Efficiency of genome-wide association studies in random cross populations

Genome-wide association studies (GWAS) with plant species have employed inbred lines panels. We evaluated the efficiency of GWAS in non-inbred and inbred populations and assessed factors affecting GWAS. Fifty samples of 800 individuals from populations with linkage disequilibrium were simulated. Individuals were genotyped for 10,000 single nucleotide polymorphisms (SNPs) and phenotyped for traits controlled by ten quantitative trait loci (QTLs) and 90 minor genes, assuming different degrees of dominance and broad sense heritabilities of 40 and 80%. The average SNP density was 0.1 centiMorgan (cM) and the QTL heritabilities ranged from 3.2 to 11.8%. The results for random cross populations evidenced that to increase the QTL detection power, the additive-dominance model must be fitted for traits controlled by dominance effects but must not be fitted for traits showing no dominance. The power of detection was maximized by increasing the sample size to 400 and the false discovery rate (FDR) to 5%. The average power of detection for the low, intermediate, and high heritability QTLs achieved 52.4, 87.0, and 100.0%, respectively. Assuming sample sizes of 400 and 800, the observed FDR was equal to or lower than the specified level of significance. The association mapping was highly precise, since at least 97% of the declared QTLs were detected by the SNP inside it (average bias of 0.4 cM). Besides controlling the FDR, relatedness (and identity by state) efficiently controls the number of significant associations outside the QTL interval (not all false positive associations). The analysis of the inbred random cross population provided essentially the same results as the non-inbred populations.