Table 1 Parameters considered in the simulation study.

From: Assessment of two statistical approaches for variance genome-wide association studies in plants

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

  1. Across all scenarios, a total of 64 unique configurations of these parameters were simulated.
  2. QTN quantitative trait nucleotides, MAF minor allele frequency, GxE genotype by environment, mQTN mean QTNs, vQTN variance QTNs.
  3. aEach epistatic effect consists of the additive-by-additive effect of two randomly selected single nucleotide polymorphisms.
  4. bThis environment-specific mQTN was simulated at the SNP in both environments, but the effect sizes differed in each environment.
  5. cThis environment-specific mQTN was simulated at different SNPs in each environment.
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