Optimizing predictions in IRRI's rice drought breeding program by leveraging 17 years of historical data and pedigree information.

Abstract

Prediction models based on pedigree and/or molecular marker information are now an inextricable part of the crop breeding programs and have led to increased genetic gains in many crops. Optimization of IRRI’s rice drought breeding program is crucial for better implementation of selections based on predictions. Historical datasets with precise and robust pedigree information have been a great resource to help optimize the prediction models in the breeding programs. Here, we leveraged 17 years of historical drought data along with the pedigree information to predict the new lines or environments and dissect the G × E interactions. Seven models ranging from basic to proposed higher advanced models incorporating interactions, and genotypic specific effects were used. These models were tested with three cross-validation schemes (CV1, CV2, and CV0) to assess the predictive ability of tested and untested lines in already observed environments and tested lines in novel or new environments. In general, the highest prediction abilities were obtained when the model accounting interactions between pedigrees (additive) and environment were included. The CV0 scheme (predicting unobserved or novel environments) reveals very low predictive abilities among the three schemes. CV1 and CV2 schemes that borrow information from the target and correlated environments have much higher predictive abilities. Further, predictive ability was lower when predicting lines in non-stress conditions using drought data as training set and/or vice-versa. When predicting the lines using the data sets under the same conditions (stress or non-stress data sets), much better prediction accuracy was obtained. These results provide conclusive evidence that modeling G × E interactions are important in predictions. Thus, considering G × E interactions would help to build enhanced genomic or pedigree-based prediction models in the rice breeding program. Further, it is crucial to borrow the correlated information from other environments to improve prediction accuracy.