One Hundred Years of Coat Colour Influences on Genetic Diversity in the Process of Development of a Composite Horse Breed
Abstract
:1. Introduction
2. Materials and Methods
2.1. Pedigree Registries and Software for Genetic Analyses
2.2. Genealogical Information
2.3. Inbreeding, Coancestry, and Nonrandom Mating Degree
2.4. Ancestral Contributions and Probabilities of Gene Origin
3. Results
3.1. Pedigree Evolution
3.2. Inbreeding, Coancestry/Kinship and Degree of Non-Random Mating
3.3. Ancestral Contributions and Probabilities of Gene Origin
3.4. Genetic Relationships between Coat Colour Subgroup
4. Discussion
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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Set | Breed | Source | Number of Animals | Males/Females | Period (Birthdates) |
---|---|---|---|---|---|
Historic | Hispano-Arabian | Spanish Union of Purebred Hispano-Arabian Horses Breeders (UEGHá) | 11,010 | 4268 males and 6742 females | January 1950 and April 2019 |
Spanish Purebred | National Association of Purebred Spanish Horse Breeders (ANCCE) | 172,797 | 83,408 males and 89,389 females | January 1884 and July 2019 | |
Arabian Purebred | Spanish Association of Arabian Horse Breeders (AECCA) | 23,293 | 11,143 males and 12,150 females | January 1898 and June 2019 | |
Current | Hispano-Arabian | Spanish Union of Purebred Hispano-Arabian Horses Breeders (UEGHá) | 9997 | 4031 males and 5966 females | December 1984 and April 2019 |
Spanish Purebred | National Association of Purebred Spanish Horse Breeders (ANCCE) | 141,357 | 69,184 males and 72,163 females | April 1984 and July 2019 | |
Arabian Purebred | Spanish Association of Arabian Horse Breeders (AECCA) | 13,576 | 6632 males and 6944 females | June 1985 and June 2019 |
Parameter | Maximum Number of Traced Generations, n | Number of Maximum Generations (Mean ± SD) | Number of Complete Generations (Mean ± SD) | Number of Equivalent Generations (Mean ± SD) | ||||
---|---|---|---|---|---|---|---|---|
Population Set | Historic | Current | Historic | Current | Historic | Current | Historic | Current |
Grey | 20.00 | 20.00 | 13.67 ± 3.47 | 14.59 ± 3.46 | 4.36 ± 1.43 | 4.65 ± 1.42 | 7.98 ± 2.09 | 8.53 ± 2.09 |
Bay | 21.00 | 21.00 | 14.01 ± 3.47 | 15.11 ± 3.46 | 4.44 ± 1.43 | 4.79 ± 1.42 | 8.03 ± 2.09 | 8.69 ± 2.09 |
Chestnut/Sorrel | 20.00 | 20.00 | 11.66 ± 3.47 | 13.54 ± 3.46 | 3.66 ± 1.43 | 4.12 ± 1.42 | 6.51 ± 2.09 | 7.51 ± 2.09 |
Black | 20.00 | 20.00 | 15.01 ± 3.46 | 15.66 ± 3.46 | 4.81 ± 1.43 | 5.01 ± 1.42 | 8.71 ± 2.09 | 9.09 ± 2.09 |
Overo | 17.00 | 17.00 | 11.24 ± 3.34 | 13.29 ± 3.21 | 3.73 ± 1.40 | 4.23 ± 1.38 | 6.57 ± 2.02 | 7.79 ± 1.95 |
Roan | 19.00 | 19.00 | 14.48 ± 3.44 | 15.42 ± 3.54 | 4.51 ± 1.42 | 4.78 ± 1.44 | 8.29 ± 2.08 | 8.84 ± 2.12 |
