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Table 2 Set of competing models compared for pearl millet and maize real data

From: Association studies including genotype by environment interactions: prospects and limits

Model

Specification

Number of parameters

  

Maize

Pearl millet

Fit1

Y = E + Qi + S + (K + e)

12

18

Fit2

Y = E + Qi + S + Qi × E + (K + e)

24

66

Fit3

Y = E + Qi + S + Qi × E + S × E + (K + e)

30

74

Fit4

Y = E + Qi + S + Qi × E + S × E + Qi × S + (K + e)

32

80

Fit5

Y = E + Qi + S + Qi × E + S × E + Qi × S + Qi × S × E + (K + e)

44

128

  1. Y is the trait, E is environmental effect (trial effect), Qi is population structure effect set by ancestry in the the ith population (from k available populations, k-1 are used in the model), S is SNP effect. K is polygenic background random effect set by kinship matrix and e is the residual. A cross between terms represents interaction effect. For each dataset, the total number of model parameters is given.