Research and Development Group, Zen-noh Embryo Transfer Center, Kamishihoro, Hokkaido, Japan
| | - Manami Urakawa
- Research and Development Group, Zen-noh Embryo Transfer Center, Kamishihoro, Hokkaido, Japan
| | - Yoshio Oono
- Research and Development Group, Zen-noh Embryo Transfer Center, Kamishihoro, Hokkaido, Japan
| | - Shinichiro Ogawa
- Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, Japan.,Division of Meat Animal and Poultry Research, Institute of Livestock and Grassland Science, NARO, Tsukuba, Ibaraki, Japan
| | - Yoshinobu Uemoto
- Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, Japan
| | - Masahiro Satoh
- Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, Japan
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6
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Ogawa S, Matsuda H, Taniguchi Y, Watanabe T, Sugimoto Y, Iwaisaki H. Estimation of the autosomal contribution to total additive genetic variability of carcass traits in Japanese Black cattle. Anim Sci J 2022; 93:e13710. [PMID: 35416392 DOI: 10.1111/asj.13710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/18/2022] [Accepted: 03/18/2022] [Indexed: 11/29/2022]
Abstract
We attempted to estimate the additive genetic variance explained by each autosome, using genotype data of 33,657 single nucleotide polymorphism (SNP) markers in 2271 Japanese Black fattened steers. Traits were cold carcass weight, ribeye area, rib thickness, subcutaneous fat thickness, estimated yield percentage, and marbling score. Two mixed linear models were used: One is that (model 1) incorporating a genomic relationship matrix (G matrix) constructed by using all available SNPs, and another (model 2), incorporating two G matrices constructed by using the SNPs on one autosome and using those on the remaining autosomes. Genomic heritabilities estimated using model 1 were moderate to high. The sums of the proportions of the additive genetic variance explained by each autosome to the total genetic variance estimated by using model 2 were >90%. For carcass weight, the proportions explained by Bos taurus autosomes 6, 8, and 14 were higher than those explained by the remaining autosomes. In some cases, the estimated proportion was close to 0. The results obtained from model 2 could provide a novel insight into the genetic architecture, such as heritability per chromosome, of carcass traits in Japanese Black cattle, although further careful investigation would be required.
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Affiliation(s)
| | | | - Yukio Taniguchi
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | | | - Yoshikazu Sugimoto
- Shirakawa Institute of Animal Genetics, Japan Livestock Technology Association, Tokyo, Japan
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Li J, Wang Y, Mukiibi R, Karisa B, Plastow GS, Li C. Integrative analyses of genomic and metabolomic data reveal genetic mechanisms associated with carcass merit traits in beef cattle. Sci Rep 2022; 12:3389. [PMID: 35232965 PMCID: PMC8888742 DOI: 10.1038/s41598-022-06567-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 02/01/2022] [Indexed: 11/09/2022] Open
Abstract
Improvement of carcass merit traits is a priority for the beef industry. Discovering DNA variants and genes associated with variation in these traits and understanding biological functions/processes underlying their associations are of paramount importance for more effective genetic improvement of carcass merit traits in beef cattle. This study integrates 10,488,742 imputed whole genome DNA variants, 31 plasma metabolites, and animal phenotypes to identify genes and biological functions/processes that are associated with carcass merit traits including hot carcass weight (HCW), rib eye area (REA), average backfat thickness (AFAT), lean meat yield (LMY), and carcass marbling score (CMAR) in a population of 493 crossbred beef cattle. Regression analyses were performed to identify plasma metabolites associated with the carcass merit traits, and the results showed that 4 (3-hydroxybutyric acid, acetic acid, citric acid, and choline), 6 (creatinine, L-glutamine, succinic acid, pyruvic acid, L-lactic acid, and 3-hydroxybutyric acid), 4 (fumaric acid, methanol, D-glucose, and glycerol), 2 (L-lactic acid and creatinine), and 5 (succinic acid, fumaric acid, lysine, glycine, and choline) plasma metabolites were significantly associated with HCW, REA, AFAT, LMY, and CMAR (P-value < 0.1), respectively. Combining the results of metabolome-genome wide association studies using the 10,488,742 imputed SNPs, 103, 160, 83, 43, and 109 candidate genes were identified as significantly associated with HCW, REA, AFAT, LMY, and