Dun | 19.00 | 19.00 | 14.14 ± 3.43 | 14.74 ± 3.47 | 4.33 ± 1.42 | 4.51 ± 1.42 | 8.00 ± 2.07 | 8.34 ± 2.08 |
White | 18.00 | 18.00 | 10.17 ± 3.43 | 15.36 ± 3.64 | 3.32 ± 1.42 | 5.08 ± 1.47 | 5.94 ± 2.07 | 8.92 ± 2.18 |
Isabelline | 18.00 | 18.00 | 9.74 ± 3.42 | 9.97 ± 3.48 | 2.93 ± 1.42 | 3.03 ± 1.43 | 5.36 ± 2.06 | 5.52 ± 2.09 |
Cremello | 18.00 | 18.00 | 9.21 ± 3.46 | 9.15 ± 3.46 | 2.88 ± 1.42 | 2.82 ± 1.42 | 5.16 ± 2.07 | 5.10 ± 2.07 |
Pearl | 19.00 | 19.00 | 13.09 ± 3.72 | 13.07 ± 1.08 | 1.63 ± 1.49 | 1.62 ± 1.49 | 4.44 ± 2.23 | 4.42 ± 2.23 |
Palomino | 19.00 | 19.00 | 15.31 ± 4.23 | 15.31 ± 4.23 | 3.94 ± 1.67 | 3.94 ± 1.67 | 8.05 ± 2.53 | 8.05 ± 2.53 |
Smokey Cream | 18.00 | 18.00 | 18.00 ± 0.00 | 18.00 ± 0.00 | 5.00 ± 0.00 | 5.00 ± 0.00 | 5.00 ± 0.00 | 9.61 ± 0.00 |
Coat Colour Subgroup | Population Sets | Inbreeding Coefficient (F), (%) | Individual Increase of Mean Inbreeding (ΔF), (%) | Maximum Inbreeding Coefficient % | Inbred Animals, % | Highly Inbred Animals, % | Average Coancestry (C), % | Average Relatedness Coefficient (ΔR), % | Non-Random Mating Rate (α) | GCI |
---|---|---|---|---|---|---|---|---|---|---|
Grey | Historic | 8.33 | 1.12 | 55.04 | 18.41 | 26.28 | 5.08 | 10.15 | 0.03 | 9.37 |
Current | 8.52 | 1.06 | 55.04 | 16.90 | 26.07 | 5.23 | 10.47 | 0.03 | 9.81 | |
Bay | Historic | 7.38 | 1.03 | 53.91 | 31.12 | 18.65 | 4.85 | 9.69 | 0.03 | 9.25 |
Current | 7.56 | 0.94 | 49.61 | 32.10 | 17.86 | 5.02 | 10.04 | 0.03 | 9.83 | |
Chestnut/Sorrel | Historic | 6.95 | 1.10 | 46.88 | 75.78 | 26.75 | 1.64 | 3.28 | 0.05 | 9.74 |
Current | 7.76 | 1.12 | 46.88 | 81.66 | 29.83 | 1.90 | 3.80 | 0.06 | 10.73 | |
Black | Historic | 7.54 | 0.96 | 45.31 | 95.27 | 16.64 | 5.18 | 10.36 | 0.03 | 9.66 |
Current | 7.64 | 0.90 | 43.38 | 98.01 | 16.21 | 5.26 | 10.51 | 0.03 | 10.00 | |
Overo | Historic | 7.81 | 1.22 | 22.72 | 90.00 | 31.25 | 3.55 | 6.42 | 0.05 | 9.59 |
Current | 7.31 | 0.98 | 17.89 | 94.29 | 25.71 | 3.55 | 7.10 | 0.04 | 9.95 | |
Roan | Historic | 7.59 | 0.95 | 28.62 | 91.16 | 21.29 | 4.71 | 9.43 | 0.03 | 9.61 |
Current | 7.87 | 0.93 | 28.62 | 93.90 | 20.19 | 4.96 | 9.91 | 0.03 | 10.03 | |
Dun | Historic | 7.19 | 1.12 | 32.42 | 89.43 | 14.00 | 4.68 | 9.35 | 0.03 | 8.69 |
Current | 7.41 | 1.09 | 32.42 | 92.72 | 14.24 | 4.76 | 9.52 | 0.03 | 8.92 | |
White | Historic | 6.25 | 1.24 | 25.00 | 64.79 | 21.13 | 4.86 | 9.71 | 0.01 | 6.98 |
Current | 8.80 | 1.01 | 21.52 | 94.87 | 28.21 | 5.31 | 10.62 | 0.04 | 9.86 | |
Isabelline | Historic | 6.78 | 1.68 | 37.19 | 7.67 | 1.49 | 2.61 | 5.21 | 0.04 | 5.85 |
Current | 6.96 | 1.67 | 37.19 | 80.77 | 14.84 | 2.63 | 5.25 | 0.04 | 5.83 | |
Cremello | Historic | 7.41 | 1.86 | 23.67 | 89.24 | 20.59 | 2.33 | 4.67 | 0.05 | 5.68 |
Current | 7.32 | 1.87 | 23.67 | 87.88 | 18.18 | 2.38 | 4.75 | 0.05 | 5.45 | |
Pearl | Historic | 2.86 | 0.60 | 22.66 | 30.26 | 8.93 | 1.20 | 2.39 | 0.02 | 4.06 |
