Annicchiarico, P. 2002. Genotype × environment interactions: Challenges and opportunities for plant breeding and cultivar recommendations. Volume 174 of FAO Plant Production and Protection Papers. 174. 115 pp.
Bernardo Júnior, L.A.Y., de Silva, C.P., de Oliveira, L.A., Nuvunga, J.J., Pires, L.P.M., Von Pinho, R.G. and Balestre, M. 2018. AMMI Bayesian models to study stability and adaptability in maize. Agronomy Journal, 110(5), pp.1765–1776. DOI: 10.2134/agronj2017.11.0668
Crossa, J., Perez-Elizalde, S., Jarquín, D., Cotes, J. M., Viele, K., Liu, G. and Cornelius, P. L. 2011. Bayesian estimation of the additive main effects and multiplicative interaction model. Crop Science, 51, pp.1458–1469. DOI: 10.2135/cropsci2010.06.0343
da Oliveira, L.A., da Silva, C.P., da Silva, A.Q., Mendes, C.T.E., Nuvunga, J.J., Nunes, J.A.R., Parrella, R.A.D.C., Baleste, M. and Filho, J.S.D.S.B. 2021. Bayesian GGE model for heteroscedastic multienvironmental trials. Crop Science, 62(3), pp.982–996. DOI: 10.1002/csc2.20696
da Silva, C.P., Mendes, C.T.E., Silva, A.Q.D., Oliveira, L.A.D., Von Pinho, R.G. and Balestre, M. 2023. Use of the reversible jump Markov Chain Monte Carlo algorithm to select multiplicative terms in the AMMI-Bayesian model. PLoS One, 18, e0279537. DOI:10.1371/journal.pone.0279537
da Silva, C.P., da Silva, A.Q., Nuvunga, J.J., Avelar, F.G., Braulio, R., Mendes, C.T.E., de Oliveira, L.A. and Bueno Filho, J.S.D.S. 2025a. Assessing the adaptability and stability of maize hybrids using a Bayesian factor analytic model. Crop Science, 65(5), e70162. DOI: 10.1002/csc2.70162
da Silva, E.V.P., Davide, L.M.C., Gianlup, C., de Oliveira, W.J.S., de Oliveira, L.A., da Silva, A.Q., da Silva, C.P., Mendes, C.T.E. and Khan, S. 2025b. Assessing the stability and adaptability of maize hybrid yield with the Bayesian AMMI model. Euphytica, 221(4), 43. DOI: 10.1007/s10681-025-03490-y
Denis, J.-B. and Pazman, A. 1999. Bias of LS estimators in nonlinear regression models with constraints. Part II: Biadditive models. Applied Mathematics, 44, pp.375–403. DOI: 10.1023/A:1023045028073
Ebrahimi, L. 2023. ‘Genotype by yield* trait’(GYT) biplot approach to evaluate resistance of soybean cultivars to Helicoverpa armigera Hübner under natural infestation conditions. Phytoparasitica, 51(4), pp.909–918. DOI: 10.1007/s12600-023-01078-7
Forkman, J. and Piepho, H.P. 2014. Parametric bootstrap methods for testing multiplicative terms in GGE and AMMI models. Biometrics, 70, pp.639–647. DOI: 10.1111/biom.12162
Gabriel, K.R. 1971. The biplot graphic display of matrices with application to principal component analysis. Biometrika, 58, pp.453–467. DOI: 10.1093/biomet/58.3.453
Gamerman, D. and Lopes, H.F. 2006. Markov chain Monte Carlo: Stochastic simulation for Bayesian inference. Chapman and Hall. DOI: 10.1201/9781482296426
Gelman, A. and Rubin, D.B. 1992. Inference from iterative simulation using multiple sequences. Statistical Science, 7, pp.457–511. DOI: 10.1214/ss/1177011136
Geman, S. and Geman, D. 1984. Stochastic relaxation, Gibbs distributions, and the Bayesian restoration of images. IEEE Transactions on Pattern Analysis and Machine Intelligence, 6, pp.721–741. DOI: 10.1109/TPAMI.1984.4767596
Geweke, J. 1992. Evaluating the accuracy of sampling-based approaches to the calculation of posterior moments. Pp. 169–193. In: L. M. Bernardo, J. Berger, A. P. Dawid, and A. F. M. Smith (eds.) Bayesian statistics. Oxford University Press.
Johnson, R.A. and Wichern, D.W. 2002. Applied multivariate statistical analysis. Fifth edition. Prentice Hall. 788 pp.
