Genomic Prediction for Abortion in Lactating Holstein Dairy Cows
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Data Sources for Genetic Evaluation
2.2. Data Editing and Trait Definition for Genetic Evaluation
2.3. Statistical Model for Genetic Evaluation
2.4. Inclusion of Abort Prediction in a Multi-Trait Selection Index
2.5. Demonstration of Evaluation Efficacy
3. Results
3.1. Data Characteristics for Genetic Evaluation
3.2. Variance Components and Summary Statistics for Genetic Evaluation
3.3. Correlations of Abortion with Other Traits
3.4. Demonstration of Evaluation Efficacy
3.4.1. Cow Abortion for the Genetic Groups
3.4.2. Holstein Haplotypes Frequencies
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Appendix A
Trait | Expected Response to Selection |
---|---|
Fat (Kg) | 9.1 |
Protein (Kg) | 5 |
Milk (Kg) | 99.3 |
Productive Life (mo.) | 1.42 |
Cow Livability (%) | 0.66 |
Somatic Cell Score (log) | −0.07 |
Residual feed Intake | −5.17 |
Body Size Composite (pts) | −0.21 |
Udder Composite (pts) | 0.27 |
Feet and Leg Composite (pts) | 0.08 |
Daughter Pregnancy Rate (%) | 0.16 |
Heifer Conception Rate (%) | 0.31 |
Early First Calving | 0.68 |
Cow Conception Rate (%) | 0.43 |
Calving Ability ($) | 5.10 |
Zoetis Mastitis (STA) | 1.54 |
Zoetis Metritis (STA) | 1.90 |
Zoetis Retained Placenta (STA) | 0.56 |
Zoetis Displaced Abomasum (STA) | 1.04 |
Zoetis Ketosis (STA) | 1.73 |
Zoetis Lameness (STA) | 1.19 |
Zoetis Calf Respiratory (STA) | 0.27 |
Zoetis Calf Scours (STA) | −0.07 |
Zoetis Calf Livability (STA) | 0.38 |
Zoetis Cow Respiratory (STA) | 0.76 |
Zoetis Cystic Ovary (STA) | 0.22 |
Zoetis Twinning (STA) | 0.61 |
Zoetis Cow Abortion (STA) | 0.19 |
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Item | Count |
---|---|
Total animals in the evaluation | 4,955,087 |
Phenotypic records total | 3,838,805 |
Animals with phenotypes | 2,038,425 |
Animals with genotypes | 1,662,251 |
Animals with genotypes and phenotypes | 109,267 |
Incidence of abortion | 11.67% |
Trait | σ2g | σ2pe | σ2hys | σ2ss | σ2e | h2 | r2 |
---|---|---|---|---|---|---|---|
Z_ABORT | 0.1235 | 0.0941 | 0.3748 | 0.0049 | 1.0 | 0.0773 | 0.1362 |
All Animals with Genotypes | |||||
---|---|---|---|---|---|
Variables * | N | Mean | Std Dev | Minimum | Maximum |
Z_Abort_PTA | 1,662,251 | −0.01 | 2.1 | −8.8 | 12.4 |
Z_Abort _STA | 1,662,251 | 99.0 | 4.8 | 71.0 | 119.0 |
Z_Abort _REL | 1,662,251 | 42.4 | 6.0 | 0.0 | 99.6 |
Animals with genotype (no phenotype, no progeny) | |||||
Z_Abort_PTA | 1,232,143 | 0.1 | 2.1 | −8.8 | 11.8 |
Z_Abort _STA | 1,232,143 | 98.8 | 4.7 | 73.0 | 119.0 |
Z_Abort _REL | 1,232,143 | 41.1 | 5.3 | 0.0 | 62.4 |
Animals with both genotype and phenotype (no progeny) | |||||
Z_Abort_PTA | 39,036 | −0.5 | 2.3 | −8.1 | 12.4 |
Z_Abort _STA | 39,036 | 100.1 | 5.1 | 71.0 | 117.0 |
Z_Abort _REL | 39,036 | 49.5 | 4.5 | 10.1 | 62.1 |
Zoetis Wellness Traits * | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
DWP$ | Z_CALF DIAR | Z_CALF RESP | Z_CALF LIV | Z_RETP | Z_METR | Z_MAST | Z_LAME | Z_KETO | Z_DA | Z_MFV | Z_TWIN | Z_RESP | Z_CYST | |
