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The phenotypic records used for fitting the models were averages over the single environment phenotypes.
Just as for the single environment case, we see that the mean robustness increases as n increases and that the lowest values are not extremely small.
The single environment and multi-environment joint analyses were performed using the QTL Network ver. 2.0 software [ 34] based on a mixed-model based composite interval mapping (MCIM).
The single environment QTL, gene−environment interactions (GEIs), and two-QTL mapping was carried out as described previously (Bhatia et al. 2014).
QTL alignment between the two detection methods showed that yield QTL on b08 and stem carbohydrate QTL on b05 were most consistent between the multilocation model and the single environment detection.
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The diagonal values (where μ x,0→1 = μ y,0→1) within each panel correspond to the single-environment model of epigenetic change discussed by Slatkin (2009).
Thus, when the environmental structure (GE) was modeled, this increased the prediction ability of unobserved individuals by about 20% with respect to the single-environment prediction model.
Several authors have proposed extensions of the single-environment GS model that accommodate G×E using either covariance functions or environmental covariates.
The locations of the mixed-model, multienvironment QTL were compared with the single-environment QTL by map location comparisons on the molecular map drawn to scale for each linkage group.
Finally, the mixed-model QTL for Stc5.1 and Stc6.1 aligned with the single-environment QTL, but this was based on only analysis in Palmira for stem TNC so this was to be expected.
Box 1a in File S4 provides an R-script that implements the single-environment model described previously using the BGLR R-package (de los Campos and Pérez-Rodriguez 2014).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com