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Journal of animal science and biotechnology2022; 13(1); 127; doi: 10.1186/s40104-022-00781-5

Fine-tuning genomic and pedigree inbreeding rates in equine population with a deep and reliable stud book: the case of the Pura Raza Española horse.

Abstract: Estimating inbreeding, which is omnipresent and inevitable in livestock populations, is a primary goal for management and animal breeding especially for those interested in mitigating the negative consequences of inbreeding. Inbreeding coefficients have been historically estimated by using pedigree information; however, over the last decade, genome-base inbreeding coefficients have come to the forefront in this field. The Pura Raza Española (PRE) horse is an autochthonous Spanish horse breed which has been recognised since 1912. The total PRE population (344,718 horses) was used to estimate Classical (F), Ballou's ancestral, Kalinowski's ancestral, Kalinowski's new and the ancestral history coefficient values. In addition, genotypic data from a selected population of 805 PRE individuals was used to determine the individual inbreeding coefficient using SNP-by-SNP-based techniques (methods of moments -F-, the diagonal elements of the genomic -F-, and hybrid matrixes -F-) and ROH measures (F). The analyse of both pedigree and genomic based inbreeding coefficients in a large and robust population such as the PRE horse, with proven parenteral information for the last 40 years and a high degree of completeness (over 90% for the last 70 years) will allow us to understand PRE genetic variability better and the correlations between the estimations will give the data greater reliability. Results: The mean values of the pedigree-based inbreeding coefficients ranged from 0.01 (F for the last 3 generations -F3-) to 0.44 (ancestral history coefficient) and the mean values of genomic-based inbreeding coefficients varied from 0.05 (F for three generations, F and F) to 0.11 (F for nine generations). Significant correlations were also found between pedigree and genomic inbreeding values, which ranged between 0.58 (F3 with F) and 0.79 (F with F). In addition, the correlations between F estimated for the last 20 generations and the pedigree-based inbreeding highlight the fact that fewer generations of genomic data are required when comparing total inbreeding values, and the opposite when ancient values are calculated. Conclusions: Ultimately, our results show that it is still useful to work with a deep and reliable pedigree in pedigree-based genetic studies with very large effective population sizes. Obtaining a satisfactory parameter will always be desirable, but the approximation obtained with a robust pedigree will allow us to work more efficiently and economically than with massive genotyping.
© 2022. The Author(s).
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Publication Date: 2022-11-07 PubMed ID: 36336696PubMed Central: PMC9639299DOI: 10.1186/s40104-022-00781-5Google Scholar: Lookup
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  • Journal Article

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

This research aimed to estimate inbreeding in the Pura Raza Española (PRE) horse population, a Spanish breed with a reliable pedigree, using both traditional pedigree methods and modern genomic techniques. The study found that both methods produced significant results, with correlations found between the estimates provided by each method.

Introduction and Methods

  • The research looked at estimating inbreeding in the Pura Raza Española (PRE) horse population. Inbreeding is common in livestock populations and can have detrimental effects. The objective was to mitigate these through careful management and breeding.
  • Historically inbreeding coefficients have been estimated using pedigree information, but more recently genomic-based coefficients have become more popular.
  • The analysis considered the total PRE population of 344,718 horses to estimate various coefficients, including Classical (F), Ballou’s ancestral, Kalinowski’s ancestral, Kalinowski’s new and the ancestral history coefficient values.
  • A smaller population of 805 PRE horses was selected to estimate individual inbreeding coefficients using SNP-by-SNP-based techniques and ROH measures. Genomic data was used for these calculations.

Results

  • The analysis revealed that the mean values of the pedigree-based inbreeding coefficients ranged from 0.01 (for the last 3 generations) to 0.44 (ancestral history coefficient).
  • The genomic-based inbreeding coefficients had mean values ranging between 0.05 (for three generations) to 0.11 (for nine generations).
  • There were significant correlations found between the two kinds of inbreeding values, highlighting the efficacy of using both traditional and modern estimation methods. Correlation values ranged from 0.58 to 0.79.
  • Fewer generations of genomic data are needed when comparing total inbreeding values, with more needed for calculating ancient inbreeding values.

Conclusions

  • The research proved that thorough and reliable pedigree is still useful in pedigree-based genetic studies, particularly in situations with large effective population sizes.
  • A robust pedigree allows for a more efficient and cost-effective process than relying solely on extensive genotyping.

Cite This Article

APA
Perdomo-González DI, Laseca N, Demyda-Peyrás S, Valera M, Cervantes I, Molina A. (2022). Fine-tuning genomic and pedigree inbreeding rates in equine population with a deep and reliable stud book: the case of the Pura Raza Española horse. J Anim Sci Biotechnol, 13(1), 127. https://doi.org/10.1186/s40104-022-00781-5

Publication

Journal of animal science and biotechnology
ISSN: 1674-9782
NlmUniqueID: 101581293
Country: England
Language: English
Volume: 13
Issue: 1
Pages: 127
PII: 127

Researcher Affiliations

Perdomo-González, Davinia Isabel
  • Departamento Agronomía, Escuela Técnica Superior de Ingeniería Agromómica, Universidad de Sevilla, Ctra Utrera Km 1, 41013, Sevilla, Spain. dperdomo@us.es.
Laseca, Nora
  • Departamento de Genética, Universidad de Córdoba, Córdoba, Spain.
Demyda-Peyrás, Sebastián
  • Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata, Argentina.
  • Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), La Plata, Argentina.
Valera, Mercedes
  • Departamento Agronomía, Escuela Técnica Superior de Ingeniería Agromómica, Universidad de Sevilla, Ctra Utrera Km 1, 41013, Sevilla, Spain.
Cervantes, Isabel
  • Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain.
Molina, Antonio
  • Departamento de Genética, Universidad de Córdoba, Córdoba, Spain.

Grant Funding

  • AGL-2017-84217-P / Ministerio de Asuntos Econu00f3micos y Transformaciu00f3n Digital, Gobierno de Espau00f1a

Conflict of Interest Statement

The authors declare that they have no competing interests.

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Citations

This article has been cited 8 times.
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