Average number of significant single-nucleotide polymorphisms (SNPs; 100 replicates) in five chromosomes (10,000 SNPs) without simulated quantitative trait loci.

Standard errors are given in parentheses. The average number of significant SNPs (Sobs) in 100 replicates was compared with the expected number (Sexp) at different significance levels using t-tests. (H0: Sobs = Sexp; H1: Sobs>Sexp; *p<0.05, **p<0.01). Significance level of 0.000005 corresponds to a nominal significance level of 0.05 after Bonferroni correction for 10000 tests. LMMped = Linear Mixed Model Including Pedigree-Based Relationship, LMMstr = Linear Mixed Model with STRUCTURE, LMMpca = Principal Component Analysis in a Linear Mixed Model, LMMgmat = Linear Mixed Model Including Genomic Relationship, LM = Linear Model, LMstr = Linear Model with STRUCTURE, LMpca = Principal Component Analysis in a Linear Model, P = admixture, K = Familial relationships.