Furthermore, we estimated the GRM from the SNPs on each chromosome (AC) and estimated the variance attributable to each chromosome by fitting the GRMs of all the chromosomes simultaneously in the model y=Xβ+∑C=122gC+ε where gC is a vector of genetic effects attributable to each chromosome and var(gC)=ACσC2 (joint analysis). The proportion of variance explained by each chromosome is defined as hC2=σC2/σP2. We also fitted one chromosome at a time in the model y = Xβ + gC + ε (separate analysis). If there is an effect of population structure, SNPs on one chromosome will be correlated with the SNPs on the other chromosomes such that hC2(sep) will be overestimated in the separate analysis.
