This function computes the following indexes proposed by Resende (2007): the harmonic mean of genotypic values (HMGV), the relative performance of the genotypic values (RPGV) and the harmonic mean of the relative performance of genotypic values (HMRPGV).
Resende_indexes(.data)
.data | An object of class |
---|
A dataframe containing the indexes.
The indexes computed with this function have been used to select genotypes with stability performance in a mixed-effect model framework. Some examples are in Alves et al (2018), Azevedo Peixoto et al. (2018), Dias et al. (2018) and Colombari Filho et al. (2013).
The HMGV index is computed as \[HMG{V_i} = \frac{E}{{\sum\limits_{j = 1}^E {\frac{1}{{G{v_{ij}}}}}}}\]
where \(E\) is the number of environments included in the analysis, \(Gv_{ij}\) is the genotypic value (BLUP) for the ith genotype in the jth environment.
The RPGV index is computed as \[RPGV_i = \frac{1}{E}{\sum\limits_{j = 1}^E {Gv_{ij}} /\mathop \mu \nolimits_j }\]
The HMRPGV index is computed as \[HMRPG{V_i} = \frac{E}{{\sum\limits_{j = 1}^E {\frac{1}{{G{v_{ij}}/{\mu _j}}}} }}\]
Alves, R.S., L. de Azevedo Peixoto, P.E. Teodoro, L.A. Silva, E.V. Rodrigues, M.D.V. de Resende, B.G. Laviola, and L.L. Bhering. 2018. Selection of Jatropha curcas families based on temporal stability and adaptability of genetic values. Ind. Crops Prod. 119:290-293. doi: 10.1016/J.INDCROP.2018.04.029
Colombari Filho, J.M., M.D.V. de Resende, O.P. de Morais, A.P. de Castro, E.P. Guimaraes, J.A. Pereira, M.M. Utumi, and F. Breseghello. 2013. Upland rice breeding in Brazil: a simultaneous genotypic evaluation of stability, adaptability and grain yield. Euphytica 192:117-129. doi: 10.1007/s10681-013-0922-2
Dias, P.C., A. Xavier, M.D.V. de Resende, M.H.P. Barbosa, F.A. Biernaski, R.A. Estopa. 2018. Genetic evaluation of Pinus taeda clones from somatic embryogenesis and their genotype x environment interaction. Crop Breed. Appl. Biotechnol. 18:55-64. doi: 10.1590/1984-70332018v18n1a8
Azevedo Peixoto, L. de, P.E. Teodoro, L.A. Silva, E.V. Rodrigues, B.G. Laviola, and L.L. Bhering. 2018. Jatropha half-sib family selection with high adaptability and genotypic stability. PLoS One 13:e0199880. doi: 10.1371/journal.pone.0199880
Resende MDV (2007) Matematica e estatistica na analise de experimentos e no melhoramento genetico. Embrapa Florestas, Colombo
Tiago Olivoto tiagoolivoto@gmail.com
# \donttest{ library(metan) res_ind <- waasb(data_ge, env = ENV, gen = GEN, rep = REP, resp = c(GY, HM))#>#>#>#>#> --------------------------------------------------------------------------- #> P-values for Likelihood Ratio Test of the analyzed traits #> --------------------------------------------------------------------------- #> model GY HM #> COMPLETE NA NA #> GEN 1.11e-05 5.07e-03 #> GEN:ENV 2.15e-11 2.27e-15 #> --------------------------------------------------------------------------- #> All variables with significant (p < 0.05) genotype-vs-environment interactionmodel_indexes <- Resende_indexes(res_ind) # Alternatively using the pipe operator %>% res_ind <- data_ge %>% waasb(ENV, GEN, REP, c(GY, HM)) %>% Resende_indexes()#>#>#>#>#> --------------------------------------------------------------------------- #> P-values for Likelihood Ratio Test of the analyzed traits #> --------------------------------------------------------------------------- #> model GY HM #> COMPLETE NA NA #> GEN 1.11e-05 5.07e-03 #> GEN:ENV 2.15e-11 2.27e-15 #> --------------------------------------------------------------------------- #> All variables with significant (p < 0.05) genotype-vs-environment interaction# }