Reproducible analysis pipeline for evaluating genotype-by-environment interaction (G×E) and optimizing multi-trait selection in lima bean (Phaseolus lunatus L.) using GGE biplot, GT biplot, and a desired-gain index.
Gérson N. C. Ferreira¹†, João P. S. Pavan¹†, Mauricio S. Araújo¹, Dayana R. Sousa¹, Michelle S. Nascimento², Vanessa G. Moura², José T. Chagas¹, Yasmin I. Retore¹, Josieli L. Silva², Maria S. S. Silva², Regina L. F. Gomes², Ângela C. A. Lopes², Maria I. Zucchi³˒⁴, José B. Pinheiro¹
† These authors contributed equally to this work.
- Genetics Diversity and Breeding Laboratory, Department of Genetics, “Luiz de Queiroz” College of Agriculture (ESALQ/USP), Piracicaba, São Paulo, Brazil
- Department of Plant Science, Federal University of Piauí (UFPI), Teresina, Piauí, Brazil
- Conservation Genetics and Genomics Group, Department of Genetics, ESALQ/USP, Piracicaba, São Paulo, Brazil
- Secretariat of Agriculture and Food Supply of São Paulo State, Piracicaba, São Paulo, Brazil
Lima bean stands out for its wide adaptation to diverse edaphoclimatic conditions and is a promising crop for low-input farming systems. However, trait expression is strongly influenced by genotype-by-environment interaction (G×E), complicating the selection of broadly adapted and stable genotypes. This study evaluated G×E interaction in 40 lima bean breeding lines across three Brazilian agro-ecological environments. Trials were conducted in a randomized complete block design with three replications. The significance of effects was tested using likelihood-ratio tests, and G×E was investigated with the GGE biplot. Simultaneous multi-trait selection was performed using the Genotype-by-Trait (GT) biplot and a desired-gain index.
- Significant G×E interaction was detected for all traits, indicating differential genotype responses across environments.
- Lines L06, L27, L14, L21, and L34 were selected as ideotypes combining high yield, stability, and overall multi-trait performance, supporting cultivation under contrasting edaphoclimatic conditions.
Keywords: Phaseolus lunatus L.; genotype-by-environment interaction; GGE biplot; multi-trait selection; stability.
Codes/– analysis scripts (model fitting, biplots, selection indices)Data/– raw/processed datasets used in the studyPlots/– figures exported from the pipeline (final and intermediate)
If you use this code, data, or results in your research, please cite:
Ferreira, G. N. C., Pavan, J. P. S., Araújo, M. S., Sousa, D. R., Nascimento, M. S., Moura, V. G., Chagas, J. T., Retore, Y. I., Silva, J. L., Silva, M. S. S., Gomes, R. L. F., Lopes, Â. C. A., Zucchi, M. I., & Pinheiro, J. B. Leveraging G×E interaction to optimize multi-trait selection in lima bean.. in review, 2026.
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