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Correlations between ROH measures and pedigree inbreeding (Fped) were calculated for 17 different populations for which pedigree-based mean inbreeding coefficients were available [11].
Mean inbreeding coefficients ± Standard Deviation in the studied litters and their parents.
Table 1 shows the mean inbreeding coefficients for males and females of the S and C lines, for each generation.
For the Holstein breed, the mean inbreeding coefficients, calculated using pedigree, were greater for genotyped cows than for the population that had only pedigree-based inbreeding coefficients.
The pedigrees of all animals were traced back to the founder populations and mean inbreeding coefficients per breed were calculated using the algorithm in [ 19].
Microsatellite genotypes within populations of both species tended to be slightly heterozygote deficient, with low positive mean inbreeding coefficients (f) across loci (Table S6).
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Comparison of the number and sum length of ROH of various sizes to the mean inbreeding coefficient and effective population size indicate that ROH provide a valuable record of a population's demographic history.
Pedigree-based estimates of the mean inbreeding coefficient, Fped, are available for 17 of the 51 populations and show highly significant and strong correlations with the very long ROH observed, peaking for the sum of ROH >10 Mb (r = 0.87, p≤0.0001).
This corresponds with a mean inbreeding coefficient of 0.83.
The observed and expected heterozygosity values were similar, with a mean inbreeding coefficient of -0.069 (Table 1).
As separate batches, both slightly positive and negative inbreeding coefficients are estimated with a mean inbreeding coefficient near zero for all three populations.
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