Genotype x environmental interaction (GxE) can lead to differences in performance of genotypes over environments. GxE analysis can be used to analyze the stability of genotypes and the value of test locations. We developed an Rlanguage program (RGxE) that computes univariate stability statistics, descriptive statistics, pooled ANOVA, genotype F ratio across location and environment, cluster analysis for location, and location correlation with average location performance. Univariate stability statistics calculated are regression slope ( b i ), deviation from regression ( S 2 d ), Shukla’s variance ( σ i 2 ), S square Wricke’s ecovalence ( W i ), and Kang’s yield stability ( YS i ). RGxE is free and intended for use by scientists studying performance of polygenic or quantitative traits over multiple environments. In the present paper we provide the RGxE program and its components along with an example input data and outputs. Additionally, the RGxE program along with associated files is also available on GitHub at https://github.com/mahendra1/RGxE, http://cucurbitbreeding.com/todd-wehner/publications/software-sas-r-project/ and http://cuke.hort.ncsu.edu/cucurbit/wehner/software.html .
KeywordsGenotype x Environment InteractionR Programming LanguageRGxEUnivariateMultivariate
Dia, M., Weindorf, D., Thompson, C., Cummings, H., Cacovean, H. and Rusu, T. (2009) Spatial Distribution of Heavy Metals in the Soils of Erath County, Texas. Studia Universitatis Babes-Bolyai, Geographia, No. 2, 99-114.
Li, Y., Gibson, J.M., Jat, P., Puggioni, G., Hasan, M., West, J.J., Vizuete, W., Sexton, K. and Serre, M. (2010) Burden of Diseases Attributed to Anthropogenic Air Pollution in the United Arab Emirates: Estimates Based on Observed Air Quality Data. Science of the Total Environment, 408, 5784-5793. https://doi.org/10.1016/j.scitotenv.2010.08.017
Jat, P. and Serre, M.L. (2016) Bayesian Maximum Entropy Space/Time Estimation of Surface Water Chloride in Maryland Using River Distances. Environmental Pollution, 219, 1148-1155. https://doi.org/10.1016/j.envpol.2016.09.020
Weindorf, D.C., Sarkar, R., Dia, M., Wang, H., Chang, Q., Haggard, B., McWhirt, A. and Wooten, A. (2008) Correlation of X-Ray Fluorescence Spectrometry and Inductively Coupled Plasma Atomic Emission Spectroscopy for Elemental Determination in Composted Products. Compost Science & Utilization, 16, 79-82. https://doi.org/10.1080/1065657X.2008.10702361
Weindorf, D., Rinard, B., Zhu, Y., Johnson, S., Haggard, B., McPherson, J., Dia, M., Spinks, C. and McWhirt, A. (2008) High Resolution Soil Survey of Capulin Volcano National Monument, New Mexico. Soil Horizons, 49, 55-62. https://doi.org/10.2136/sh2008.3.0055
Dia, M., Wehner, T.C., Hassell, R., Price, D.S., Boyhan, G.E., Olson, S., King, S., Davis, A.R., Tolla, G.E., Bernier, J., Juarez, B., Sari, N., Solmaz, I. and Aras, V. (2012) Stability of Fruit Yield in Watermelon Genotypes Tested in Multiple US Environments. Proceedings of the Xth EUCARPIA Meeting on Genetics and Breeding of Cucurbitaceae, Antalya, Turkey, 15-18 October 2012, 84-88.
Dia, M., Wehner, T.C., Hassell, R., Price, D.S., Boyhan, G.E., Olson, S., King, S., Davis, A.R., Tolla, G.E., Bernier, J., Juarez, B., Sari, N., Solmaz, I. and Aras V.(2012) Mega-Environment Identification for Watermelon Yield Testing in the USProceedings of the Xth EUCARPIA Meeting on Genetics and Breeding of Cucurbitaceae, Antalya, Turkey, 15-18 October 2012, 385-390.
Kumar, R., Dia, M. and Wehner, T.C. (2013) Implications of Mating Behavior in Watermelon Breeding. HortScience, 48, 960-964.
