Incorporation of causative quantitative trait nucleotides in single-step GBLUP

Table 2 Number of eigenvalues explaining 90, 95 or 98% of the variance for genomic relationship matrices

Options used to construct the genomic relation matrix: 60 k non-coding SNPs (60 k), all causative QTN (QTN), the top 10% causative SNPs (QTN10), blending at 5% (BL5) or 1% (BL1), weighted by the 3rd iteration of the single-step GWAS (GWAS3), and weighted by true QTN effects (TRUE) for datasets with 100 or 1000 causative QTN
^a10 eigenvalues explained 76% of the variance of \({\mathbf{G}}\) for the 100-QTN scenario
^b100 eigenvalues explained 71% of the variance of \({\mathbf{G}}\)
^cEigenvalues after number of QTN (100 or 1000) had values approaching 0 (below 10E−4)
^dSimulated true weights for QTN and a constant equal to the minimum QTN value for SNPs

ISSN: 1297-9686