DeepMap: A deep learning-based model with a four-line code for prediction-based breeding in crops

ABSTRACT Prediction of phenotype through genotyping data using the emerging machine or deep learning technology has been proven successful in genomic prediction. We present here a graphical processing unit (GPU) enabled DeepMap configurable deep learning-based python package for the genomic prediction of quantitative phenotype traits. We found that deep learning captures non-linear patterns more efficiently than conventional statistical methods. Furthermore, we suggest an additional module inclusion of epistasis interactions and training of the model on Graphical Processing Units (GPUs) in addition to Central Processing Unit (CPU) to enhance efficiency and increase the model’s performance. We developed and demonstrated the application of DeepMap using a 3K rice genome panel and 1K-Rice Custom Amplicon (1kRiCA) data for several phenotypic traits including days to 50% flowering (DTF), number of productive tillers (NPT), panicle length (PL), plant height (PH), and plot yield (PY). We have found that DeepMap outperformed the best existing state-of-the-art models by giving higher predictive correlation and low mean squared error for the datasets studied. This prediction performance was higher than other compared models in the range of 13-31%. Similarly for Dataset-2, significantly higher predictions were observed than the compared models (16-20% higher prediction ability). On Dataset-3, we have also shown the better and versatile performance of our model across crops (wheat, maize, and soybean) for yield and yield-related traits. This demonstrates the potentiality of the framework and ease of use for future research in crop improvement. The DeepMap is accessible at https://test.pypi.org/project/DeepMap-1.0/ . Short Summary DeepMap is a deep learning-based breeder-friendly python package to perform genomic prediction. It utilizes epistatic interactions for data augmentation and outperforms the existing state-of-the-art machine/deep learning models such as Bayesian LASSO, GBLUP, DeepGS, and dualCNN. DeepMap developed for rice and tested across crops such as maize, wheat, soybean etc.