1. Distribution of eigenvalues from an eigendecomposition of the genomic relatedness matrix for all 110 lines excluding one large eigenvalue where .
Distribution of eigenvalues from an eigendecomposition of the genomic relatedness matrix for all 110 lines excluding one large eigenvalue where . Eigendecomposition of the genomic relatedness matrix, X, which was scaled by equation 2.8 in Bryc et al. (2013) using values of N = 3,709,328 and M = 110. Here, N corresponds to the number of SNPs used to estimate X and M is the number of lines. Only SNPs with without missing data were used for this analysis. The red vertical line corresponds to the significance threshold, t, for declaring an eigenvalue larger than that expected for a random relatedness matrix. t = (1 + F) /2 and corresponds to a value of with our expected inbreeding coefficient (F) of after 20 generations of full-sib mating. The two largest eigenvalues were significant, (not plotted) and .
Adam J. Reddiex et al. G3 2018;8:
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