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The percentage of genetic variance explained by each QTL for each trait was calculated using the given sizes and the multinomial nature of those sizes; the calculation mirrored the development presented in the Methods section.
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Phenotypic correlations between traits within years and between years for each trait were calculated using the non-parametric Spearman correlation coefficient.
The percentage of phenotypic variation explained by all detected QTLs for one trait was calculated using a linear regression fitting the QTLs detected for each trait as factors.
The genetic correlations of the five milk trait Igenity scores with the equivalent recorded trait were calculated using ASReml and the appropriate final model for each of the two traits.
The means, standard deviations, results of analysis of variance for each trait, and correlations among traits were calculated using SAS Enterprise Guide 7.1 (SAS Institute Inc., Cary, North Carolina, USA).
The average clustering coefficients for each of the 354 studied traits were calculated using clustering coefficients of contributing genes in the corresponding epistasis subnetworks (Li et al. 2010).
Phenotypic correlation coefficients among the traits were calculated using Genstat [16].
Correlations between phenotypic traits were calculated using least-square RIL means (PROC CORR, SAS v.9.2).
The correlations between the different traits were calculated using the Statgraphics Plus 4.0 software.
Pearson correlations among four growth traits were calculated using pairwise comparison.
Correlation among leaf traits and years was calculated using Pearson's correlation coefficients.
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