Current | 2.91 | 0.61 | 22.66 | 30.91 | 9.09 | 1.16 | 2.33 | 0.02 | 4.04 | |
Palomino | Historic | 4.75 | 0.70 | 11.10 | 62.50 | 12.50 | 3.69 | 7.38 | 0.01 | 9.44 |
Current | 4.75 | 0.70 | 11.10 | 62.50 | 12.50 | 3.69 | 7.38 | 0.01 | 9.44 | |
Smokey Cream | Historic | 1.81 | 0.20 | 1.81 | 1.00 | 0.00 | 3.65 | 7.30 | −0.02 | 15.07 |
Current | 1.81 | 0.21 | 1.81 | 1.00 | 0.00 | 3.65 | 7.30 | −0.02 | 15.07 |
Coat Colour Subgroup | Population Set | Base Population (One or More Unknown Parents) | Actual Base Population (One Unknown Parent = Half Founder) | Number of Founders, n | Number of Ancestors, n | Effective Number of Non-Founders (Nef) | Number of Founder Equivalents (fe) | Effective Number of Ancestors (fa) | Founder Genome Equivalents (fg) | fa/fe Ratio | fg/fe Ratio |
---|---|---|---|---|---|---|---|---|---|---|---|
Grey | Historic | 1503.00 | 331.00 | 1172.00 | 2144.00 | 14.66 | 26.50 | 17.00 | 9.23 | 0.64 | 0.35 |
Current | 277.00 | 49.00 | 228.00 | 1138.00 | 12.99 | 26.03 | 17.00 | 8.67 | 0.65 | 0.33 | |
Bay | Historic | 600.00 | 84.00 | 516.00 | 1490.00 | 16.14 | 25.14 | 17.00 | 9.83 | 0.68 | 0.39 |
Current | 128.00 | 28.00 | 100.00 | 840.00 | 14.31 | 25.68 | 17.00 | 9.19 | 0.66 | 0.36 | |
Chestnut/Sorrel | Historic | 558.00 | 88.00 | 470.00 | 1283.00 | 20.26 | 58.99 | 31.00 | 15.08 | 0.53 | 0.26 |
Current | 108.00 | 22.00 | 86.00 | 762.00 | 17.44 | 58.61 | 27.00 | 13.44 | 0.46 | 0.23 | |
Black | Historic | 84.00 | 22.00 | 62.00 | 500.00 | 13.67 | 22.41 | 15.00 | 8.49 | 0.67 | 0.38 |
Current | 23.00 | 3.00 | 20.00 | 383.00 | 12.74 | 23.25 | 15.00 | 8.23 | 0.65 | 0.35 | |
Overo | Historic | 4.00 | 0.00 | 4.00 | 106.00 | 16.89 | 51.02 | 29.00 | 12.69 | 0.57 | 0.25 |
Current | 2.00 | 0.00 | 2.00 | 52.00 | 14.04 | 45.66 | 26.00 | 10.74 | 0.57 | 0.24 | |
Roan | Historic | 5.00 | 0.00 | 5.00 | 195.00 | 15.38 | 31.39 | 20.00 | 10.32 | 0.64 | 0.33 |
Current | 1.00 | 0.00 | 1.00 | 177.00 | 13.70 | 28.97 | 19.00 | 9.30 | 0.66 | 0.32 | |
Dun | Historic | 14.00 | 2.00 | 12.00 | 210.00 | 13.30 | 27.76 | 18.00 | 8.99 | 0.65 | 0.32 |
Current | 31.00 | 21.00 | 10.00 | 191.00 | 12.21 | 28.60 | 18.00 | 8.56 | 0.63 | 0.30 | |
White | Historic | 5.00 | 0.00 | 5.00 | 107.00 | 17.72 | 13.55 | 10.00 | 7.68 | 0.64 | 0.35 |
Current | 1.00 | 0.00 | 1.00 | 69.00 | 9.89 | 23.10 | 15.00 | 6.93 | 0.65 | 0.33 | |
Isabelline | Historic | 11.00 | 0.00 | 11.00 | 138.00 | 12.51 | 26.40 | 12.00 | 8.49 | 0.68 | 0.39 |
Current | 11.00 | 0.00 | 11.00 | 129.00 | 10.52 | 27.46 | 10.00 | 7.61 | 0.66 | 0.36 | |
Cremello | Historic | 4.00 | 0.00 | 4.00 | 27.00 | 8.79 | 28.17 | 9.00 | 6.70 | 0.53 | 0.26 |
Current | 4.00 | 0.00 | 4.00 | 26.00 | 8.37 | 26.66 | 9.00 | 6.37 | 0.46 | 0.23 | |
Pearl | Historic | 9.00 | 0.00 | 9.00 | 39.00 | 14.53 | 32.87 | 16.00 | 10.08 | 0.67 | 0.38 |
