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An interactive biplot implementation in R for modeling genotype-by-environment interaction

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Abstract

Classical and GGE biplot methods are graphical procedures that allow multivariate data to be analyzed. In particular, the GGE biplot displays the genotype main effect (G) and the genotype by environment interaction (GE) in two-way data. The GGE biplot originates from data graphical analysis of multi-environment trials (MET). Thus, agronomists, crop scientists and geneticists are potential users of this method. However, it can also be used to visualize and analyze other types of data. In this paper, we propose a new interactive computational implementation in R language to perform the main functions of the classical and GGE biplot methods, so it is also useful for MET data visual analysis. This implementation is organized in an R package named GGEBiplotGUI . This package is the only interactive, noncommercial and open source software that currently exists, offering a free alternative to available commercial software. In addition, it can be used without to practically have knowledge of the R programming language. Here, we present and discuss the capabilities and features of the GGEBiplotGUI package and illustrate them by using real data. The GGEBiplotGUI package graphically addresses the questions that a researcher likely asks. This R package is not only a tool for visual data analysis of multi-environment trials, useful for plant breeders and geneticists, in order to study yields from genotypes and interactions between genotype and environment, but also data from other areas can be analyzed by the GGEBiplotGUI package.

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Acknowledgments

The authors wish to thank the Editor-in-Chief, Professor George Christakos, an Associate Editor, and anonymous referees for their comments on an earlier version of this manuscript, which resulted in this improved version. The research of Victor Leiva was partially supported by FONDECYT 1120879 grant from the Chilean government.

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Authors and Affiliations

  1. Departamento de Estadística, Universidad de Salamanca, Salamanca, Spain

    Elisa Frutos & M. Purificación Galindo

  2. Departamento de Estadística, Universidad de Valparaíso, Avda. Gran Bretaña 1111, Playa Ancha, Valparaiso, Chile

    Víctor Leiva

Authors
  1. Elisa Frutos
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  2. M. Purificación Galindo
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  3. Víctor Leiva
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Correspondence to Víctor Leiva.

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Frutos, E., Galindo, M.P. & Leiva, V. An interactive biplot implementation in R for modeling genotype-by-environment interaction. Stoch Environ Res Risk Assess 28, 1629–1641 (2014). https://doi.org/10.1007/s00477-013-0821-z

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