Yan, W., Pageau, D., Frégeau-Reid, J. and Durand, J. (2011) Assessing the Representativeness and Repeatability of Test Locations for Genotype Evaluation. Crop Science, 51, 1603-1610. https://doi.org/10.2135/cropsci2011.01.0016
Smith, A.B., Cullis, B.R. and Thompson, R. (2005) The Analysis of Crop Cultivar Breeding and Evaluation Trials: An Overview of Current Mixed Model Approaches. Journal of Agricultural Science, 143, 449-462. https://doi.org/10.1017/S0021859605005587
Wricke, G. (1962) Evaluation Method for Recording Ecological Differences in Field Trials. Z Pflanzenzücht, 47, 92-96.
Shukla, G.K. (1972) Genotype Stability Analysis and Its Application to Potato Regional Trails. Crop Science, 11, 184-190.
Kang, M.S., Miller, J.D. and Darrah, L.L. (1987) A Note on Relationship between Stability Variance and Ecovalence. Journal of Heredity, 78, 107. https://doi.org/10.1093/oxfordjournals.jhered.a110322
Kang, M.S. (1993) Simultaneous Selection for Yield and Stability in Crop Performance Trials: Consequences for Growers. Agronomy Journal, 85, 754-757. https://doi.org/10.2134/agronj1993.00021962008500030042x
Mekbib, F. (2003) Yield Stability in Common Beans (Phaseolus vulgaris L.) Genotypes. Euphytica, 130, 147-153.
Fan, X.M., Kang, M., Chen, H., Zhang, Y., Tan, J. and Xu, C. (2007) Yield Stability of Maize Hybrids Evaluated in Multi-Environment Trials in Yunnan, China. Agronomy Journal, 99, 220-228. https://doi.org/10.2134/agronj2006.0144
Dia, M., Wehner, T.C. and Arellano, C. (2016) Analysis of Genotype × Environment Interaction (G × E) Using SAS Programming. Agronomy Journal, 108, 1838-1852. https://doi.org/10.2134/agronj2016.02.0085
RStudio Team (2015) RStudio: Integrated Development for R. RStudio, Inc., Boston, MA (Computer Software v0.98.1074). http://www.rstudio.com/
R Core Team (2015) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. http://www.R-project.org/
Wickham, H. and Francois, R. (2015) dplyr: A Grammar of Data Manipulation. R Package Version 0.4.3. http://CRAN.R-project.org/package=dplyr
Wickham, H. (2016) tidyr: Easily Tidy Data with ‘spread()’ and ‘gather()’ Functions. R package Version 0.4.1. http://CRAN.R-project.org/package=tidyr
Robinson, D. (2015) broom: Convert Statistical Analysis Objects into Tidy Data Frames. R Package Version 0.4.0. http://CRAN.R-project.org/package=broom
Mendiburu, F.D. (2015) agricolae: Statistical Procedures for Agricultural Research. R Package Version 1.2-3. http://CRAN.R-project.org/package=agricolae
Bates, D., Maechler, M., Bolker, B. and Walker, S. (2015) Fitting Linear Mixed-Effects Models Using lme4. Journal of Statistical Software, 67, 1-48. https://doi.org/10.18637/jss.v067.i01
Singmann, H., Bolker, B. and Westfall, J. (2015) afex: Analysis of Factorial Experiments. R Package Version 0.15-2. http://CRAN.R-project.org/package=afex
Maechler, M., Rousseeuw, P., Struyt, A. and Hubert, M. (2015) cluster: Cluster Analysis Basics and Extensions. R Package Version 2.0.1.
Dia, M., Wehner, T.C., Hassell, R., Price, D.S., Boyhan, G.E., Olson, S., King, S., Davis, A.R. andTolla, G.E. (2016) Genotype × Environment Interaction and Stability Analysis for Watermelon Fruit Yield in the U.S. Crop Science, 56, 1645-1661. https://doi.org/10.2135/cropsci2015.10.0625
Dia, M., Wehner, T.C., Hassell, R., Price, D.S., Boyhan, G.E., Olson, S., King S., Davis, A.R. and Tolla, G.E. (2016) Values of Locations for Representing Mega-Environments and for Discriminating Yield of Watermelon in the U.S. Crop Science, 56, 1726-1735. https://doi.org/10.2135/cropsci2015.11.0698
Dia, M., Wehner, T.C., Perkins-Veazie, P., Hassell, R., Price, D.S., Boyhan, G.E., Olson, S., King, S., Davis, A.R., Tolla, G.E., Bernier, J. and Juarez, B. (2016) Stability of Fruit Quality Traits in Diverse Watermelon Cultivars Tested in Multiple Environments. Horticulture Research, 3, Article No. 16066. https://doi.org/10.1038/hortres.2016.66