Z_Abort | 0.017 | 0.013 | 0.078 | 0.190 | 0.285 | 0.189 | 0.087 | 0.068 | 0.037 | 0.039 | 0.069 | 0.284 | 0.145 | 0.013 |
CDCB Traits ** | ||||||||||||||
NM$ | Milk | Fat | Prot | PL | LIV | SCS | DPR | HCR | CCR | |||||
Z_Abort | −0.180 | −0.224 | −0.254 | −0.264 | −0.016 | 0.184 | −0.005 | 0.289 | 0.051 | 0.236 |
Z_Abort STA Genetic Group | Marginal Means (Incidence) | SEM | Abortion Cost per Cow ($) |
---|---|---|---|
Worst 25% | 0.166 a | 0.013 | 92 |
25–50% | 0.136 b | 0.011 | 76 |
50–75% | 0.115 c | 0.010 | 64 |
Best 25% | 0.110 c | 0.010 | 61 |
Lactation Group | Marginal Means (Incidence) | SEM |
---|---|---|
Lact 1 | 0.112 a | 0.009 |
Lact 2 | 0.120 a | 0.010 |
Lact 3 | 0.140 b | 0.012 |
Lact 4 | 0.154 b | 0.016 |
DPR gPTA Genetic Group | Marginal Means (Incidence) | SEM | Abortion Cost per Cow ($) |
---|---|---|---|
Worst 25% | 0.151 a | 0.013 | USD 84 |
25–50% | 0.127 bc | 0.011 | USD 71 |
50–75% | 0.133 b | 0.011 | USD 74 |
Best 25% | 0.116 c | 0.010 | USD 64 |
HH0 | HH1 | HH2 | HH3 | HH4 | HH5 | |
---|---|---|---|---|---|---|
AI Bulls | 2.6% | 0.4% | 1.6% | 2.4% | 0.2% | 4.8% |
Abort | 4.4% | 2.5% | 4.7% | 6.4% | 1.6% | 2.8% |
No Abort | 4.7% | 2.6% | 3.7% | 6.9% | 1.1% | 3.2% |
Carrier × carrier matings (n) | 1 | 1 | 1 | 0 | 0 | 1 |
Z_Abort STA Genetic Group | HH0 | HH1 | HH2 | HH3 | HH4 | HH5 |
---|---|---|---|---|---|---|
Worst 25% | 4.5 | 2.7 | 5.0 a | 6.1 | 0.1 | 2.5 |
25–50% | 3.9 | 2.6 | 4.2 a | 5.9 | 0.1 | 3.4 |
50–75% | 5.2 | 3.9 | 4.1 a | 8.7 | 0.1 | 3.3 |
Best 25% | 4.2 | 2.5 | 2.1 b | 6.7 | 0.04 | 4.7 |
p-Value | 0.19 | 0.83 | <0.001 | 0.07 | 0.05 | 0.24 |
DPR gPTA Genetic Group | |||||
---|---|---|---|---|---|
Worst 25% | 25–50% | 50–75% | Best 25% | ||
Z_Abort STA Genetic Group | Worst 25% | 8.2 | 6.8 | 5.3 | 3.9 |
25–50% | 6.8 | 6.8 | 6.3 | 5.7 | |
50–75% | 5.4 | 6.1 | 7.3 | 7.2 | |
Best 25% | 4.2 | 5.6 | 6.4 | 8.1 |
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Wijma, R.; Weigel, D.J.; Vukasinovic, N.; Gonzalez-Peña, D.; McGovern, S.P.; Fessenden, B.C.; McNeel, A.K.; Di Croce, F.A. Genomic Prediction for Abortion in Lactating Holstein Dairy Cows. Animals 2022, 12, 2079. https://doi.org/10.3390/ani12162079
Wijma R, Weigel DJ, Vukasinovic N, Gonzalez-Peña D, McGovern SP, Fessenden BC, McNeel AK, Di Croce FA. Genomic Prediction for Abortion in Lactating Holstein Dairy Cows. Animals. 2022; 12(16):2079. https://doi.org/10.3390/ani12162079
Chicago/Turabian StyleWijma, Robert, Daniel J. Weigel, Natascha Vukasinovic, Dianelys Gonzalez-Peña, Shaileen P. McGovern, Brenda C. Fessenden, Anthony K. McNeel, and Fernando A. Di Croce. 2022. "Genomic Prediction for Abortion in Lactating Holstein Dairy Cows" Animals 12, no. 16: 2079. https://doi.org/10.3390/ani12162079
APA StyleWijma, R., Weigel, D. J., Vukasinovic, N., Gonzalez-Peña, D., McGovern, S. P., Fessenden, B. C., McNeel, A. K., & Di Croce, F. A. (2022). Genomic Prediction for Abortion in Lactating Holstein Dairy Cows. Animals, 12(16), 2079. https://doi.org/10.3390/ani12162079