RGxE: An R Program for Genotype x Environment Interaction Analysis

Abstract

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 (bi), deviation from regression (S2d), Shukla’s variance (σi2), S square Wricke’s ecovalence (Wi), and Kang’s yield stability (YSi). 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.