Genomics-based plant disease resistance prediction using machine learning

Plant disease outbreaks continuously challenge food security and sustainability. Traditional chemical methods used to treat diseases have environmental and health concerns, raising the need to enhance inherent plant disease resistance mechanisms. Traits, including disease resistance, can be linked to specific loci in the genome and identifying these markers facilitates targeted breeding approaches. Several methods, including genome-wide association studies and genomic selection, have been used to identify important markers and select varieties with desirable traits. However, these traditional approaches may not fully capture the non-linear characteristics of the effect of genomic variation on traits. Machine learning, known for its data-mining abilities, offers an opportunity to enhance the accuracy of the existing trait association approaches. It has found applications in predicting various agronomic traits across several species. However, its use in disease resistance prediction remains limited. This review highlights the potential of machine learning as a complementary tool for predicting the genetic loci contributing to pathogen resistance. We provide an overview of traditional trait prediction methods, summarize machine-learning applications, and address the challenges and opportunities associated with machine learning-based crop disease resistance prediction.