Table 1.

Parameters considered in the simulation study.

dScenario	nQTN	Species	Heritability	Targeted MAF	Sample size	Allelic effect
Null	0	Maize; Arabidopsis	0.00	N/A	500; Maximum	N/A
Epistasisa	3 epistatic QTNsa	Maize; Arabidopsis	0.30; 0.80	0.10	500; Maximum	0.75 for all 3 QTNs;
GxE	2 mQTNs in 2 environments	Maize; Arabidopsis	0.70	0.30	500; Maximum	Env.1: 0.2b, 0.5c Env.2: 0.8b, 0.5c
vQTN	1 mQTN 1 vQTN	Maize; Arabidopsis	0.63; 0.33	0.10; 0.40	500; Maximum	mQTN: 0.25 vQTN: 0.1; 0.5; 0.9

Across all scenarios, a total of 64 unique configurations of these parameters were simulated.

QTN quantitative trait nucleotides, MAF minor allele frequency, GxE genotype by environment, mQTN mean QTNs, vQTN variance QTNs.

^aEach epistatic effect consists of the additive-by-additive effect of two randomly selected single nucleotide polymorphisms.

^bThis environment-specific mQTN was simulated at the SNP in both environments, but the effect sizes differed in each environment.

^cThis environment-specific mQTN was simulated at different SNPs in each environment.