CMAR (P-value < 1 × 10-5), respectively. By applying functional enrichment analyses for candidate genes of each trait, 26, 24, 26, 24, and 28 significant cellular and molecular functions were predicted for HCW, REA, AFAT, LMY, and CMAR, respectively. Among the five topmost significantly enriched biological functions for carcass merit traits, molecular transport and small molecule biochemistry were two top biological functions associated with all carcass merit traits. Lipid metabolism was the most significant biological function for LMY and CMAR and it was also the second and fourth highest biological function for REA and HCW, respectively. Candidate genes and enriched biological functions identified by the integrative analyses of metabolites with phenotypic traits and DNA variants could help interpret the results of previous genome-wide association studies for carcass merit traits. Our integrative study also revealed additional potential novel genes associated with these economically important traits. Therefore, our study improves understanding of the molecular and biological functions/processes that influence carcass merit traits, which could help develop strategies to enhance genomic prediction of carcass merit traits with incorporation of metabolomic data. Similarly, this information could guide management practices, such as nutritional interventions, with the purpose of boosting specific carcass merit traits.
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Affiliation(s)
- Jiyuan Li
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Yining Wang
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada.,Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada
| | - Robert Mukiibi
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Scotland, UK
| | - Brian Karisa
- Results Driven Agriculture Research, Edmonton, AB, Canada
| | - Graham S Plastow
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada.
| | - Changxi Li
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada. .,Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada.
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Bedhane M, van der Werf J, de las Heras-Saldana S, Lim D, Park B, Na Park M, Seung Hee R, Clark S. The accuracy of genomic prediction for meat quality traits in Hanwoo cattle when using genotypes from different SNP densities and preselected variants from imputed whole genome sequence. ANIMAL PRODUCTION SCIENCE 2022. [DOI: 10.1071/an20659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Context
Genomic prediction is the use of genomic data in the estimation of genomic breeding values (GEBV) in animal breeding. In beef cattle breeding programs, genomic prediction increases the rates of genetic gain by increasing the accuracy of selection at earlier ages.
Aims
The objectives of the study were to examine the effect of single-nucleotide polymorphism (SNP) density and to evaluate the effect of using SNPs preselected from imputed whole-genome sequence for genomic prediction.
Methods
Genomic and phenotypic data from 2110 Hanwoo steers were used to predict GEBV for marbling score (MS), meat texture (MT), and meat colour (MC) traits. Three types of SNP densities including 50k, high-density (HD), and whole-genome sequence data and preselected SNPs from genome-wide association study (GWAS) were used for genomic prediction analyses. Two scenarios (independent and dependent discovery populations) were used to select top significant SNPs. The accuracy of GEBV was assessed using random cross-validation. Genomic best linear unbiased prediction (GBLUP) was used to predict the breeding values for each trait.
Key results
Our result showed that very similar prediction accuracies were observed across all SNP densities used in the study. The prediction accuracy among traits ranged from 0.29±0.05 for MC to 0.46±0.04 for MS. Depending on the studied traits, up to 5% of prediction accuracy improvement was obtained when the preselected SNPs from GWAS analysis were included in the prediction analysis.
Conclusions
High SNP density such as HD and the whole-genome sequence data yielded a similar prediction accuracy in Hanwoo beef cattle. Therefore, the 50K SNP chip panel is sufficient to capture the relationships in a breed with a small effective population size such as the Hanwoo cattle population. Preselected variants improved prediction accuracy when they were included in the genomic prediction model.
Implications
The estimated genomic prediction accuracies are moderately accurate in Hanwoo cattle and for searching for SNPs that are more productive could increase the accuracy of estimated breeding values for the studied traits.
