Genomic Predictions in Korean Hanwoo Cows: A Comparative Analysis of Genomic BLUP and Bayesian Methods for Reproductive Traits
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Ethics Statement
2.2. Animal Phenotypes
2.3. Genotyping and Quality Control
2.4. Statistical Analysis
2.4.1. Estimation of Variance Components
2.4.2. Estimation of Breeding Values
Genomic Best Linear Unbiased Prediction Model (GBLUP)
Bayesian Model
with probability π | |
with probability (1 − π) |
2.4.3. Cross Validation
2.4.4. Accuracy of Genomic Prediction
2.4.5. Estimation of Genomic Heritability
3. Results and Discussion
3.1. Description of SNP Statistics
3.2. Genomic Relationship Matrix
3.3. Estimation of Heritability
3.4. Evaluation of GEBV Prediction Accuracy
3.5. Bias in Genomic Prediction Accuracy
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Methods | Traits | Number of Animals | Mean | SD | Minimum | Maximum |
---|---|---|---|---|---|---|
Pedigree-based analysis | AFC (days) | 11,348 | 748.74 | 85.75 | 447 | 1060 |
CI (days) | 8878 | 376.41 | 51.94 | 242 | 600 | |
GL (days) | 11,348 | 287.19 | 8.20 | 206 | 395 | |
NAIPC (1–4) | 11,348 | 1.45 | 0.81 | 1 | 7 | |
Genome-based analysis | AFC (days) | 10,148 | 736.18 | 64.43 | 556 | 934 |
CI (days) | 7994 | 370.56 | 40.04 | 300 | 497 | |
GL (days) | 10,426 | 286.62 | 4.91 | 275 | 303 | |
NAIPC (1–4) | 11,204 | 1.44 | 0.79 | 1 | 4 |
Traits | ± SE | |||
---|---|---|---|---|
AFC | 0.070 ± 0.02 | 284.06 | 3756.37 | 4040.43 |
CI | 0.026 ± 0.04 | 42.35 | 1612.31 | 1654.66 |
GL | 0.102 ± 0.02 | 2.15 | 18.83 | 20.98 |
NAIPC | 0.055 ± 0.01 | 0.03 | 0.52 | 0.55 |
Method | Traits | |||
---|---|---|---|---|
GBLUP | AFC | 156.09 | 0.55 | 0.039 |
CI | 35.95 | 0.85 | 0.022 | |
GL | 1.29 | 0.60 | 0.061 | |
NAIPC | 0.02 | 0.56 | 0.030 | |
BayesB | AFC | 161.09 | 0.57 | 0.040 |
CI | 37.00 | 0.87 | 0.022 | |
GL | 1.32 | 0.61 | 0.063 | |
NAIPC | 0.01 | 0.43 | 0.024 | |
BayesLASSO | AFC | 159.28 | 0.56 | 0.039 |
CI | 39.71 | 0.94 | 0.024 | |
GL | 1.23 | 0.57 | 0.059 | |
NAIPC | 0.02 | 0.57 | 0.031 | |
BayesR | AFC | 167.33 | 0.59 | 0.041 |
CI | 39.73 | 0.94 | 0.020 | |
GL | 1.29 | 0.60 | 0.061 | |
NAIPC | 0.01 | 0.47 | 0.026 |
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Haque, M.A.; Lee, Y.-M.; Ha, J.-J.; Jin, S.; Park, B.; Kim, N.-Y.; Won, J.-I.; Kim, J.-J. Genomic Predictions in Korean Hanwoo Cows: A Comparative Analysis of Genomic BLUP and Bayesian Methods for Reproductive Traits. Animals 2024, 14, 27. https://doi.org/10.3390/ani14010027
Haque MA, Lee Y-M, Ha J-J, Jin S, Park B, Kim N-Y, Won J-I, Kim J-J. Genomic Predictions in Korean Hanwoo Cows: A Comparative Analysis of Genomic BLUP and Bayesian Methods for Reproductive Traits. Animals. 2024; 14(1):27. https://doi.org/10.3390/ani14010027
Chicago/Turabian StyleHaque, Md Azizul, Yun-Mi Lee, Jae-Jung Ha, Shil Jin, Byoungho Park, Nam-Young Kim, Jeong-Il Won, and Jong-Joo Kim. 2024. "Genomic Predictions in Korean Hanwoo Cows: A Comparative Analysis of Genomic BLUP and Bayesian Methods for Reproductive Traits" Animals 14, no. 1: 27. https://doi.org/10.3390/ani14010027