Performance prediction of crosses in plant breeding through genotype by environment interactions

Performance prediction of potential crosses plays a significant role in plant breeding, which aims to produce new crop varieties that have higher yields, require fewer resources, and are more adaptable to the changing environments. In the 2020 Syngenta crop challenge, Syngenta challenged participants to predict the yield performance of a list of potential breeding crosses of inbreds and testers based on their historical yield data in different environments. They released a dataset that contained the observed yields for 294,128 corn hybrids through the crossing of 593 unique inbreds and 496 unique testers across multiple environments between 2016 and 2018. To address this challenge, we designed a new predictive approach that integrates random forest and an optimization model for G x E interaction detection. Our computational experiment found that our approach achieved a relative root-mean-square-error (RMSE) of 0.0869 for the validation data, outperforming other state-of-the-art models such as factorization machine and extreme gradient boosting tree. Our model was also able to detect genotype by environment interactions that are potentially biologically insightful. This model won the first place in the 2020 Syngenta crop challenge in analytics.