Assessment of the Genetic Diversity of a Local Pig Breed Using Pedigree and SNP Data
Abstract
:1. Introduction
2. Materials and Methods
2.1. Animals
2.2. Pedigree Analysis
2.3. SNP Analysis
3. Results
3.1. Quality of the Pedigree
3.2. Analysis Based on the Pedigree Data
3.3. SNP Data Analysis
4. Discussion
4.1. Analysis Based on Pedigree Data
4.2. SNP Data Analysis
5. 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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Parameter (Unit) | Sire | Dam | Total |
---|---|---|---|
Total number of animals in pedigree | 507 | 1466 | 1971 |
Reference population in pedigree | 47 | 277 | 324 |
Number of evaluated herds | 12 | 11 | 12 |
Average number of: dams in a herd | 15.3 | ||
Sires in a herd | 2.71 | ||
Number of offspring selected per dam | 1.71 | ||
Number of offspring selected per sire | 4.50 | ||
Number of sires per dam | 1.19 | ||
Number of dams per sire | 3.02 |
Year of Evaluation | Generation Interval (in Years) in Different Paths 1 | ||||
---|---|---|---|---|---|
SS | SD | DS | DD | Population | |
2005 | 3.6 | 2.4 | 2.3 | 2.4 | 2.6 |
2010 | 1.8 | 2.0 | 2.3 | 2.4 | 2.1 |
2015 | 2.3 | 2.3 | 1.8 | 2.1 | 2.2 |
2020 | 3.3 | 2.8 | 2.2 | 2.2 | 2.6 |
Mean | 3.0 | 2.5 | 2.6 | 2.2 | 2.5 |
Year | Animals | Sires | Dams | |||
---|---|---|---|---|---|---|
n 1 in Total | F 2 | n in Total | F | n in Total | F | |
2018 | 75 | 7.49% | 26 | 7.03% | 54 | 6.82% |
2019 | 103 | 8.11% | 24 | 7.37% | 73 | 7.21% |
2020 | 126 | 8.10% | 32 | 6.67% | 82 | 7.43% |
FAnN | FAnO | FAnT | FSrN | FSrO | FSrT | FDmN | FDmO | FDmT | |
---|---|---|---|---|---|---|---|---|---|
Avg. | 2.31 | 5.64 | 7.95 | 2.15 | 5.49 | 7.64 | 2.32 | 5.65 | 7.97 |
s.d. | 2.51 | 0.71 | 2.61 | 1.54 | 0.71 | 1.79 | 1.6 | 2.61 | 1.83 |
Min. | 0.00 | 2.87 | 4.31 | 0.00 | 2.87 | 5.05 | 0.00 | 3.14 | 4.31 |
Max | 9.38 | 7.86 | 14.46 | 5.47 | 7.26 | 12.11 | 9.38 | 7.86 | 14.46 |
ROH Class | No. of ROH | FROH (%) | ||||
---|---|---|---|---|---|---|
± SD | Min | Max | ± SD | Min | Max | |
1 Mb | 41.931 ± 8.974 | 21 | 71 | 10.810 ± 3.634 | 3.225 | 23.663 |
2 Mb | 38.477 ± 8.725 | 19 | 68 | 10.571 ± 3.637 | 3.097 | 23.289 |
4 Mb | 21.190 ± 5.834 | 8 | 36 | 9.308 ± 3.578 | 2.438 | 23.486 |
8 Mb | 9.500 ± 3.941 | 1 | 21 | 6.722 ± 3.320 | 0.333 | 20.430 |
16 Mb | 3.517 ± 2.190 | 0 | 10 | 3.984 ± 2.758 | 0 | 14.801 |
FROH1 | FROH2 | FROH4 | FROH8 | FROH16 | Fhat1 | Fhat2 | Fhat3 | |
---|---|---|---|---|---|---|---|---|
FPED | 0.519 | 0.513 | 0.510 | 0.542 | 0.491 | −0.026 | 0.508 | 0.307 |
FROH1 | 0.998 | 0.967 | 0.895 | 0.795 | 0.222 | 0.844 | 0.659 | |
FROH2 | 0.964 | 0.889 | 0.797 | 0.220 | 0.838 | 0.651 | ||
FROH4 | 0.942 | 0.834 | 0.262 | 0.830 | 0.689 | |||
FROH8 | 0.893 | 0.288 | 0.785 | 0.686 | ||||
FROH16 | 0.237 | 0.716 | 0.585 | |||||
Fhat1 | 0.032 | 0.771 | ||||||
Fhat2 | 0.606 |
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Krupa, E.; Moravčíková, N.; Krupová, Z.; Žáková, E. Assessment of the Genetic Diversity of a Local Pig Breed Using Pedigree and SNP Data. Genes 2021, 12, 1972. https://doi.org/10.3390/genes12121972
Krupa E, Moravčíková N, Krupová Z, Žáková E. Assessment of the Genetic Diversity of a Local Pig Breed Using Pedigree and SNP Data. Genes. 2021; 12(12):1972. https://doi.org/10.3390/genes12121972
Chicago/Turabian StyleKrupa, Emil, Nina Moravčíková, Zuzana Krupová, and Eliška Žáková. 2021. "Assessment of the Genetic Diversity of a Local Pig Breed Using Pedigree and SNP Data" Genes 12, no. 12: 1972. https://doi.org/10.3390/genes12121972
APA StyleKrupa, E., Moravčíková, N., Krupová, Z., & Žáková, E. (2021). Assessment of the Genetic Diversity of a Local Pig Breed Using Pedigree and SNP Data. Genes, 12(12), 1972. https://doi.org/10.3390/genes12121972