Current | 9.00 | 0.00 | 9.00 | 38.00 | 14.67 | 32.83 | 17.00 | 10.14 | 0.65 | 0.35 | |
Palomino | Historic | 0.00 | 0.00 | 0.00 | 19.00 | 8.85 | 42.81 | 17.00 | 7.33 | 0.57 | 0.25 |
Current | 0.00 | 0.00 | 0.00 | 19.00 | 8.85 | 42.51 | 17.00 | 7.33 | 0.57 | 0.24 | |
Smokey Cream | Historic | 0.00 | 0.00 | 0.00 | 1.00 | 1.01 | 37.35 | 1.00 | 0.98 | 0.46 | 0.23 |
Current | 0.00 | 0.00 | 0.00 | 1.00 | 0.00 | 0.00 | 1.00 | 0.00 | 0.39 | 0.19 |
Coat Colour Subgroup | Population Set | Genetic Diversity GD (%) | Genetic Diversity Loss GDL (%) | GDL Due to Genetic Drift since Founders (%) | GDL Due to Bottlenecks and Genetic Drift since Founders (GL) (%) | GDL Due to Unequal Founder Contributions (%) | Ancestors Explaining 25% of the Gene Pool (n) | Ancestors Explaining 50% of the Gene Pool (n) | Ancestors Explaining 75% of the Gene Pool (n) |
---|---|---|---|---|---|---|---|---|---|
Grey | Historic | 95 | 5 | 2 | 4 | 5 | 2 | 6 | 20 |
Current | 94 | 6 | 2 | 4 | 6 | 2 | 6 | 18 | |
Bay | Historic | 95 | 5 | 2 | 3 | 5 | 2 | 6 | 22 |
Current | 95 | 5 | 2 | 3 | 5 | 2 | 6 | 20 | |
Chestnut/Sorrel | Historic | 97 | 3 | 1 | 2 | 3 | 3 | 12 | 48 |
Current | 96 | 4 | 1 | 3 | 4 | 3 | 11 | 35 | |
Black | Historic | 94 | 6 | 2 | 4 | 6 | 2 | 6 | 17 |
Current | 94 | 6 | 2 | 4 | 6 | 2 | 6 | 17 | |
Overo | Historic | 96 | 4 | 1 | 3 | 4 | 4 | 11 | 28 |
Current | 95 | 5 | 1 | 4 | 5 | 4 | 10 | 23 | |
Roan | Historic | 95 | 5 | 2 | 3 | 5 | 3 | 8 | 26 |
Current | 95 | 5 | 2 | 4 | 5 | 3 | 7 | 22 | |
Dun | Historic | 94 | 6 | 2 | 4 | 6 | 2 | 7 | 17 |
Current | 94 | 6 | 2 | 4 | 6 | 3 | 7 | 17 | |
White | Historic | 93 | 7 | 4 | 3 | 7 | 2 | 4 | 16 |
Current | 93 | 7 | 2 | 5 | 7 | 2 | 6 | 15 | |
Isabelline | Historic | 94 | 6 | 2 | 4 | 6 | 2 | 4 | 16 |
Current | 93 | 7 | 2 | 5 | 7 | 2 | 4 | 15 | |
Cremello | Historic | 93 | 7 | 2 | 6 | 7 | 2 | 4 | 12 |
Current | 92 | 8 | 2 | 6 | 8 | 2 | 4 | 11 | |
Pearl | Historic | 95 | 5 | 2 | 3 | 5 | 2 | 7 | 18 |
Current | 95 | 5 | 2 | 3 | 5 | 2 | 7 | 18 | |
Palomino | Historic | 93 | 7 | 1 | 6 | 7 | 3 | 7 | 12 |
Current | 93 | 7 | 1 | 6 | 7 | 3 | 7 | 12 | |
Smokey Cream | Historic | 49 | 51 | 1 | 50 | 51 | 1 | 1 | 1 |
Current | 0 | 0 | N/A | N/A | N/A | 1 | 1 | 1 |
Parameter | Population Set | Effective Population Size Calculated through of the Individual Inbreeding Rate | Effective Size of the Population Calculated through the Individual Coancestry Rate | Number of Equivalent Subpopulations | Rate of Loss Heterozygosity Due to Inbreeding per Generation | ||
---|---|---|---|---|---|---|---|
Coat Colour Subgroup | |||||||
Grey | Historic | 96.15 | 16.13 | 0.17 | 0.005 | ||
Current | 138.89 | 10.06 | 0.07 | 0.004 | |||
Bay | Historic | 44.64 | 4.93 | 0.11 | 0.011 | ||
Current | 47.17 | 4.78 | 0.10 | 0.011 | |||
Chestnut/Sorrel | Historic | 48.54 | 5.16 | 0.11 | 0.010 | ||
