Joint modeling of spatial variability and within-row interplot competition to increase the efficiency of plant improvement

Trials in the early stages of selection are often subject to variation arising from spatial variability and interplot competition, which can seriously bias the assessment of varietal performance and reduce genetic progress. An approach to jointly model both sources of bias is presented. It models genotypic and residual competition and also global and extraneous spatial variation. Variety effects were considered random and residual maximum likelihood was used for parameter estimation. Competition at the residual level was examined using two special simultaneous autoregressive models. An equal-roots second-order autoregressive (EAR(2)) model is proposed for trials where competition is dominant. An equal-roots third-order autoregressive (EAR(3)) model allows for competition and spatial variability. These models are applied to two yield data sets from an Australian sugarcane selection program. One data set is in the paper and the other is in supplementary material available online. To determine the effect of simultaneously adjusting for spatial variability and interplot competition on selection, the percentages of superior varieties in common in the top 15% for the joint model and classical approaches were compared. Agreement between the two approaches was 45 and 84%. Hence, for some trials there are large differences in varieties advanced to the next stage of selection.