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Kim EH, Kang HC, Sun DW, Myung CH, Kim JY, Lee DH, Lee SH, Lim HT. Estimation of breeding value and accuracy using pedigree and genotype of Hanwoo cows (Korean cattle). J Anim Breed Genet 2021; 139:281-291. [PMID: 34902178 DOI: 10.1111/jbg.12661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 11/03/2021] [Accepted: 11/22/2021] [Indexed: 11/29/2022]
Abstract
The genetic improvement of Hanwoo is dependent on the estimated breeding value (EBV) of pedigree-based Korean proven bull's number, and the genetic evaluation for cows is difficult due to insufficient pedigree and test records. Genomic selection involves utilizing the individual's genotype to estimate the breeding value (BV) and is determined to be an appropriate evaluation method for cows who lack test information. This study used pedigree and genotype to estimate and analyse BV and accuracy of Hanwoo cows in the Gyeongnam area using pedigree best linear unbiased prediction (PBLUP) and genomic best linear unbiased prediction (GBLUP). The test group acquired pedigree and genotype of 919 Hanwoo cows in the Gyeongnam area. The traits used for analysis were carcass weight (CWT), eye muscle areas (EMA), backfat thickness (BFT) and marbling score (MS). PBLUP used Reference group 1 containing the pedigree and phenotype of 919 Hanwoo cows and 545,483 heads to construct the numeric relationship matrix and estimated the EBV and accuracy. GBLUP used Reference group 2 containing the genotype and phenotype of 919 Hanwoo cows and 17,226 heads to construct the genomic relationship matrix and estimated the genomic EBV (GEBV) and accuracy. In the order of CWT, EMA, BFT and MS, the accuracy of PBLUP was 0.488, 0.480, 0.482 and 0.486 while the accuracy of GBLUP was higher with 0.779, 0.758, 0.766 and 0.791. And for 104 cows without relationship coefficient on pedigree to the reference group, the accuracy as PBLUP was estimated to be 0, but for GBLUP, it was possible to estimate the accuracy for all individuals. If GBLUP is applied to cows raised in general farms, the genetic evaluation can be performed even on animals without pedigree and high-accuracy estimation, enabling selection of excellent cows. Accordingly, by securing the genetic diversity of cows, it is expected to increase the profitability of farms by decreasing the inbreeding rate and increasing efficiency of elite calf production.
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Affiliation(s)
- Eun-Ho Kim
- Department of Animal Science, Gyeongsang National University, Jinju, Korea
| | - Ho-Chan Kang
- Department of Animal Science and Biotechnology, Gyeongsang National University, Jinju, Korea
| | - Du-Won Sun
- Institute of Agriculture and Life Science, Gyeongsang National University, Jinju, Korea
| | - Cheol-Hyun Myung
- Department of Animal Science, Gyeongsang National University, Jinju, Korea
| | - Ji-Yeong Kim
- Department of Animal Science, Gyeongsang National University, Jinju, Korea
| | - Doo-Ho Lee
- Department of Animal Science and Biotechnology, Chungnam National University, Daejeon, Korea
| | - Seung-Hwan Lee
- Department of Animal Science and Biotechnology, Chungnam National University, Daejeon, Korea
| | - Hyun-Tae Lim
- Department of Animal Science, Gyeongsang National University, Jinju, Korea.,Department of Animal Science and Biotechnology, Gyeongsang National University, Jinju, Korea.,Institute of Agriculture and Life Science, Gyeongsang National University, Jinju, Korea
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10
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Komiya R, Ogawa S, Aonuma T, Satoh M. Performance of using opposing homozygotes for paternity testing in Japanese Black cattle. J Anim Breed Genet 2021; 139:113-124. [PMID: 34499371 DOI: 10.1111/jbg.12649] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/20/2021] [Accepted: 09/01/2021] [Indexed: 11/30/2022]
Abstract
Genome-wide single nucleotide polymorphism (SNP) markers in Japanese Black cattle enable genomic prediction and verifying parent-offspring relationships. We assessed the performance of opposing homozygotes (OH) for paternity testing in Japanese Black cattle, using SNP genotype information of 50 sires and 3,420 fattened animals, 1,945 of which were fathered by the 50 genotyped sires. The number of OH was counted for each sire-progeny pair in 28,764 SNPs with minor allele frequencies of ≥0.05 in this population. Across all pairs of animals, the number of OH tended to increase as the pedigree-based coefficient of relationship decreased. With a threshold of 288 (1% of SNPs) for paternity testing, most sire-progeny pairs were detected as true relationships. The frequency of Mendelian inconsistencies was 2.4%, reflecting the high accuracy of pedigree information in Japanese Black cattle population. The results indicate the utility of OH for paternity testing in Japanese Black cattle.