Josse, J., van Eeuwijk, F., Piepho, H.P. and Denis, J.-B. 2014. Another look at Bayesian analysis of AMMI models for genotype-environment data. Journal of Agricultural, Biological, and Environmental Statistics, 19, pp.240–257. DOI: 10.1007/s13253-014-0168-z
Khan, M.M.H., Rafii, M.Y., Ramlee, S.I., Jusoh, M. and Al Mamun, M. 2021. AMMI and GGE biplot analysis for yield performance and stability assessment of selected Bambara groundnut (Vigna subterranea L. Verdc.) genotypes under the multi-environmental trials (METs). Scientific Reports, 11, e22791. DOI: 10.1038/s41598-021-01411-2
Kona, P., Ajay, B. C., Gangadhara, K., Kumar, N., Choudhary, R.R., Mahatma, M.K., Singh, S., Reddy, K.K., Bera, S.K., Sangh, C., Rani, K., Chavada, Z. and Solanki, K.D. 2024. AMMI and GGE biplot analysis of genotype by environment interaction for yield and yield contributing traits in confectionery groundnut. Scientific Reports, 14, e2943. DOI: 10.1038/s41598-024-52938-z
Nascimento, A.C.C., Nascimento, M., Sagae, V.S., Destro, V., Nardino, M., Olivoto, T. and Jarquín, D. 2025. Bayesian AMMI‐based indexes for genotype selection: Integrating novel stability measures for enhanced G× E inference. Crop Science, 65(5), e70140. DOI: 10.1002/csc2.70140
Olivoto, T., Lúcio, A.D.C., Silva, J.A.G., Marchioro, V.S., Souza, V.Q. and Jost, E. 2019. Mean performance and stability in multi-environment trials I: Combining features of AMMI and BLUP techniques. Agronomy Journal, 111, pp.2949–2960. DOI: 10.2134/agronj2019.03.0220
Perez-Elizalde, S., Jarquín, D. and Crossa, J. 2012. A general Bayesian estimation method of linear-bilinear models applied to plant breeding trials with genotype × environment interaction. Journal of Agricultural, Biological, and Environmental Statistics, 17, pp.15–37. DOI: 10.1007/s13253-011-0063-9
R Core Team. 2024. R: the R project for statistical computing. https://www.r-project.org
Raftery, A.E. and Lewis, S.M. 1992. One long run with diagnostics: Implementation strategies for Markov chain Monte Carlo. Statistical Science, 7, pp.493–497. DOI: 10.1214/ss/1177011143
Shiri, M.R., Estakhr, A., Najafinezhad, H., Hassanzadeh Moghaddam, H., Shirkhani, A. and Ataei, R. 2024. Employing Bayesian probabilistic approach for risk assessment in selection and recommendation of new maize (Zea mays L.) hybrids. Seed and Plant, 40, pp.295–320 (in Persian). DOI: 10.22092/spj.2025.368724.1410
Shiri, M., Estakhr, A., Fareghi, Sh., Najafinezhad, H., Khorasani, S.K., Eshraghi-Nejad, M., Afarinesh, A., Anvari, K. and Ebrahimi, L. 2025a. Evaluating the efficiency of AMMI, GGE biplot, and HO-AMMI stability analysis models for selecting high-yielding and stable maize hybrids in multi-environment trials. Advanced Environmental Science, 23(2), pp.461–476 (in Persian). DOI: 10.48308/envs.2024.1421
Shiri, M., Estakhr, A., Shikhani, A., Mosavat, A. and Bahmankar, M. 2025b. The risk analysis for high-potential and stable cultivars recommendation in maize. Iranian Journal of Field Crop Science, 56(2), pp.77–90 (in Persian). DOI: 10.22059/ijfcs.2024.384144.655108
Shiri, M., Moharramnejad, S., Estakhr, A., Fareghi, S., Najafinezhad, H., Khavari Khorasani, S., Afarinesh, A. and Eshraghi-Nejad, M. 2025c. Strategic risk analysis for the selection of stable and high-potential maize genotypes in multi-environment trials. PLoS One, 20(6), e0325454. DOI: 10.1371/journal.pone.0325454
Smith, B. J. 2007. boa: An R package for MCMC output convergence assessment and posterior inference. Journal of Statistical Software, 21, pp.1-37. DOI: 10.18637/jss.v021.i11
Teodoro, P.E., Azevedo, C.F., Farias, F.J.C., Alves, R.S., de Azevedo Peixoto, L., Ribeiro, L.P., Paulo de Carvalho, L. and Bhering, L.L. 2019. Adaptability of cotton (Gossypium hirsutum) genotypes analysed using a Bayesian AMMI model. Crop and Pasture Science, 70(7), pp.615–621. DOI: 10.1071/CP18318
Viele, K. and Srinivasan, C. 2000. Parsimonious estimation of multiplicative interaction in analysis of variance using Kullback—Leibler information. Journal of Statistical Planning and Inference, 84, pp.201–219. DOI: 10.1016/S0378-3758(99)00151-2
Yang, R.-C., Crossa, J., Cornelius, P.L. and Burgueño, J. 2009. Biplot analysis of genotype × environment interaction: Proceed with caution. Crop Science, 49, pp.1564–1576. DOI: 10.2135/cropsci2008.11.0665