Abstract

Background

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 -FHOM-, the diagonal elements of the genomic -FG-, and hybrid matrixes -FH-) and ROH measures (FRZ). 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 (Ffor the last 3 generations -F3-) to 0.44 (ancestral history coefficient) and the mean values of genomic-based inbreeding coefficients varied from 0.05 (FRZfor three generations,FHandFHOM) to 0.11 (FRZfor nine generations). Significant correlations were also found between pedigree and genomic inbreeding values, which ranged between 0.58 (F3 withFHOM) and 0.79 (FwithFRZ). In addition, the correlations betweenFRZestimated 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.

Data Availability

The dataset supporting the results of this study was supplied by the National Association of Pura Raza Española Horse Breeders (ANCCE). The datasets generated and/or analysed during the current study are available from the corresponding author upon reasonable request.

Abbreviations

  • AHC:: Ancestral history coefficient
  • F :: Wright classical inbreeding value
  • fa:: Number of ancestors
  • Fa_Bal:: Ballou’s ancestral inbreeding
  • Fa_Kal:: Kalinowski’s ancestral inbreeding
  • fe:: Number of founders
  • F G :: Genomic inbreeding value by the diagonal elements of the genomic matrix
  • F H :: Genomic inbreeding value by the diagonal elements of the hybrid matrix
  • F HOM :: Genomic inbreeding value applying the method-of-moments methodology
  • F i j :: Partial inbreeding coefficients
  • Fnew_Kal:: Kalinowski’s new inbreeding
  • F RZ :: Genomic inbreeding value applying the RZooROH R package
  • F3:: Classical inbreeding considering 3 generations
  • F6:: Classical inbreeding considering 6 generations
  • F9:: Classical inbreeding considering 9 generations
  • IBD:: Identity by descent
  • ROH:: Runs of homozygosity

References

Acknowledgements

We wish to thank the Pura Raza Española Horse Breeders Association for the data.

Funding

This research was funded by the AGL-2017-84217-P Research project from Ministerio de Economía, Industria y Competitividad, Gobierno de España.

Ethics Declaration

Ethics approval and consent to participate

Not applicable.

Consent for publication

Not applicable.

Competing interests

The authors declare that they have no competing interests.

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