Although the reliability of the pedigree haplotype depends on the number of SNPs in the respective haplotype blocks, we could identify the ancestral origin of the pedigree haplotypes in 60.9% of the Koshihikari genome.
The gain in reliability from genomic information was calculated as the difference between the realised reliability of the pedigree-based EBV and the combined GEBV of the validation bulls.
In addition, reliability of the pedigree index (PI) for bulls in the test datasets was calculated using the data of bulls born before the cut-off date to divide reference and test datasets, but each partner based their calculations on different datasets.
Based on data from the Dairy Association of China, the reliability of a conventional pedigree index (calculated as 0.5*sire EBV + 0.25*maternal grandsire EBV) in the CH population was 0.12 for milk production traits.
For example, the difference between the reliability of genomic and pedigree predictions in generation 21 was 17 % larger when based on reliability of selection than when based on base PEV reliability, which indicates that genotyping un-phenotyped females might be more valuable than previously suggested, e.g., [ 20– 20].
Table 2 shows that reliability decreased when less than 3 generations of pedigree data were used, and the reliability of the prediction increased only very slightly when the number of generations of pedigree used was greater than 3. Table 3 shows variance components estimated by ASReml using IBS, IBD and IBS + IBD information.
In addition to the more standard quantitative uncertainty assessment (number, units and the spread of those numbers), the NUSAP approach also includes an evaluation of the reliability of the information (assessment) and its the scientific basis (pedigree).
To investigate the effect of the number of generations in the pedigree, which defines the base generation with non-IBD individuals, on the reliability of the GW-EBV with IBD information, we performed iterative peeling using 1, 2, 3, 4 and 5 generations of pedigree data, respectively.
Analysis of the pedigrees revealed good pedigree completeness and depth [ 1].
Thus, the reliabilities of genomic predictions based on the CH reference population were of similar magnitude as the reliabilities of a pedigree index, and the genomic predictions based on the joint reference population gave much higher reliabilities than those based on a pedigree index.
