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

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 coefcients have been historically estimated by using pedigree information; however, over the last decade, genome-base inbreeding coefcients have come to the forefront in this feld. The Pura Raza Española (PRE) horse is an autochthonous Spanish horse breed which has been recognised since 1912. The total PRE popula‑ tion (344,718 horses) was used to estimate Classical (F), Ballou’s ancestral, Kalinowski’s ancestral, Kalinowski’s new and the ancestral history coefcient values. In addition, genotypic data from a selected population of 805 PRE individu‑ als was used to determine the individual inbreeding coefcient 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 coefcients 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 estima‑ tions will give the data greater reliability. Results: The mean values of the pedigree-based inbreeding coefcients ranged from 0.01 (F for the last 3 genera‑ tions -F3-) to 0.44 (ancestral history coefcient) and the mean values of genomic-based inbreeding coefcients varied from 0.05 (FRZ for three generations, FH and FHOM) to 0.11 (FRZ for nine generations). Signifcant correlations were also found between pedigree and genomic inbreeding values, which ranged between 0.58 (F3 with FHOM) and 0.79 (F with FRZ). In addition, the correlations between FRZ estimated for the last 20 generations and the pedigree-based inbreed‑ ing 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 pedigreebased genetic studies with very large efective population sizes. Obtaining a satisfactory parameter will always be desirable, but the approximation obtained with a robust pedigree will allow us to work more efciently and economi‑ cally than with massive genotyping.