Current | 53.19 | 4.98 | 0.09 | 0.009 | |||
Black | Historic | 45.45 | 15.24 | 0.34 | 0.011 | ||
Current | 44.64 | 13.16 | 0.29 | 0.011 | |||
Overo | Historic | 52.08 | 4.83 | 0.09 | 0.010 | ||
Current | 55.56 | 4.76 | 0.09 | 0.009 | |||
Roan | Historic | 40.98 | 7.79 | 0.19 | 0.012 | ||
Current | 51.02 | 7.04 | 0.14 | 0.010 | |||
Dun | Historic | 60.98 | 6.35 | 0.10 | 0.008 | ||
Current | 75.76 | 6.35 | 0.08 | 0.007 | |||
White | Historic | 44.64 | 5.35 | 0.12 | 0.011 | ||
Current | 45.87 | 5.25 | 0.11 | 0.011 | |||
Isabelline | Historic | 40.32 | 5.15 | 0.13 | 0.012 | ||
Current | 49.50 | 4.71 | 0.10 | 0.010 | |||
Cremello | Historic | 29.76 | 9.60 | 0.32 | 0.017 | ||
Current | 29.94 | 9.52 | 0.32 | 0.017 | |||
Pearl | Historic | 26.88 | 10.71 | 0.40 | 0.019 | ||
Current | 26.74 | 10.53 | 0.39 | 0.019 | |||
Palomino | Historic | 83.33 | 20.92 | 0.25 | 0.006 | ||
Current | 81.97 | 21.46 | 0.26 | 0.006 | |||
Smokey Cream | Historic | N/A | N/A | N/A | N/A | ||
Current | N/A | N/A | N/A | N/A |
Parameters | Coat Colour Subgroup | |
---|---|---|
Populational Set | Historic | Current |
FIS (Inbreeding coefficient relative to the subpopulation) | 0.029 | 0.018 |
FST (Correlation between random gametes drawn from the subpopulation relative to the total population) | 0.004 | 0.014 |
FIT (Inbreeding coefficient relative to the total population) | 0.033 | 0.032 |
Mean inbreeding within subpopulations | 0.079 | 0.057 |
Mean number of horses per subpopulation | 12,943.75 | 10,308.81 |
Number of Nei genetic distances | 78 | 78 |
Average Nei genetic distance | 0.004 | 0.014 |
Mean coancestry within subpopulations | 0.052 | 0.040 |
Self coancestry | 0.540 | 0.528 |
Mean coancestry in the metapopulation | 0.048 | 0.026 |
Subpopulations | 13 | 13 |
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Marín Navas, C.; Delgado Bermejo, J.V.; McLean, A.K.; León Jurado, J.M.; Torres, A.R.d.l.B.y.R.d.; Navas González, F.J. One Hundred Years of Coat Colour Influences on Genetic Diversity in the Process of Development of a Composite Horse Breed. Vet. Sci. 2022, 9, 68. https://doi.org/10.3390/vetsci9020068
Marín Navas C, Delgado Bermejo JV, McLean AK, León Jurado JM, Torres ARdlByRd, Navas González FJ. One Hundred Years of Coat Colour Influences on Genetic Diversity in the Process of Development of a Composite Horse Breed. Veterinary Sciences. 2022; 9(2):68. https://doi.org/10.3390/vetsci9020068
Chicago/Turabian StyleMarín Navas, Carmen, Juan Vicente Delgado Bermejo, Amy Katherine McLean, José Manuel León Jurado, Antonio Rodríguez de la Borbolla y Ruiberriz de Torres, and Francisco Javier Navas González. 2022. "One Hundred Years of Coat Colour Influences on Genetic Diversity in the Process of Development of a Composite Horse Breed" Veterinary Sciences 9, no. 2: 68. https://doi.org/10.3390/vetsci9020068