Level of Inbreeding in Norik of Muran Horse: Pedigree vs. Genomic Data

Abstract

The objective of this study was to analyse the level of pedigree and genomic inbreeding in a herd of the Norik of Muran horses. The pedigree file included 1374 animals (603 stallions and 771 mares), while the reference population consisted of animals that were genotyped by using 70k SNP platform (n = 25). The trend of pedigree inbreeding was expressed as the probability that an animal has two identical alleles by descent according to classical formulas. The trend of genomic inbreeding was derived from the distribution of runs of homozygosity (ROHs) with various length in the genome based on the assumption that these regions reflect the autozygosity originated from past generations of ancestors. A maximum of 19 generations was found in pedigree file. As expected, the highest level of pedigree completeness was found in first five generations. Subsequent quality control of genomic data resulted in totally 54432 SNP markers covering 2.242 Mb of the autosomal genome. The pedigree analysis showed that in current generation can be expected the pedigree inbreeding at level 0.23% (ΔFPEDi = 0.19 ± 1.17%). Comparable results was obtained also by the genomic analysis, when the inbreeding in current generation reached level 0.11%. Thus, in term of genetic diversity both analyses reflected sufficient level of variability across analysed population of Norik of Muran horses.

Suitability of Pedigree Information and Genomic Methods for Analyzing Inbreeding of Polish Cold-Blooded Horses Covered by Conservation Programs

“…Previous studies [ 33 ], reported that the ROH segments of 2–4 Mb represent the inbreeding of distant generations of the ancestors (13–25 generations ago), which cannot usually be captured using pedigree information. The ROH segments > 8 Mb represent the proportion of autozygosity originated from ancestors that were born 6–7 generations ago and the ROH longer than 16 Mb reflect ancestors that were born 3–6 generations ago [ 34 ]. This was also visible in our data in which the correlation coefficient between F PED and F ROH tended to increase along with the increase of the number of generations registered in pedigree data.…”

Fine‐scale estimation of inbreeding rates, runs of homozygosity and genome‐wide heterozygosity levels in the Mangalarga Marchador horse breed

“…The genomic coefficients derived from animals/populations can be calculated without pedigree records or incomplete pedigree information. The inbreeding coefficients of many horse breeds—including Arabian (Al Abri, König von Borstel, Strecker, & Brooks, 2017), Lipizzan (Grilz‐Seger et al., 2019), Thoroughbred (Fawcett et al., 2019), Saxon‐Thuringian (Metzger et al., 2015) and Norik of Muran (Kasarda et al., 2019)—have been studied in a genomic‐wide view.…”

Genetic Variability in the Italian Heavy Draught Horse from Pedigree Data and Genomic Information

“…A number of recent studies in livestock species have focused on the estimation of genetic diversity using both pedigree data and molecular information: in cattle [4,5], pigs [6], and horses. In horses, genetic diversity was estimated using pedigree data and microsatellites (e.g., in thoroughbred horses [7], Franches-Montagnes [8], and Belgian Draught horse [9]) and, more recently, using pedigree and high-density SNP information (Norik of Muran horses [10]).…”