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Affiliation(s)
- Ryota Komiya
- Faculty of Agriculture, Tohoku University, Sendai, Japan
| | - Shinichiro Ogawa
- Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Tatsuya Aonuma
- Miyagi Prefectural Livestock Experiment Station, Osaki, Japan
| | - Masahiro Satoh
- Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
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11
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Wang Y, Zhang F, Mukiibi R, Chen L, Vinsky M, Plastow G, Basarab J, Stothard P, Li C. Genetic architecture of quantitative traits in beef cattle revealed by genome wide association studies of imputed whole genome sequence variants: II: carcass merit traits. BMC Genomics 2020; 21:38. [PMID: 31931697 PMCID: PMC6958779 DOI: 10.1186/s12864-019-6273-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 11/12/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Genome wide association studies (GWAS) were conducted on 7,853,211 imputed whole genome sequence variants in a population of 3354 to 3984 animals from multiple beef cattle breeds for five carcass merit traits including hot carcass weight (HCW), average backfat thickness (AFAT), rib eye area (REA), lean meat yield (LMY) and carcass marbling score (CMAR). Based on the GWAS results, genetic architectures of the carcass merit traits in beef cattle were elucidated. RESULTS The distributions of DNA variant allele substitution effects approximated a bell-shaped distribution for all the traits while the distribution of additive genetic variances explained by single DNA variants conformed to a scaled inverse chi-squared distribution to a greater extent. At a threshold of P-value < 10-5, 51, 33, 46, 40, and 38 lead DNA variants on multiple chromosomes were significantly associated with HCW, AFAT, REA, LMY, and CMAR, respectively. In addition, lead DNA variants with potentially large pleiotropic effects on HCW, AFAT, REA, and LMY were found on chromosome 6. On average, missense variants, 3'UTR variants, 5'UTR variants, and other regulatory region variants exhibited larger allele substitution effects on the traits in comparison to other functional classes. The amounts of additive genetic variance explained per DNA variant were smaller for intergenic and intron variants on all the traits whereas synonymous variants, missense variants, 3'UTR variants, 5'UTR variants, downstream and upstream gene variants, and other regulatory region variants captured a greater amount of additive genetic variance per sequence variant for one or more carcass merit traits investigated. In total, 26 enriched cellular and molecular functions were identified with lipid metabolisms, small molecular biochemistry, and carbohydrate metabolism being the most significant for the carcass merit traits. CONCLUSIONS The GWAS results have shown that the carcass merit traits are controlled by a few DNA variants with large effects and many DNA variants with small effects. Nucleotide polymorphisms in regulatory, synonymous, and missense functional classes have relatively larger impacts per sequence variant on the variation of carcass merit traits. The genetic architecture as revealed by the GWAS will improve our understanding on genetic controls of carcass merit traits in beef cattle.
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Affiliation(s)
- Yining Wang
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB Canada
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB Canada
| | - Feng Zhang
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB Canada
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB Canada
- State Key Laboratory for Swine Genetics, Breeding and Production Technology, Jiangxi Agricultural University, Nanchang, Jiangxi China
- Present Address: Institute of Translational Medicine, Nanchang University, Nanchang, Jiangxi China
| | - Robert Mukiibi
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB Canada
| | - Liuhong Chen
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB Canada
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB Canada
| | - Michael Vinsky
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB Canada
| | - Graham Plastow
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB Canada
| | - John Basarab
- Alberta Agriculture and Forestry, Lacombe Research and Development Centre, 6000 C&E Trail, Lacombe, AB Canada
| | - Paul Stothard
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB Canada
| | - Changxi Li
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB Canada
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB Canada
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